Title: Fast Compressed Neural Networks for R
Description: Provides an interface to kernel routines from the FCNN C++ library.
FCNN is based on a completely new Artificial Neural Network representation that
offers unmatched efficiency, modularity, and extensibility. FCNN4R provides
standard teaching (backpropagation, Rprop, simulated annealing, stochastic
gradient) and pruning algorithms (minimum magnitude, Optimal Brain Surgeon),
but it is first and foremost an efficient computational engine. Users can
easily implement their algorithms by taking advantage of fast gradient computing
routines, as well as network reconstruction functionality (removing weights
and redundant neurons, reordering inputs, merging networks). Networks can be
exported to C functions in order to integrate them into virtually any software
solution.
Author: Grzegorz Klima <gklima@users.sourceforge.net>
Maintainer: Grzegorz Klima <gklima@users.sourceforge.net>
Diff between FCNN4R versions 0.5.0 dated 2015-10-12 and 0.6.0 dated 2015-12-31
FCNN4R-0.5.0/FCNN4R/man/mlp_net-single-weight-access.Rd |only FCNN4R-0.5.0/FCNN4R/man/mlp_net-weight-indexing.Rd |only FCNN4R-0.6.0/FCNN4R/DESCRIPTION | 27 FCNN4R-0.6.0/FCNN4R/MD5 | 107 - FCNN4R-0.6.0/FCNN4R/NAMESPACE | 7 FCNN4R-0.6.0/FCNN4R/R/dataset.R |only FCNN4R-0.6.0/FCNN4R/R/fcnn4r.R |only FCNN4R-0.6.0/FCNN4R/R/mlp_gteach.R | 7 FCNN4R-0.6.0/FCNN4R/R/mlp_net.R | 595 +++++----- FCNN4R-0.6.0/FCNN4R/R/mlp_plot.R | 14 FCNN4R-0.6.0/FCNN4R/R/mlp_prune.R | 16 FCNN4R-0.6.0/FCNN4R/R/mlp_teach.R | 183 ++- FCNN4R-0.6.0/FCNN4R/man/FCNN4R-package.Rd | 46 FCNN4R-0.6.0/FCNN4R/man/is.mlp_net.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_actvfunc2str.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_check_inout.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_check_w.Rd | 14 FCNN4R-0.6.0/FCNN4R/man/mlp_eval.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_export_C.Rd | 14 FCNN4R-0.6.0/FCNN4R/man/mlp_net-MSE-gradients.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_net-absolute-weight-indices.Rd |only FCNN4R-0.6.0/FCNN4R/man/mlp_net-accessing-individual-weights.Rd |only FCNN4R-0.6.0/FCNN4R/man/mlp_net-class.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_net-combining-two-networks.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_net-export-import.Rd | 38 FCNN4R-0.6.0/FCNN4R/man/mlp_net-general-information.Rd | 5 FCNN4R-0.6.0/FCNN4R/man/mlp_net-manipulating-network-inputs.Rd |only FCNN4R-0.6.0/FCNN4R/man/mlp_net-names.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_net-weights-access.Rd | 2 FCNN4R-0.6.0/FCNN4R/man/mlp_net.Rd | 4 FCNN4R-0.6.0/FCNN4R/man/mlp_plot.Rd | 11 FCNN4R-0.6.0/FCNN4R/man/mlp_prune_mag.Rd | 12 FCNN4R-0.6.0/FCNN4R/man/mlp_prune_obs.Rd | 10 FCNN4R-0.6.0/FCNN4R/man/mlp_rm_neurons.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_rnd_weights.Rd | 4 FCNN4R-0.6.0/FCNN4R/man/mlp_set_activation.Rd | 19 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_bp.Rd | 22 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_grprop.Rd | 6 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_rprop.Rd | 20 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_sa.Rd | 12 FCNN4R-0.6.0/FCNN4R/man/mlp_teach_sgd.Rd |only FCNN4R-0.6.0/FCNN4R/man/read-write-fcnndataset.Rd |only FCNN4R-0.6.0/FCNN4R/src/Makevars | 2 FCNN4R-0.6.0/FCNN4R/src/Makevars.win | 2 FCNN4R-0.6.0/FCNN4R/src/dataset.cpp |only FCNN4R-0.6.0/FCNN4R/src/fcnn/activation.h | 58 FCNN4R-0.6.0/FCNN4R/src/fcnn/error.h | 3 FCNN4R-0.6.0/FCNN4R/src/fcnn/export.cpp | 455 ++++--- FCNN4R-0.6.0/FCNN4R/src/fcnn/export.h | 27 FCNN4R-0.6.0/FCNN4R/src/fcnn/level1.h | 2 FCNN4R-0.6.0/FCNN4R/src/fcnn/level2.cpp | 68 - FCNN4R-0.6.0/FCNN4R/src/fcnn/level2.h | 8 FCNN4R-0.6.0/FCNN4R/src/fcnn/level3.cpp | 56 FCNN4R-0.6.0/FCNN4R/src/fcnn/level3.h | 12 FCNN4R-0.6.0/FCNN4R/src/fcnn/struct.cpp | 245 +++- FCNN4R-0.6.0/FCNN4R/src/fcnn/struct.h | 46 FCNN4R-0.6.0/FCNN4R/src/fcnn/utils.cpp | 32 FCNN4R-0.6.0/FCNN4R/src/fcnn/utils.h | 7 FCNN4R-0.6.0/FCNN4R/src/fcnn/version.h |only FCNN4R-0.6.0/FCNN4R/src/interface.cpp | 316 +++-- 60 files changed, 1655 insertions(+), 933 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
is more familiar to experienced R users. Also, implements various functions
related to topic modeling. It works well with with the "lda" package by J.
Chang.
Author: "Thomas W. Jones <jones.thos.w@gmail.com>"
Maintainer: Thomas W. Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 1.5.0 dated 2015-12-30 and 1.5.1 dated 2015-12-31
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- src/CalcLikelihoodC.cpp | 13 +++++++------ src/CalcSumSquares.cpp | 2 +- src/HellingerMat.cpp | 8 +++++--- src/Hellinger_cpp.cpp | 6 +++--- src/JSD_cpp.cpp | 6 +++--- src/JSDmat.cpp | 6 +++--- 8 files changed, 33 insertions(+), 30 deletions(-)
Title: Interface to 'Sunlight' Foundation 'APIs'
Description: Interface to three 'Sunlight' Foundation 'APIs' (http://
sunlightfoundation.com/api/) for government data, including the
Congress 'API' 'v3', the Capitol Words 'API', and the Open States
'API'. 'Sunlight' Foundation is a 'nonpartison' 'nonprofit' that collects and
provides data on government activities, and those that influence government.
Functions are provided to interact with each of the three 'APIs'.
Author: Scott Chamberlain [aut, cre],
Thomas J. Leeper [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rsunlight versions 0.4.0 dated 2015-07-01 and 0.4.2 dated 2015-12-31
rsunlight-0.4.0/rsunlight/R/ie_contr.R |only rsunlight-0.4.0/rsunlight/R/ie_contr_bundled.R |only rsunlight-0.4.0/rsunlight/R/ie_earmarks.R |only rsunlight-0.4.0/rsunlight/R/ie_entities.R |only rsunlight-0.4.0/rsunlight/R/ie_epa.R |only rsunlight-0.4.0/rsunlight/R/ie_faca.R |only rsunlight-0.4.0/rsunlight/R/ie_getcontracts.R |only rsunlight-0.4.0/rsunlight/R/ie_getgrants.R |only rsunlight-0.4.0/rsunlight/R/ie_getlobbying.R |only rsunlight-0.4.0/rsunlight/R/ie_individuals.R |only rsunlight-0.4.0/rsunlight/R/ie_industries.R |only rsunlight-0.4.0/rsunlight/R/ie_misconduct.R |only rsunlight-0.4.0/rsunlight/R/ie_organizations.R |only rsunlight-0.4.0/rsunlight/R/ie_politicians.R |only rsunlight-0.4.0/rsunlight/data/ie_sectors.rda |only rsunlight-0.4.0/rsunlight/man/ie_contr.Rd |only rsunlight-0.4.0/rsunlight/man/ie_contr_bundled.Rd |only rsunlight-0.4.0/rsunlight/man/ie_contracts.Rd |only rsunlight-0.4.0/rsunlight/man/ie_earmarks.Rd |only rsunlight-0.4.0/rsunlight/man/ie_entities.Rd |only rsunlight-0.4.0/rsunlight/man/ie_epa.Rd |only rsunlight-0.4.0/rsunlight/man/ie_faca.Rd |only rsunlight-0.4.0/rsunlight/man/ie_grants.Rd |only rsunlight-0.4.0/rsunlight/man/ie_individuals.Rd |only rsunlight-0.4.0/rsunlight/man/ie_industries.Rd |only rsunlight-0.4.0/rsunlight/man/ie_lobbying.Rd |only rsunlight-0.4.0/rsunlight/man/ie_misconduct.Rd |only rsunlight-0.4.0/rsunlight/man/ie_organizations.Rd |only rsunlight-0.4.0/rsunlight/man/ie_politicians.Rd |only rsunlight-0.4.0/rsunlight/man/ie_sectors.Rd |only rsunlight-0.4.2/rsunlight/DESCRIPTION | 20 - rsunlight-0.4.2/rsunlight/MD5 | 127 ++++------ rsunlight-0.4.2/rsunlight/NAMESPACE | 11 rsunlight-0.4.2/rsunlight/R/cg_bills.R | 14 + rsunlight-0.4.2/rsunlight/R/cg_committees.R | 4 rsunlight-0.4.2/rsunlight/R/cg_legislators.R | 12 rsunlight-0.4.2/rsunlight/R/cw_timeseries.R | 4 rsunlight-0.4.2/rsunlight/R/defunct.R |only rsunlight-0.4.2/rsunlight/R/query.R | 8 rsunlight-0.4.2/rsunlight/R/rsunlight-package.R | 17 - rsunlight-0.4.2/rsunlight/R/tbldf.R | 7 rsunlight-0.4.2/rsunlight/R/zzz.R | 12 rsunlight-0.4.2/rsunlight/README.md | 79 +----- rsunlight-0.4.2/rsunlight/build/vignette.rds |binary rsunlight-0.4.2/rsunlight/inst/doc/rsunlight_vignette.Rmd | 127 ---------- rsunlight-0.4.2/rsunlight/inst/doc/rsunlight_vignette.html | 122 +-------- rsunlight-0.4.2/rsunlight/inst/ignore/rt_ind_exp.R |only rsunlight-0.4.2/rsunlight/inst/ignore/rt_new_filing.R |only rsunlight-0.4.2/rsunlight/inst/img/unnamed-chunk-10-1.png |binary rsunlight-0.4.2/rsunlight/man/cg_amendments.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_bills.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_committees.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_districts.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_documents.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_floor_updates.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_hearings.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_legislators.Rd | 35 +- rsunlight-0.4.2/rsunlight/man/cg_nominations.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_upcoming_bills.Rd | 2 rsunlight-0.4.2/rsunlight/man/cg_votes.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_dates.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_phrases.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_text.Rd | 2 rsunlight-0.4.2/rsunlight/man/cw_timeseries.Rd | 14 - rsunlight-0.4.2/rsunlight/man/ie_contr-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_contr_bundled-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_contracts-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_earmarks-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_entities-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_epa-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_faca-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_grants-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_individuals-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_industries-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_lobbying-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_organizations-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_politicians-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/ie_sectors-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/os_billlookup.Rd | 2 rsunlight-0.4.2/rsunlight/man/os_billsearch.Rd | 2 rsunlight-0.4.2/rsunlight/man/os_legislatorsearch.Rd | 2 rsunlight-0.4.2/rsunlight/man/os_statemetasearch.Rd | 2 rsunlight-0.4.2/rsunlight/man/rsunlight-defunct.Rd |only rsunlight-0.4.2/rsunlight/man/rsunlight-package.Rd | 15 - rsunlight-0.4.2/rsunlight/man/sessions.Rd | 2 rsunlight-0.4.2/rsunlight/man/type_sum.Rd | 2 rsunlight-0.4.2/rsunlight/tests/testthat/test-cg_bills.R |only rsunlight-0.4.2/rsunlight/tests/testthat/test-cg_legislators.R |only rsunlight-0.4.2/rsunlight/tests/testthat/test-trunc_mat.R |only rsunlight-0.4.2/rsunlight/vignettes/rsunlight_vignette.Rmd | 127 ---------- 90 files changed, 227 insertions(+), 566 deletions(-)
Title: Extreme Value Analysis with Goodness-of-Fit Testing
Description: Goodness-of-fit tests for selection of r in the r-largest order
statistics (GEVr) model. Goodness-of-fit tests for threshold selection in the
peaks-over-threshold approach. Random number generation and density functions
for the GEVr distribution. Profile likelihood for return level estimation
using the GEVr and generalized pareto distributions. P-value adjustments for
sequential, multiple testing error control.
Author: Brian Bader [aut, cre],
Jun Yan [aut]
Maintainer: Brian Bader <brianbader@mail.com>
Diff between eva versions 0.1.1 dated 2015-12-29 and 0.1.2 dated 2015-12-31
DESCRIPTION | 8 +-- MD5 | 88 +++++++++++++++++++------------------- R/gevr.R | 19 ++++---- R/gevrEd.R | 10 ++-- R/gevrFit.R | 3 - R/gevrMultScore.R | 9 ++- R/gevrPbScore.R | 9 ++- R/gevrProfShape.R | 7 +-- R/gevrRl.R | 13 +++-- R/gevrSeqTests.R | 20 ++++---- R/gpd.R | 104 +++++++++++++++++++++++---------------------- R/gpdAd.R | 7 +-- R/gpdCvm.R | 7 +-- R/gpdImAsym.R | 11 ++-- R/gpdImPb.R | 9 ++- R/gpdMultScore.R | 9 ++- R/gpdPbScore.R | 7 +-- R/gpdProfShape.R | 7 +-- R/gpdRl.R | 11 ++-- R/gpdSeqTests.R | 17 +++---- R/lowestoft.R | 2 R/mrlPlot.R | 7 +-- R/pSeqStop.R | 9 ++- inst/doc/introduction.html | 2 man/gevr.Rd | 3 - man/gevrEd.Rd | 10 +--- man/gevrFit.Rd | 3 - man/gevrMultScore.Rd | 10 +--- man/gevrPbScore.Rd | 10 +--- man/gevrProfShape.Rd | 8 +-- man/gevrRl.Rd | 15 ++---- man/gevrSeqTests.Rd | 25 +++------- man/gpd.Rd | 37 +++++++++------- man/gpdAd.Rd | 8 +-- man/gpdCvm.Rd | 8 +-- man/gpdImAsym.Rd | 13 ++--- man/gpdImPb.Rd | 11 +--- man/gpdMultScore.Rd | 8 +-- man/gpdPbScore.Rd | 8 +-- man/gpdProfShape.Rd | 8 +-- man/gpdRl.Rd | 13 ++--- man/gpdSeqTests.Rd | 23 +++------ man/lowestoft.Rd | 2 man/mrlPlot.Rd | 2 man/pSeqStop.Rd | 10 +--- 45 files changed, 309 insertions(+), 321 deletions(-)
Title: Estimation and Comparison of Dynamic Treatment Regimes
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials.
Author: Xinyu Tang [aut, cre],
Maria Melguizo [aut]
Maintainer: Xinyu Tang <xtang@uams.edu>
Diff between DTR versions 1.6 dated 2015-05-06 and 1.7 dated 2015-12-31
DESCRIPTION | 14 ++++----- MD5 | 14 ++++----- NAMESPACE | 4 -- R/plot.CHR.R | 75 ++++++++++++++++-------------------------------- R/plot.DTR.R | 80 ++++++++++++++++++---------------------------------- inst/NEWS.Rd | 6 +++ man/DTR-internal.Rd | 5 --- man/DTR-package.Rd | 4 +- 8 files changed, 78 insertions(+), 124 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut, cre],
Joe Cheng [aut],
Yihui Xie [aut],
Jonathan McPherson [aut],
Winston Chang [aut],
Jeff Allen [aut],
Hadley Wickham [aut],
Aron Atkins [aut],
Rob Hyndman [aut],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rmarkdown versions 0.9 dated 2015-12-22 and 0.9.1 dated 2015-12-31
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/beamer_presentation.R | 4 ++-- R/html_resources.R | 2 +- R/pdf_document.R | 6 +++--- R/render.R | 12 +++++++++--- R/tufte_handout.R | 2 +- inst/NEWS | 9 +++++++++ man/beamer_presentation.Rd | 4 ++-- man/pdf_document.Rd | 4 ++-- man/tufte_handout.Rd | 4 ++-- tests/testthat/test-resources.R | 13 +++++++++++++ 12 files changed, 59 insertions(+), 31 deletions(-)
Title: Financial Functions & More
Description: This fills the gaps credit analysts and loan modellers at
Optimum Credit identify in the existing R code body.
It allows for the production of documentation with less coding,
replicates a number of Microsoft Excel functions useful for
modelling loans (without rounding), and other helpful functions
for producing charts and tables. It also has some additional scales for
use, including a GBP scale.
Author: Stephanie Locke [aut, cre]
Maintainer: Stephanie Locke <stephanie.g.locke@gmail.com>
Diff between optiRum versions 0.37.1 dated 2015-11-07 and 0.37.3 dated 2015-12-31
optiRum-0.37.1/optiRum/inst/doc/index.Rmd |only optiRum-0.37.1/optiRum/inst/doc/presentation.Rmd |only optiRum-0.37.1/optiRum/vignettes |only optiRum-0.37.3/optiRum/DESCRIPTION | 10 ++-- optiRum-0.37.3/optiRum/MD5 | 28 +++++------- optiRum-0.37.3/optiRum/NAMESPACE | 9 +++- optiRum-0.37.3/optiRum/NEWS | 10 ++++ optiRum-0.37.3/optiRum/R/optiRum-package.r | 6 +- optiRum-0.37.3/optiRum/R/theme_optimum.R | 35 +++++++++++++--- optiRum-0.37.3/optiRum/README.md | 4 - optiRum-0.37.3/optiRum/build/vignette.rds |binary optiRum-0.37.3/optiRum/inst/doc/index.html | 10 ++-- optiRum-0.37.3/optiRum/inst/doc/presentation.html | 6 +- optiRum-0.37.3/optiRum/man/theme_optimum.Rd | 4 - optiRum-0.37.3/optiRum/tests/testthat/datatabletest.Rnw | 2 optiRum-0.37.3/optiRum/tests/testthat/datatabletest.pdf |binary 16 files changed, 79 insertions(+), 45 deletions(-)
Title: Default Color Maps from 'matplotlib'
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph] (Continuous scale),
Bob Rudis [ctb, cph] (Combined scales)
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3.1 dated 2015-10-11 and 0.3.2 dated 2015-12-31
DESCRIPTION | 19 ++++++++------- MD5 | 24 +++++++++---------- NAMESPACE | 2 - R/scales.R | 45 ++++++++++++++++++++++++++++-------- R/viridis.R | 24 +++++++++++-------- build/vignette.rds |binary inst/doc/intro-to-viridis.Rmd | 2 - inst/doc/intro-to-viridis.html | 50 +++++++++++++++++++++++++---------------- man/scale_viridis.Rd | 14 +++++++++-- man/viridis.Rd | 16 ++++++++----- man/viridis.map.Rd | 2 - man/viridis_pal.Rd | 9 +++++-- vignettes/intro-to-viridis.Rmd | 2 - 13 files changed, 134 insertions(+), 75 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI (http://vcg.isti.cnr.it),
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk (svn://
svn.code.sf.net/p/vcg/code/trunk/vcglib) and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager; the authors of VCGLIB for the included version of the
code
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.13.1 dated 2015-12-22 and 0.13.1.1 dated 2015-12-31
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/Rvcg-package.R | 4 ++-- inst/NEWS.Rd | 10 +++++++++- man/Rvcg-package.Rd | 4 ++-- src/vcglib/vcg/math/base.h | 12 +++++++----- 6 files changed, 29 insertions(+), 19 deletions(-)
Title: D3 JavaScript Network Graphs from R
Description: Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey
graphs from 'R'.
Author: Christopher Gandrud [aut, cre],
J.J. Allaire [aut],
Kenton Russell [aut],
B.W. Lewis [ctb],
Kevin Kuo [ctb],
Charles Sese [ctb],
Peter Ellis [ctb],
Jonathan Owen [ctb],
Jennifer Rogers [ctb]
Maintainer: Christopher Gandrud <christopher.gandrud@gmail.com>
Diff between networkD3 versions 0.2.6 dated 2015-10-11 and 0.2.8 dated 2015-12-31
networkD3-0.2.6/networkD3/data/MisLinks.tab |only networkD3-0.2.6/networkD3/data/MisNodes.tab |only networkD3-0.2.6/networkD3/man/energy.Rd |only networkD3-0.2.6/networkD3/man/flare.Rd |only networkD3-0.2.8/networkD3/DESCRIPTION | 10 + networkD3-0.2.8/networkD3/MD5 | 50 ++++---- networkD3-0.2.8/networkD3/NAMESPACE | 2 networkD3-0.2.8/networkD3/NEWS | 71 +++++++----- networkD3-0.2.8/networkD3/R/data-definitions.R | 46 +------ networkD3-0.2.8/networkD3/R/sankeyNetwork.R | 42 +++++-- networkD3-0.2.8/networkD3/README.md | 24 ++-- networkD3-0.2.8/networkD3/data/MisLinks.rda |only networkD3-0.2.8/networkD3/data/MisNodes.rda |only networkD3-0.2.8/networkD3/inst/htmlwidgets/forceNetwork.js | 36 ++---- networkD3-0.2.8/networkD3/inst/htmlwidgets/sankeyNetwork.js | 47 ++++++- networkD3-0.2.8/networkD3/man/JS.Rd | 2 networkD3-0.2.8/networkD3/man/MisLinks.Rd | 7 - networkD3-0.2.8/networkD3/man/MisNodes.Rd | 9 + networkD3-0.2.8/networkD3/man/as.radialNetwork.Rd | 3 networkD3-0.2.8/networkD3/man/chordNetwork.Rd | 21 +-- networkD3-0.2.8/networkD3/man/dendroNetwork.Rd | 3 networkD3-0.2.8/networkD3/man/diagonalNetwork.Rd | 5 networkD3-0.2.8/networkD3/man/forceNetwork.Rd | 3 networkD3-0.2.8/networkD3/man/networkD3-package.Rd | 2 networkD3-0.2.8/networkD3/man/networkD3-shiny.Rd | 6 - networkD3-0.2.8/networkD3/man/radialNetwork.Rd | 5 networkD3-0.2.8/networkD3/man/sankeyNetwork.Rd | 31 +++-- networkD3-0.2.8/networkD3/man/saveNetwork.Rd | 4 networkD3-0.2.8/networkD3/man/simpleNetwork.Rd | 3 29 files changed, 253 insertions(+), 179 deletions(-)
Title: Default Color Maps from 'matplotlib' (Lite Version)
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness. This is the 'lite' version of the more complete 'viridis' package
that can be found at <https://cran.r-project.org/package=viridis>.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridisLite versions 0.1 dated 2015-11-13 and 0.1.1 dated 2015-12-31
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- R/viridis.R | 31 ++++++++++++++++--------------- man/viridis.Rd | 17 ++++++++++------- 4 files changed, 35 insertions(+), 30 deletions(-)
Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 3.0 dated 2015-10-29 and 3.1 dated 2015-12-31
DESCRIPTION | 8 ++-- MD5 | 48 +++++++++++++------------- NEWS | 5 ++ R/fitsde.R | 10 ++--- R/ftpsde.R | 36 +++++++++---------- R/rsde.R | 36 +++++++++---------- R/snssde.R | 80 ++++++++++++++++++++++---------------------- R/st.int.R | 12 +++--- R/zzz.r | 6 +-- build/vignette.rds |binary inst/doc/FitSDE.Rnw | 7 ++- inst/doc/FitSDE.pdf |binary inst/doc/Introduction.Rnw | 2 - inst/doc/Introduction.pdf |binary inst/doc/SDEs.Rnw | 4 +- inst/doc/SDEs.pdf |binary inst/doc/Thumbs.db |binary man/Sim.DiffProc-package.Rd | 4 +- man/bridgesde2d.Rd | 2 - man/fitsde.Rd | 5 +- vignettes/Core_FitSDE.tex | 29 ++++++++------- vignettes/FitSDE.Rnw | 7 ++- vignettes/Introduction.Rnw | 2 - vignettes/SDEs.Rnw | 4 +- vignettes/Thumbs.db |binary 25 files changed, 157 insertions(+), 150 deletions(-)
Title: Paralellised Versions of Constraint Based Causal Discovery
Algorithms
Description: Parallelise constraint based causality discovery and causal inference methods. The parallelised algorithms in the package will generate the same results as that of the 'pcalg' package but will be much more efficient.
Author: Thuc Duy Le, Tao Hoang, Shu Hu, and Liang Zhang
Maintainer: Thuc Duy Le <Thuc.Le@unisa.edu.au>
Diff between ParallelPC versions 1.1 dated 2015-10-02 and 1.2 dated 2015-12-31
DESCRIPTION | 10 +- MD5 | 53 ++++++------ NAMESPACE | 64 +++++++-------- inst |only man/IDA_parallel.Rd | 112 +++++++++++++------------- man/IDA_stable.Rd | 82 +++++++++---------- man/cor2.Rd | 74 ++++++++--------- man/fci_parallel.Rd | 196 +++++++++++++++++++++++------------------------ man/fci_stable.Rd | 146 +++++++++++++++++------------------ man/jointIDA_direct.Rd | 76 +++++++++--------- man/jointIDA_parallel.Rd | 112 +++++++++++++------------- man/mccor.Rd | 70 ++++++++-------- man/mcmig.Rd | 70 ++++++++-------- man/mczf.Rd | 70 ++++++++-------- man/mig.Rd | 70 ++++++++-------- man/migsh.Rd | 70 ++++++++-------- man/pcSelect_parallel.Rd | 144 +++++++++++++++++----------------- man/pcSelect_stable.Rd | 108 ++++++++++++------------- man/pc_parallel.Rd | 174 ++++++++++++++++++++--------------------- man/pc_stable.Rd | 122 ++++++++++++++--------------- man/rfci_parallel.Rd | 184 ++++++++++++++++++++++---------------------- man/rfci_stable.Rd | 128 +++++++++++++++--------------- man/skeleton_parallel.Rd | 138 ++++++++++++++++----------------- man/skeleton_stable.Rd | 102 ++++++++++++------------ man/smccor.Rd | 70 ++++++++-------- man/smcmig.Rd | 70 ++++++++-------- man/smczf.Rd | 70 ++++++++-------- man/zf.Rd | 70 ++++++++-------- 28 files changed, 1328 insertions(+), 1327 deletions(-)
Title: Symbolic Computation and More with Multivariate Polynomials
Description: Symbolic computing with multivariate polynomials in R.
Author: David Kahle [aut, cre]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between mpoly versions 0.1.0 dated 2015-05-01 and 1.0.0 dated 2015-12-31
mpoly-0.1.0/mpoly/R/is.linear.R |only mpoly-0.1.0/mpoly/R/is.mpoly.R |only mpoly-0.1.0/mpoly/R/is.mpolyList.R |only mpoly-0.1.0/mpoly/R/is.wholenumber.R |only mpoly-0.1.0/mpoly/man/is.linear.Rd |only mpoly-0.1.0/mpoly/man/is.mpoly.Rd |only mpoly-0.1.0/mpoly/man/is.mpolyList.Rd |only mpoly-1.0.0/mpoly/DESCRIPTION | 14 mpoly-1.0.0/mpoly/MD5 | 129 ++++---- mpoly-1.0.0/mpoly/NAMESPACE | 24 + mpoly-1.0.0/mpoly/NEWS | 55 +++ mpoly-1.0.0/mpoly/R/LCM.R | 5 mpoly-1.0.0/mpoly/R/as.function.mpoly.R | 103 +++++- mpoly-1.0.0/mpoly/R/as.function.mpolyList.R | 18 - mpoly-1.0.0/mpoly/R/as.mpoly.R | 55 +++ mpoly-1.0.0/mpoly/R/bernstein.R |only mpoly-1.0.0/mpoly/R/bezier.R |only mpoly-1.0.0/mpoly/R/burst.R | 8 mpoly-1.0.0/mpoly/R/chebyshev.R |only mpoly-1.0.0/mpoly/R/deriv.mpoly.R | 7 mpoly-1.0.0/mpoly/R/grobner.R | 14 mpoly-1.0.0/mpoly/R/help.R | 10 mpoly-1.0.0/mpoly/R/hermite.R |only mpoly-1.0.0/mpoly/R/jacobi.R |only mpoly-1.0.0/mpoly/R/laguerre.R |only mpoly-1.0.0/mpoly/R/legendre.R |only mpoly-1.0.0/mpoly/R/mp.R | 59 +++ mpoly-1.0.0/mpoly/R/mpoly.R | 9 mpoly-1.0.0/mpoly/R/mpolyList.R | 29 + mpoly-1.0.0/mpoly/R/mpolyListArithmetic.R | 2 mpoly-1.0.0/mpoly/R/partitions.R | 5 mpoly-1.0.0/mpoly/R/permutations.R | 3 mpoly-1.0.0/mpoly/R/plug.R |only mpoly-1.0.0/mpoly/R/predicates.R |only mpoly-1.0.0/mpoly/R/print.mpoly.R | 20 - mpoly-1.0.0/mpoly/R/print.mpolyList.R | 13 mpoly-1.0.0/mpoly/R/reorder.mpoly.R | 5 mpoly-1.0.0/mpoly/R/round.mpoly.R | 13 mpoly-1.0.0/mpoly/R/swap.R |only mpoly-1.0.0/mpoly/R/terms.mpoly.R | 4 mpoly-1.0.0/mpoly/R/tuples.R | 56 ++- mpoly-1.0.0/mpoly/README.md | 372 ++++++++++++++++++++++--- mpoly-1.0.0/mpoly/man/LCM.Rd | 5 mpoly-1.0.0/mpoly/man/as.function.mpoly.Rd | 34 +- mpoly-1.0.0/mpoly/man/as.function.mpolyList.Rd | 26 + mpoly-1.0.0/mpoly/man/as.mpoly.Rd | 22 - mpoly-1.0.0/mpoly/man/bernstein.Rd |only mpoly-1.0.0/mpoly/man/bernsteinApprox.Rd |only mpoly-1.0.0/mpoly/man/bezier.Rd |only mpoly-1.0.0/mpoly/man/bezierFunction.Rd |only mpoly-1.0.0/mpoly/man/burst.Rd | 7 mpoly-1.0.0/mpoly/man/chebyshev.Rd |only mpoly-1.0.0/mpoly/man/deriv.mpoly.Rd | 5 mpoly-1.0.0/mpoly/man/gradient.Rd | 2 mpoly-1.0.0/mpoly/man/grobner.Rd | 16 - mpoly-1.0.0/mpoly/man/hermite.Rd |only mpoly-1.0.0/mpoly/man/insert.Rd | 6 mpoly-1.0.0/mpoly/man/is.wholenumber.Rd | 6 mpoly-1.0.0/mpoly/man/jacobi.Rd |only mpoly-1.0.0/mpoly/man/laguerre.Rd |only mpoly-1.0.0/mpoly/man/legendre.Rd |only mpoly-1.0.0/mpoly/man/mp.Rd | 27 + mpoly-1.0.0/mpoly/man/mpoly.Rd | 22 - mpoly-1.0.0/mpoly/man/mpolyArithmetic.Rd | 6 mpoly-1.0.0/mpoly/man/mpolyEqual.Rd | 6 mpoly-1.0.0/mpoly/man/mpolyList.Rd | 17 - mpoly-1.0.0/mpoly/man/mpolyListArithmetic.Rd | 4 mpoly-1.0.0/mpoly/man/partitions.Rd | 7 mpoly-1.0.0/mpoly/man/permutations.Rd | 5 mpoly-1.0.0/mpoly/man/plug.Rd |only mpoly-1.0.0/mpoly/man/predicates.Rd |only mpoly-1.0.0/mpoly/man/print.mpoly.Rd | 13 mpoly-1.0.0/mpoly/man/print.mpolyList.Rd | 13 mpoly-1.0.0/mpoly/man/reorder.mpoly.Rd | 10 mpoly-1.0.0/mpoly/man/round.mpoly.Rd | 7 mpoly-1.0.0/mpoly/man/swap.Rd |only mpoly-1.0.0/mpoly/man/terms.mpoly.Rd | 3 mpoly-1.0.0/mpoly/man/tuples.Rd | 23 + mpoly-1.0.0/mpoly/man/vars.Rd | 6 mpoly-1.0.0/mpoly/tests/testthat/test-mp.r | 2 80 files changed, 978 insertions(+), 354 deletions(-)
Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@mcmaster.ca>
Diff between markophylo versions 1.0.3 dated 2015-11-05 and 1.0.4 dated 2015-12-31
DESCRIPTION | 9 +- MD5 | 18 ++--- NEWS | 7 ++ R/custom-general14.R | 141 +++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/estimaterates.Rmd | 5 + inst/doc/estimaterates.html | 129 ++++++++++++++++++++-------------------- man/markophylo-package.Rd | 4 - tests/testthat/test-main.R | 33 +++++----- vignettes/estimaterates.Rmd | 5 + 10 files changed, 183 insertions(+), 168 deletions(-)
Title: Fractional ARIMA (and Other Long Memory) Time Series Modeling
Description: Simulates, fits, and predicts long-memory and anti-persistent time
series, possibly mixed with ARMA, regression, transfer-function components.
Exact methods (MLE, forecasting, simulation) are used.
Author: Justin Q. Veenstra [aut, cre],
A.I. McLeod [aut]
Maintainer: Justin Q. Veenstra <justin.veenstra@gmail.com>
Diff between arfima versions 1.3-3 dated 2015-12-28 and 1.3-4 dated 2015-12-31
DESCRIPTION | 6 MD5 | 10 R/arfima.R | 2429 ++++++++++++++++++++++++++++----------------------------- R/arfimaFit.R | 1 man/SeriesJ.Rd | 92 +- man/arfima.Rd | 2 6 files changed, 1275 insertions(+), 1265 deletions(-)