Title: Test Analysis Modules
Description:
Includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models).
Latent regression models and plausible value imputation are
also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <a.robitzsch@bifie.at>
Diff between TAM versions 1.7-1 dated 2015-06-05 and 1.8-0 dated 2015-06-26
DESCRIPTION | 10 - MD5 | 55 +++++----- NAMESPACE | 10 + R/IRT.informationCurve.R |only R/calc_exp_TK.R | 31 ++++- R/mml.3pl.calc_prob.v5.R | 4 R/plot.IRT.informationCurves.R |only R/plotDevianceTAM.R | 2 R/tam.latreg.R | 3 R/tam.mml.2pl.R | 8 + R/tam.mml.3pl.R | 18 ++- R/tam.mml.3pl.est.guessing.R | 28 ++++- R/tam.mml.3pl.est.slopes.R | 3 R/tam.mml.3pl.preproc.R | 34 +++++- R/tam.mml.R | 79 ++++++-------- R/tam.mml.mfr.R | 10 + R/tamaan.3pl.trait.R | 3 R/tamaanify.R | 15 +- R/tamaanify.modelconstraint.loadings.R | 2 R/tamaanify.proc.items.R | 12 ++ R/tamaanify.proc.loadings.B.fixed.R | 10 + R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R | 22 +++- inst/NEWS | 69 ++++++++---- man/IRT.informationCurves.Rd |only man/TAM-package.Rd | 2 man/tam.mml.3pl.Rd | 33 +++++- man/tam.mml.Rd | 17 ++- man/tamaanify.Rd | 1 src/tam_calcexp.cpp | 134 ++++++++++++++++++++++++- src/tam_mml_3pl_helper_functions.cpp | 20 ++- 30 files changed, 487 insertions(+), 148 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 0.12.1 dated 2015-06-23 and 0.12.2 dated 2015-06-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/Rvcg-package.R | 4 ++-- man/Rvcg-package.Rd | 4 ++-- src/Rmarch.cpp | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-)
Title: Latent Budget Analysis for Compositional Data
Description: Latent budget analysis is a method for the analysis of a two-way contingency table with an exploratory variable and a response variable. It is specially designed for compositional data.
Author: Enio G. Jelihovschi <eniojelihovs@gmail.com> and
Ivan Bezerra Allaman <ivanalaman@gmail.com>
Maintainer: Enio G. Jelihovschi <eniojelihovs@gmail.com>
Diff between lba versions 1.0 dated 2015-01-22 and 1.2 dated 2015-06-26
ChangeLog |only DESCRIPTION | 10 +++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 22 ++++++++++++++++++++++ R/goodnessfit.R | 12 ++++++------ R/lba.ls.fe.R | 9 +++++++++ R/lba.ls.logit.R | 29 ++++++++++++++++++++++++++++- R/lba.mle.R | 2 +- R/lba.mle.fe.R | 18 ++++++++++++++++++ R/lba.mle.logit.R | 27 +++++++++++++++++++++++++++ R/plot.lba.R | 12 ++++++++---- R/summary.lba.ls.fe.R | 14 ++++++++++---- R/summary.lba.ls.logit.R | 22 ++++++++++++++-------- R/summary.lba.mle.fe.R | 14 ++++++++++---- R/summary.lba.mle.logit.R | 22 ++++++++++++++-------- README.md |only man/lba.Rd | 6 ++++-- 17 files changed, 192 insertions(+), 57 deletions(-)
Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.4 dated 2015-06-04 and 1.2.5 dated 2015-06-26
icenReg-1.2.4/icenReg/data/mice_data.RData |only icenReg-1.2.4/icenReg/man/mice_data.Rd |only icenReg-1.2.5/icenReg/DESCRIPTION | 10 icenReg-1.2.5/icenReg/MD5 | 35 +- icenReg-1.2.5/icenReg/NEWS |only icenReg-1.2.5/icenReg/R/Utilities.R | 144 +++++++++-- icenReg-1.2.5/icenReg/R/user_functions.R | 98 ++++--- icenReg-1.2.5/icenReg/data/essIncData.RData |only icenReg-1.2.5/icenReg/data/essIncData_small.RData |only icenReg-1.2.5/icenReg/data/miceData.RData |only icenReg-1.2.5/icenReg/man/diag_baseline.Rd | 36 +- icenReg-1.2.5/icenReg/man/diag_covar.Rd | 40 +-- icenReg-1.2.5/icenReg/man/essIncData.Rd |only icenReg-1.2.5/icenReg/man/essIncData_small.Rd |only icenReg-1.2.5/icenReg/man/ic_par.Rd | 11 icenReg-1.2.5/icenReg/man/ic_sp.Rd | 8 icenReg-1.2.5/icenReg/man/miceData.Rd |only icenReg-1.2.5/icenReg/man/simIC_weib.Rd | 2 icenReg-1.2.5/icenReg/src/icenReg_files/basicUtilities.cpp | 15 - icenReg-1.2.5/icenReg/src/icenReg_files/ic_par.cpp | 66 +++-- icenReg-1.2.5/icenReg/src/icenReg_files/ic_par.h | 11 icenReg-1.2.5/icenReg/src/icenReg_files/ic_sp_ch.cpp | 160 ++++++++++--- icenReg-1.2.5/icenReg/src/icenReg_files/ic_sp_ch.h | 49 +++ 23 files changed, 489 insertions(+), 196 deletions(-)
Title: Additive and Multiplicative Effects Models for Networks and
Relational Data
Description: Analysis of dyadic network and relational data using additive and
multiplicative effects (AME) models. The basic model includes
regression terms, the covariance structure of the social relations model
(Warner, Kenny and Stoto (1979), Wong (1982)), and multiplicative factor
models (Hoff(2009)). Four different link functions accommodate different
relational data structures, including binary/network data (bin), normal
relational data (nrm), ordinal relational data (ord) and data from
fixed-rank nomination schemes (frn). Several of these link functions are
discussed in Hoff, Fosdick, Volfovsky and Stovel (2013). Development of this
software was supported in part by NIH grant R01HD067509.
Author: Peter Hoff, Bailey Fosdick, Alex Volfovsky, Yanjun He
Maintainer: Peter Hoff <pdhoff@uw.edu>
Diff between amen versions 1.0 dated 2015-02-26 and 1.1 dated 2015-06-26
amen-1.0/amen/R/rs2_rep.R |only amen-1.0/amen/data/YX_bin.rda |only amen-1.0/amen/data/YX_bin_long.rda |only amen-1.0/amen/data/YX_cbin.rda |only amen-1.0/amen/data/YX_frn.rda |only amen-1.0/amen/data/YX_nrm.rda |only amen-1.0/amen/data/YX_ord.rda |only amen-1.0/amen/data/YX_rrl.rda |only amen-1.0/amen/data/conflict90s.RData |only amen-1.0/amen/man/conflict90s.Rd |only amen-1.1/amen/DESCRIPTION | 33 - amen-1.1/amen/MD5 | 215 ++++++----- amen-1.1/amen/NAMESPACE | 13 amen-1.1/amen/R/Xbeta.R | 12 amen-1.1/amen/R/addlines.R |only amen-1.1/amen/R/ame.R | 324 +++++++++++----- amen-1.1/amen/R/ame_rep.R | 674 ++++++++++++++++++++--------------- amen-1.1/amen/R/amen-package.R | 93 +++- amen-1.1/amen/R/circplot.R |only amen-1.1/amen/R/design_array.R | 11 amen-1.1/amen/R/el2sm.R |only amen-1.1/amen/R/gofstats.R | 7 amen-1.1/amen/R/mhalf.R | 9 amen-1.1/amen/R/netplot.R |only amen-1.1/amen/R/plot.ame.R | 43 -- amen-1.1/amen/R/rUV_fc.R | 63 --- amen-1.1/amen/R/rUV_rep_fc.R | 62 --- amen-1.1/amen/R/rUV_sym_fc.R |only amen-1.1/amen/R/rZ_bin_fc.R | 28 - amen-1.1/amen/R/rZ_cbin_fc.R | 51 -- amen-1.1/amen/R/rZ_frn_fc.R | 59 --- amen-1.1/amen/R/rZ_nrm_fc.R | 13 amen-1.1/amen/R/rZ_ord_fc.R | 36 - amen-1.1/amen/R/rZ_rrl.R | 52 -- amen-1.1/amen/R/raSab_bin_fc.R | 27 - amen-1.1/amen/R/raSab_cbin_fc.R | 31 - amen-1.1/amen/R/raSab_frn_fc.R | 24 - amen-1.1/amen/R/rbeta_ab_fc.R | 84 ---- amen-1.1/amen/R/rbeta_ab_rep_fc.R | 94 ---- amen-1.1/amen/R/rmvnorm.R | 9 amen-1.1/amen/R/rrho_mh.R | 22 - amen-1.1/amen/R/rrho_mh_rep.R | 29 - amen-1.1/amen/R/rs2_fc.R | 10 amen-1.1/amen/R/rs2_rep_fc.R |only amen-1.1/amen/R/simY_bin.R | 15 amen-1.1/amen/R/simY_frn.R | 30 - amen-1.1/amen/R/simY_nrm.R | 14 amen-1.1/amen/R/simY_ord.R | 20 - amen-1.1/amen/R/simY_rrl.R | 24 - amen-1.1/amen/R/simZ.R | 12 amen-1.1/amen/R/sm2el.R |only amen-1.1/amen/R/summary.ame.R | 34 - amen-1.1/amen/R/xnet.R |only amen-1.1/amen/R/zscores.R | 9 amen-1.1/amen/build |only amen-1.1/amen/data/IR90s.RData |only amen-1.1/amen/data/YX_bin.RData |only amen-1.1/amen/data/YX_bin_long.RData |only amen-1.1/amen/data/YX_cbin.RData |only amen-1.1/amen/data/YX_frn.RData |only amen-1.1/amen/data/YX_nrm.RData |only amen-1.1/amen/data/YX_ord.RData |only amen-1.1/amen/data/YX_rrl.RData |only amen-1.1/amen/data/coldwar.RData |binary amen-1.1/amen/data/comtrade.RData |binary amen-1.1/amen/data/datalist | 3 amen-1.1/amen/data/sheep.RData |only amen-1.1/amen/inst |only amen-1.1/amen/man/IR90s.Rd |only amen-1.1/amen/man/Xbeta.Rd | 14 amen-1.1/amen/man/YX_bin.Rd | 3 amen-1.1/amen/man/YX_bin_long.Rd | 3 amen-1.1/amen/man/YX_cbin.Rd | 3 amen-1.1/amen/man/YX_frn.Rd | 3 amen-1.1/amen/man/YX_nrm.Rd | 3 amen-1.1/amen/man/YX_ord.Rd | 3 amen-1.1/amen/man/YX_rrl.Rd | 3 amen-1.1/amen/man/addhealthc3.Rd | 5 amen-1.1/amen/man/addhealthc9.Rd | 3 amen-1.1/amen/man/addlines.Rd |only amen-1.1/amen/man/ame.Rd | 28 - amen-1.1/amen/man/ame_rep.Rd | 29 - amen-1.1/amen/man/amen-package.Rd | 5 amen-1.1/amen/man/circplot.Rd |only amen-1.1/amen/man/coldwar.Rd | 7 amen-1.1/amen/man/comtrade.Rd | 22 - amen-1.1/amen/man/design_array.Rd | 7 amen-1.1/amen/man/dutchcollege.Rd | 6 amen-1.1/amen/man/el2sm.Rd |only amen-1.1/amen/man/gofstats.Rd | 3 amen-1.1/amen/man/lazegalaw.Rd | 3 amen-1.1/amen/man/mhalf.Rd | 11 amen-1.1/amen/man/netplot.Rd |only amen-1.1/amen/man/plot.ame.Rd | 38 - amen-1.1/amen/man/rUV_fc.Rd | 55 -- amen-1.1/amen/man/rUV_rep_fc.Rd | 63 --- amen-1.1/amen/man/rUV_sym_fc.Rd |only amen-1.1/amen/man/rZ_bin_fc.Rd | 30 - amen-1.1/amen/man/rZ_cbin_fc.Rd | 51 -- amen-1.1/amen/man/rZ_frn_fc.Rd | 62 --- amen-1.1/amen/man/rZ_nrm_fc.Rd | 13 amen-1.1/amen/man/rZ_ord_fc.Rd | 34 - amen-1.1/amen/man/rZ_rrl_fc.Rd | 48 -- amen-1.1/amen/man/raSab_bin_fc.Rd | 28 - amen-1.1/amen/man/raSab_cbin_fc.Rd | 30 - amen-1.1/amen/man/raSab_frn_fc.Rd | 24 - amen-1.1/amen/man/rbeta_ab_fc.Rd | 86 ---- amen-1.1/amen/man/rbeta_ab_rep_fc.Rd | 95 ---- amen-1.1/amen/man/rmvnorm.Rd | 11 amen-1.1/amen/man/rrho_mh.Rd | 24 - amen-1.1/amen/man/rrho_mh_rep.Rd | 30 - amen-1.1/amen/man/rs2_fc.Rd | 12 amen-1.1/amen/man/rs2_rep_fc.Rd | 17 amen-1.1/amen/man/rwish.Rd | 3 amen-1.1/amen/man/sampsonmonks.Rd | 3 amen-1.1/amen/man/sheep.Rd |only amen-1.1/amen/man/simY_bin.Rd | 17 amen-1.1/amen/man/simY_frn.Rd | 30 - amen-1.1/amen/man/simY_nrm.Rd | 16 amen-1.1/amen/man/simY_ord.Rd | 21 - amen-1.1/amen/man/simY_rrl.Rd | 26 - amen-1.1/amen/man/simZ.Rd | 14 amen-1.1/amen/man/sm2el.Rd |only amen-1.1/amen/man/summary.ame.Rd | 24 - amen-1.1/amen/man/xnet.Rd |only amen-1.1/amen/man/zscores.Rd | 10 amen-1.1/amen/vignettes |only 127 files changed, 1033 insertions(+), 2335 deletions(-)
Title: Functions for Calibrating Control Charts
Description: Calibration of thresholds of control charts such as
CUSUM charts based on past data, taking estimation error into account.
Author: Axel Gandy <a.gandy@imperial.ac.uk> and Jan Terje Kvaloy <jan.t.kvaloy@uis.no>.
Maintainer: Axel Gandy <a.gandy@imperial.ac.uk>
Diff between spcadjust versions 0.1-3 dated 2014-08-26 and 0.9 dated 2015-06-26
DESCRIPTION | 14 - MD5 | 35 ++ R/main.R | 17 + build |only inst/doc/CUSUM_LinearRegression.R |only inst/doc/CUSUM_LinearRegression.Rmd |only inst/doc/CUSUM_LinearRegression.html |only inst/doc/CUSUM_LogisticRegression.R |only inst/doc/CUSUM_LogisticRegression.Rmd |only inst/doc/CUSUM_LogisticRegression.html |only inst/doc/CUSUM_NormalNormal.R |only inst/doc/CUSUM_NormalNormal.Rmd |only inst/doc/CUSUM_NormalNormal.html |only inst/doc/Methods.pdf |only inst/doc/Shewhart_NormalNormal.R |only inst/doc/Shewhart_NormalNormal.Rmd |only inst/doc/Shewhart_NormalNormal.html |only inst/doc/papers.bib |only inst/doc/spcadjust-intro.R | 401 +++++++++++++++------------------ inst/doc/spcadjust-intro.pdf |binary man/SPCShew-class.Rd | 5 man/SPCShewNormalCenterScale-class.Rd | 25 +- vignettes/CUSUM_LinearRegression.Rmd |only vignettes/CUSUM_LogisticRegression.Rmd |only vignettes/CUSUM_NormalNormal.Rmd |only vignettes/Shewhart_NormalNormal.Rmd |only vignettes/spcadjust-intro.Rnw | 131 +++++++--- vignettes/spcadjustClasses.pdf |binary 28 files changed, 362 insertions(+), 266 deletions(-)
Title: Entrez in R
Description: Provides an R interact to the NCBI's EUtils API allowing
users to search databases like genbank and pubmed, process the resulting
files and pull data into their R sessions.
Author: David Winter [aut, cre],
Scott Chamberlain [ctb]
Maintainer: David Winter <david.winter@gmail.com>
Diff between rentrez versions 0.4.1 dated 2015-03-03 and 0.4.2 dated 2015-06-26
DESCRIPTION | 12 ++++---- MD5 | 42 ++++++++++++++-------------- NAMESPACE | 2 - NEWS | 4 ++ build/vignette.rds |binary inst/doc/rentrez_tutorial.R | 61 ++++++++++++++++------------------------- inst/doc/rentrez_tutorial.html | 8 ++--- man/entrez_citmatch.Rd | 2 - man/entrez_db_links.Rd | 2 - man/entrez_db_searchable.Rd | 2 - man/entrez_db_summary.Rd | 2 - man/entrez_dbs.Rd | 2 - man/entrez_fetch.Rd | 2 - man/entrez_global_query.Rd | 2 - man/entrez_info.Rd | 2 - man/entrez_link.Rd | 2 - man/entrez_post.Rd | 2 - man/entrez_search.Rd | 2 - man/entrez_summary.Rd | 2 - man/parse_pubmed_xml.Rd | 2 - man/rentrez.Rd | 2 - tests/testthat/test_webenv.r | 4 +- 22 files changed, 76 insertions(+), 85 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013).
Author: Gerta Rücker [aut],
Guido Schwarzer [aut, cre],
Ulrike Krahn [aut],
Jochem König [aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 0.7-0 dated 2015-02-04 and 0.8-0 dated 2015-06-26
DESCRIPTION | 10 +++++----- MD5 | 17 ++++++++++------- NAMESPACE | 4 +++- NEWS | 26 ++++++++++++++++++++++++-- R/netmeta.R | 2 +- R/netrank.R |only R/print.netmeta.R | 4 ++-- R/print.netrank.R |only man/netgraph.Rd | 46 +++++++++++++++++++++++++++------------------- man/netmeta.Rd | 27 ++++++++++++++++++--------- man/netrank.Rd |only 11 files changed, 90 insertions(+), 46 deletions(-)
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the 'FME' package.
If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions.
Please note that no warranty is implied for correctness of results or fitness
for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9-38 dated 2015-06-23 and 0.9-39 dated 2015-06-26
mkin-0.9-38/mkin/NEWS |only mkin-0.9-38/mkin/inst/staticdocs |only mkin-0.9-39/mkin/DESCRIPTION | 10 +-- mkin-0.9-39/mkin/MD5 | 42 +++++++------- mkin-0.9-39/mkin/NAMESPACE | 5 + mkin-0.9-39/mkin/NEWS.md |only mkin-0.9-39/mkin/R/mkinparplot.R | 2 mkin-0.9-39/mkin/R/mmkin.R |only mkin-0.9-39/mkin/R/plot.mmkin.R |only mkin-0.9-39/mkin/README.md | 3 - mkin-0.9-39/mkin/inst/doc/FOCUS_D.html | 17 +++-- mkin-0.9-39/mkin/inst/doc/FOCUS_L.html | 74 ++++++++++++------------- mkin-0.9-39/mkin/inst/doc/FOCUS_Z.R | 2 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.Rnw | 2 mkin-0.9-39/mkin/inst/doc/FOCUS_Z.pdf |binary mkin-0.9-39/mkin/inst/doc/compiled_models.html | 42 +++++++------- mkin-0.9-39/mkin/inst/doc/mkin.pdf |binary mkin-0.9-39/mkin/man/DFOP.solution.Rd | 2 mkin-0.9-39/mkin/man/Extract.mmkin.Rd |only mkin-0.9-39/mkin/man/FOMC.solution.Rd | 2 mkin-0.9-39/mkin/man/HS.solution.Rd | 2 mkin-0.9-39/mkin/man/mkinresplot.Rd | 13 +--- mkin-0.9-39/mkin/man/mmkin.Rd |only mkin-0.9-39/mkin/man/plot.mkinfit.Rd | 10 +-- mkin-0.9-39/mkin/man/plot.mmkin.Rd |only mkin-0.9-39/mkin/vignettes/FOCUS_Z.Rnw | 2 26 files changed, 115 insertions(+), 115 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 1.1-0 dated 2015-06-12 and 1.2-0 dated 2015-06-26
DESCRIPTION | 8 +- MD5 | 122 ++++++++++++++++++++--------------------- R/jomo1.MCMCchain.R | 10 +-- R/jomo1.R | 10 +-- R/jomo1cat.MCMCchain.R | 34 ++++++++--- R/jomo1cat.R | 37 +++++++++--- R/jomo1con.MCMCchain.R | 22 ++++--- R/jomo1con.R | 25 +++++--- R/jomo1mix.MCMCchain.R | 34 ++++++++--- R/jomo1mix.R | 37 +++++++++--- R/jomo1ran.MCMCchain.R | 22 +++---- R/jomo1ran.R | 22 +++---- R/jomo1rancat.MCMCchain.R | 45 ++++++++++----- R/jomo1rancat.R | 48 +++++++++++----- R/jomo1rancathr.MCMCchain.R | 47 +++++++++++---- R/jomo1rancathr.R | 52 ++++++++++++----- R/jomo1rancon.MCMCchain.R | 33 ++++++----- R/jomo1rancon.R | 36 +++++++----- R/jomo1ranconhr.MCMCchain.R | 35 +++++++---- R/jomo1ranconhr.R | 40 ++++++++----- R/jomo1ranmix.MCMCchain.R | 45 ++++++++++----- R/jomo1ranmix.R | 48 +++++++++++----- R/jomo1ranmixhr.MCMCchain.R | 47 +++++++++++---- R/jomo1ranmixhr.R | 52 ++++++++++++----- man/jomo1.MCMCchain.Rd | 12 +++- man/jomo1.Rd | 9 ++- man/jomo1cat.MCMCchain.Rd | 11 ++- man/jomo1cat.Rd | 10 +++ man/jomo1con.MCMCchain.Rd | 10 ++- man/jomo1con.Rd | 9 ++- man/jomo1mix.MCMCchain.Rd | 13 ++++ man/jomo1mix.Rd | 9 ++- man/jomo1ran.MCMCchain.Rd | 12 +++- man/jomo1ran.Rd | 11 +++ man/jomo1rancat.MCMCchain.Rd | 13 +++- man/jomo1rancat.Rd | 10 ++- man/jomo1rancathr.MCMCchain.Rd | 11 +++ man/jomo1rancathr.Rd | 10 +++ man/jomo1rancon.MCMCchain.Rd | 11 ++- man/jomo1rancon.Rd | 9 ++- man/jomo1ranconhr.MCMCchain.Rd | 12 ++-- man/jomo1ranconhr.Rd | 10 ++- man/jomo1ranmix.MCMCchain.Rd | 12 +++- man/jomo1ranmix.Rd | 9 ++- man/jomo1ranmixhr.MCMCchain.Rd | 12 +++- man/jomo1ranmixhr.Rd | 9 ++- src/MCMCjomo1con.c | 18 ++---- src/MCMCjomo1mix.c | 22 ++----- src/MCMCjomo1rancon.c | 23 ++----- src/MCMCjomo1ranconhf.c | 23 ++----- src/MCMCjomo1ranconhr.c | 29 +++------ src/MCMCjomo1ranmix.c | 26 +++----- src/MCMCjomo1ranmixhf.c | 27 +++------ src/MCMCjomo1ranmixhr.c | 32 ++++------ src/jomo1con.c | 8 +- src/jomo1mix.c | 12 ++-- src/jomo1rancon.c | 12 ++-- src/jomo1ranconhf.c | 12 ++-- src/jomo1ranconhr.c | 18 +++--- src/jomo1ranmix.c | 16 ++--- src/jomo1ranmixhf.c | 16 ++--- src/jomo1ranmixhr.c | 22 +++---- 62 files changed, 906 insertions(+), 555 deletions(-)
Title: Racing for Unbalanced Methods Selection
Description: A dataset is said to be unbalanced when the class of interest (minority class) is much rarer than normal behaviour (majority class). The cost of missing a minority class is typically much higher that missing a majority class. Most learning systems are not prepared to cope with unbalanced data and several techniques have been proposed. This package implements some of most well-known techniques and propose a racing algorithm to select adaptively the most appropriate strategy for a given unbalanced task.
Author: Andrea Dal Pozzolo, Olivier Caelen and Gianluca Bontempi
Maintainer: Andrea Dal Pozzolo <adalpozz@ulb.ac.be>
Diff between unbalanced versions 1.1 dated 2014-02-05 and 2.0 dated 2015-06-26
DESCRIPTION | 17 +++--- MD5 | 51 ++++++++++--------- NAMESPACE | 4 - R/ubBalance.R | 122 ++++++++++++++++++++++++---------------------- R/ubCNN.R | 2 R/ubENN.R | 19 ++++--- R/ubNCL.R | 102 ++++++++++++++++++-------------------- R/ubOSS.R | 19 ++++--- R/ubOver.R | 60 +++++++++++----------- R/ubRacing.R |only R/ubSMOTE.R | 4 - R/ubSmoteExs.R | 21 +++++-- R/ubTomek.R | 9 +-- R/ubUnder.R | 73 +++++++++++++-------------- R/unbalanced-internal.R |only data/ubIonosphere.rda |binary man/ubBalance.Rd | 30 ++++++----- man/ubCNN.Rd | 2 man/ubENN.Rd | 2 man/ubIonosphere.Rd | 4 - man/ubNCL.Rd | 2 man/ubOSS.Rd | 4 - man/ubOver.Rd | 5 + man/ubRacing.Rd |only man/ubSMOTE.Rd | 2 man/ubTomek.Rd | 2 man/ubUnder.Rd | 19 ++++--- man/unbalanced-package.Rd | 42 +++++++++------ 28 files changed, 334 insertions(+), 283 deletions(-)
Title: A Parallel-Voting Version of the Support-Vector-Machine
Algorithm
Description: By sampling your data, running the Support-Vector-Machine algorithm on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular Support-Vector-Machine and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelSVM versions 0.1-8 dated 2015-06-03 and 0.1-9 dated 2015-06-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/parallelSVM-package.Rd | 1 + 3 files changed, 7 insertions(+), 6 deletions(-)
Title: A Parallel-Voting Algorithm for many Classifiers
Description: By sampling your data, running the provided classifier on these samples in parallel on your own machine and letting your models vote on a prediction, we return much faster predictions than the regular machine learning algorithm and possibly even more accurate predictions.
Author: Wannes Rosiers (InfoFarm)
Maintainer: Wannes Rosiers <wannes.rosiers@infofarm.be>
Diff between parallelML versions 1.1 dated 2015-06-23 and 1.2 dated 2015-06-26
DESCRIPTION | 8 +++--- MD5 | 20 ++++++++------- NAMESPACE | 1 R/convertAverage.R |only R/parallelML.R | 8 +++--- R/predictML.R | 28 +++++++++++++++++++-- R/trainSample.R | 60 +++++++++++++++++++++++++++++----------------- man/convertAverage.Rd |only man/parallelML-package.Rd | 1 man/parallelML.Rd | 29 +++++++++++++++++++++- man/predictML.Rd | 24 +++++++++++++++++- man/trainSample.Rd | 15 +++++++++-- 12 files changed, 150 insertions(+), 44 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between KFAS versions 1.1.1 dated 2015-04-29 and 1.1.2 dated 2015-06-26
ChangeLog | 6 DESCRIPTION | 8 MD5 | 89 +++--- NAMESPACE | 1 R/KFAS-package.R | 4 R/KFS.R | 695 +++++++++++++++++++++++++-------------------------- R/SSMarima.R | 130 ++++----- R/SSMcustom.R | 151 +++++------ R/SSMcycle.R | 173 ++++++------ R/SSModel.R | 433 ++++++++++++++++--------------- R/SSMregression.R | 344 ++++++++++++------------- R/SSMseasonal.R | 235 ++++++++--------- R/SSMtrend.R | 183 ++++++------- R/approxSSM.R | 32 +- R/checkModel.R | 95 +++--- R/coef.KFS.R | 10 R/deviance.KFS.R | 7 R/extract.SSModel.R | 199 +++++++------- R/fitSSM.R | 6 R/hatvalues.KFS.R | 6 R/importanceSSM.R | 146 +++++----- R/initTheta.R | 51 +-- R/internalResids.R | 71 ++--- R/interval.R | 162 +++++------ R/ldl.R | 15 - R/logLik.SSModel.R | 189 ++++++------- R/mvInnovations.R | 12 R/predict.SSModel.R | 128 ++++----- R/print.objects.R | 59 ++-- R/residuals.KFS.R | 163 ++++++----- R/rstandard.KFS.R | 32 +- R/signals.R | 110 ++++---- R/simHelper.R | 11 R/simulateSSM.R | 138 +++++----- R/subset.SSModel.R | 11 R/transformSSM.R | 250 +++++++++--------- build/vignette.rds |binary inst/CITATION | 2 inst/doc/KFAS.pdf |binary man/KFS.Rd | 3 man/SSModel.Rd | 44 ++- man/alcohol.Rd | 4 man/mvInnovations.Rd |only src/approx.f95 | 6 src/gloglik.f95 | 12 src/ngloglik.f95 | 2 46 files changed, 2239 insertions(+), 2189 deletions(-)
Title: A Collection of Network Data Sets for the 'igraph' Package
Description: A small collection of various network data sets,
to use with the 'igraph' package: the Enron email network, various food webs,
interactions in the immunoglobulin protein, the karate club network,
Koenigsberg's bridges, visuotactile brain areas of the macaque monkey,
UK faculty friendship network, domestic US flights network, etc.
Author: Gabor Csardi <csardi.gabor@gmail.com>
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between igraphdata versions 0.2.2 dated 2015-04-09 and 1.0.0 dated 2015-06-26
DESCRIPTION | 18 +-- LICENSE | 27 +++++ MD5 | 31 +++--- README.md |only data/Koenigsberg.rda |binary data/UKfaculty.rda |binary data/USairports.rda |binary data/enron.rda |only data/foodwebs.rda |binary data/immuno.rda |binary data/karate.rda |binary data/kite.rda |only data/macaque.rda |binary data/rfid.rda |only data/yeast.rda |binary inst/getdata.R | 256 +++++++++++++++++++++++++++++++++++++++++++++++++-- man/enron.Rd |only man/karate.Rd | 3 man/kite.Rd |only man/rfid.Rd |only 20 files changed, 305 insertions(+), 30 deletions(-)
Title: Improved Access for Blind Users
Description: Blind users do not have access to the graphical output from R without printing the content of graph windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.
Author: A. Jonathan R. Godfrey [aut, cre], Greg Snow [ctb], James Curtis [ctb], Paul Murrell [ctb], Timothy Bilton [ctb], Yihui Xie [ctb]
Maintainer: A. Jonathan R. Godfrey <a.j.godfrey@massey.ac.nz>
Diff between BrailleR versions 0.20 dated 2015-05-30 and 0.22.0 dated 2015-06-26
BrailleR-0.20/BrailleR/inst/PREFERENCES |only BrailleR-0.22.0/BrailleR/DESCRIPTION | 13 +- BrailleR-0.22.0/BrailleR/MD5 | 36 +++--- BrailleR-0.22.0/BrailleR/NAMESPACE | 3 BrailleR-0.22.0/BrailleR/R/BRLThis.R |only BrailleR-0.22.0/BrailleR/R/MakeBatch.R | 2 BrailleR-0.22.0/BrailleR/R/MakeRprofile.R |only BrailleR-0.22.0/BrailleR/R/Options.R | 79 +++++++++++++ BrailleR-0.22.0/BrailleR/R/Premiere100.R |only BrailleR-0.22.0/BrailleR/R/SVGThis.R |only BrailleR-0.22.0/BrailleR/R/VIMethod1_JG.R | 4 BrailleR-0.22.0/BrailleR/R/zzz.R | 10 + BrailleR-0.22.0/BrailleR/inst/DEFAULTS |only BrailleR-0.22.0/BrailleR/inst/NEWS | 23 +++ BrailleR-0.22.0/BrailleR/inst/doc/BrailleRHistory.html | 29 ++--- BrailleR-0.22.0/BrailleR/inst/doc/Ex1histograms.html | 98 ++++++++--------- BrailleR-0.22.0/BrailleR/inst/fonts |only BrailleR-0.22.0/BrailleR/man/BRLThis.Rd |only BrailleR-0.22.0/BrailleR/man/BrailleR-package.Rd | 10 - BrailleR-0.22.0/BrailleR/man/Embossers.Rd |only BrailleR-0.22.0/BrailleR/man/MakeRprofile.Rd |only BrailleR-0.22.0/BrailleR/man/Options.Rd | 4 BrailleR-0.22.0/BrailleR/man/SVGThis.Rd |only BrailleR-0.22.0/BrailleR/man/SetOptions.Rd | 33 +++++ 24 files changed, 244 insertions(+), 100 deletions(-)
Title: Genetic Association Studies
Description: Some procedures including EIGENSTRAT (a procedure for
detecting and correcting for population stratification through
searching for the eigenvectors in genetic association studies),
PCoC (a procedure for correcting for population stratification
through calculating the principal coordinates and the clustering
of the subjects), Tracy-Wisdom test (a procedure for detecting
the significant eigenvalues of a matrix), distance regression (a
procedure for detecting the association between a distance matrix
and some independent variants of interest), single-marker test (a
procedure for identifying the association between the genotype at
a biallelic marker and a trait using the Wald test or the Fisher
exact test), MAX3 (a procedure for testing for the association
between a single nucleotide polymorphism and a binary phenotype
using the maximum value of the three test statistics derived for
the recessive, additive, and dominant models), nonparametric trend
test (a procedure for testing for the association between a genetic
variant and a non-normal distributed quantitative trait based on the
nonparametric risk), and nonparametric MAX3 (a procedure for testing
for the association between a biallelic single nucleotide polymorphism
and a quantitative trait using the maximum value of the three
nonparametric trend tests derived for the recessive, additive, and
dominant models), which are commonly used in genetic association studies.
Author: Lin Wang [aut],
Wei Zhang [aut],
Qizhai Li [aut],
Weicheng Zhu [ctb]
Maintainer: Lin Wang <wanglin2009@amss.ac.cn>
Diff between AssocTests versions 0.0-1 dated 2015-06-21 and 0.0-2 dated 2015-06-26
DESCRIPTION | 8 ++++---- MD5 | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-13 1.6
2012-06-28 1.2
2012-04-06 1.1
Title: Treemap Visualization
Description: A treemap is a space-filling visualization of hierarchical
structures. This package offers great flexibility to draw treemaps.
Author: Martijn Tennekes
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between treemap versions 2.2 dated 2014-03-31 and 2.3 dated 2015-06-26
DESCRIPTION | 12 - MD5 | 54 ++--- NAMESPACE | 2 NEWS | 8 R/comp2col.R | 13 - R/createRec.R | 4 R/dens2col.R | 6 R/itreemap.R | 2 R/pkg.R | 4 R/str2rect.R | 40 ++- R/tmColorsLegend.R | 10 R/tmDrawRect.R | 20 + R/treecolors.R | 2 R/treefunctions.R | 2 R/treegraph.R | 19 + R/treemap.R | 21 +- R/treepalette.R | 4 R/value2col.R | 6 man/GNI2010.Rd | 9 man/business.Rd | 16 - man/itreemap.Rd | 33 --- man/random.hierarchical.data.Rd | 87 ++------ man/tmPlot.Rd | 4 man/treecolors.Rd | 14 - man/treegraph.Rd | 127 ++++-------- man/treemap-package.Rd | 24 +- man/treemap.Rd | 414 +++++++++++----------------------------- man/treepalette.Rd | 85 ++------ 28 files changed, 395 insertions(+), 647 deletions(-)
Title: Soil Physical Analysis
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva <anderson.agro@hotmail.com>
Diff between soilphysics versions 2.3 dated 2015-05-09 and 2.4 dated 2015-06-26
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS | 7 + R/iwc.R | 9 +- R/llwr.R | 193 ++++++++++++++++++++++++++++----------------- man/iwc.Rd | 21 ++-- man/llwr.Rd | 74 +++++++++++------ man/soilphysics-package.Rd | 78 ++++++------------ 8 files changed, 240 insertions(+), 166 deletions(-)
Title: Computational Routines for Proton and Ion Radiotherapy
Description: R interface to the open-source, ANSI C library libamtrack (http://libamtrack.dkfz.org). libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams. It is designed for research in proton and ion dosimetry and radiotherapy. libamtrack also provides many auxiliary physics routines for proton and ion beams. Original package and C-to-R conversion routines developed by Felix A. Klein.
Author: Steffen Greilich and the libamtrack team
Maintainer: Steffen Greilich <s.greilich@dkfz.de>
Diff between libamtrack versions 0.6.1 dated 2015-05-22 and 0.6.2 dated 2015-06-26
libamtrack-0.6.1/libamtrack/man/AT.Bethe.mean.energy.loss.MeV.Rd |only libamtrack-0.6.1/libamtrack/man/AT.Vavilov.energy.loss.distribution.Rd |only libamtrack-0.6.1/libamtrack/man/AT.energy.loss.FWHM.Rd |only libamtrack-0.6.1/libamtrack/man/AT.energy.loss.distribution.Rd |only libamtrack-0.6.1/libamtrack/man/AT.energy.loss.mode.Rd |only libamtrack-0.6.1/libamtrack/man/AT.lambda.from.energy.loss.Rd |only libamtrack-0.6.2/libamtrack/DESCRIPTION | 13 libamtrack-0.6.2/libamtrack/MD5 | 173 - libamtrack-0.6.2/libamtrack/NAMESPACE | 94 libamtrack-0.6.2/libamtrack/R/initial.R | 2 libamtrack-0.6.2/libamtrack/R/libamtrack.R | 385 ++- libamtrack-0.6.2/libamtrack/configure | 922 ++----- libamtrack-0.6.2/libamtrack/configure.ac | 36 libamtrack-0.6.2/libamtrack/man/AT.A.from.particle.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.CSDA.energy.after.slab.E.MeV.u.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.CSDA.range.Bethe.g.cm2.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.D.RDD.Gy.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.E.MeV.u.from.momentum.MeV.c.u.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.E.from.beta.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Gauss.IDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.Gauss.PDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.I.eV.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Landau.IDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.Landau.PDF.Rd | 11 libamtrack-0.6.2/libamtrack/man/AT.Mass.Stopping.Power.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Mass.Stopping.Power.with.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Rutherford.SDCS.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.Stopping.Power.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Stopping.Power.with.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Vavilov.IDF.Rd |only libamtrack-0.6.2/libamtrack/man/AT.Vavilov.PDF.Rd | 11 libamtrack-0.6.2/libamtrack/man/AT.WEPL.Bethe.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.Z.from.particle.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.atomic.weight.from.Z.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.average.A.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.average.Z.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.beam.par.physical.to.technical.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.beam.par.technical.to.physical.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.beta.from.E.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.dose.Gy.from.fluence.cm2.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.dose.weighted.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.dose.weighted.LET.MeV.cm2.g.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.effective.Z.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.effective.charge.from.E.MeV.u.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.electron.density.m3.from.material.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.gauss.Rd |only libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.landau.Rd |only libamtrack-0.6.2/libamtrack/man/AT.energy.loss.from.lambda.vavilov.Rd |only libamtrack-0.6.2/libamtrack/man/AT.energy.straggling.MeV2.cm2.g.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.energy.straggling.after.slab.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.fluence.cm2.from.dose.Gy.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.fluence.weighted.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.fluence.weighted.LET.MeV.cm2.g.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.gamma.from.E.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.get.materials.data.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.kappa.Rd | 15 libamtrack-0.6.2/libamtrack/man/AT.lambda.landau.from.energy.loss.Rd |only libamtrack-0.6.2/libamtrack/man/AT.lambda.max.Rd |only libamtrack-0.6.2/libamtrack/man/AT.lambda.mean.Rd |only libamtrack-0.6.2/libamtrack/man/AT.lambda.vavilov.from.energy.loss.Rd |only libamtrack-0.6.2/libamtrack/man/AT.max.E.transfer.MeV.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.max.E.transfer.MeV.new.Rd |only libamtrack-0.6.2/libamtrack/man/AT.max.electron.ranges.m.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.mean.energy.loss.keV.Rd |only libamtrack-0.6.2/libamtrack/man/AT.mean.number.of.tracks.contrib.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.momentum.MeV.c.u.from.E.MeV.u.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.nuclear.spin.from.particle.no.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.particle.no.from.Z.and.A.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.r.RDD.m.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.run.CPPSC.method.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.run.GSM.method.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.run.IGK.method.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.set.user.material.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.set.user.material.from.composition.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.stopping.power.ratio.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.total.D.Gy.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.total.fluence.cm2.Rd | 4 libamtrack-0.6.2/libamtrack/man/AT.translate.dose.into.DSB.distribution.Rd | 2 libamtrack-0.6.2/libamtrack/man/AT.xi.keV.Rd |only libamtrack-0.6.2/libamtrack/man/libamtrack-package.Rd | 4 libamtrack-0.6.2/libamtrack/src/AT.c | 4 libamtrack-0.6.2/libamtrack/src/AT.h | 4 libamtrack-0.6.2/libamtrack/src/AT_CernlibFuns.c |only libamtrack-0.6.2/libamtrack/src/AT_CernlibFuns.h |only libamtrack-0.6.2/libamtrack/src/AT_EnergyLoss.c | 1240 ++++------ libamtrack-0.6.2/libamtrack/src/AT_EnergyLoss.h | 517 ++-- libamtrack-0.6.2/libamtrack/src/AT_PhysicsRoutines.c | 113 libamtrack-0.6.2/libamtrack/src/AT_PhysicsRoutines.h | 73 libamtrack-0.6.2/libamtrack/src/AT_R_Wrapper.c | 650 ++++- libamtrack-0.6.2/libamtrack/src/AT_R_Wrapper.h | 137 - libamtrack-0.6.2/libamtrack/src/AT_SPC.c | 11 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataBethe.c | 176 + libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataBethe.h | 75 libamtrack-0.6.2/libamtrack/src/AT_StoppingPowerDataFromFile.c | 2 libamtrack-0.6.2/libamtrack/src/CERNLIBFUNS.f |only libamtrack-0.6.2/libamtrack/src/Makevars.in | 8 libamtrack-0.6.2/libamtrack/src/config.h | 26 99 files changed, 2928 insertions(+), 1908 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between igraph versions 1.0.0 dated 2015-06-24 and 1.0.1 dated 2015-06-26
DESCRIPTION | 6 ++-- MD5 | 42 ++++++++++++++++---------------- R/adjacency.R | 28 ++++++++++----------- R/attributes.R | 22 ++++++++-------- R/centrality.R | 22 ++++++++-------- R/conversion.R | 10 +++---- R/make.R | 25 ++++++++++++++++++- R/structural.properties.R | 14 +++++----- R/topology.R | 20 +++++++-------- man/arpack.Rd | 22 ++++++++-------- man/as.directed.Rd | 10 +++---- man/canonical_permutation.Rd | 20 +++++++-------- man/graph_from_adjacency_matrix.Rd | 28 ++++++++++----------- man/igraph-attribute-combination.Rd | 22 ++++++++-------- man/make_.Rd | 28 ++++++++++++++++++++- man/transitivity.Rd | 14 +++++----- src/Makevars.in | 2 - src/Makevars.win | 4 --- src/gengraph_graph_molloy_hash.cpp | 4 +-- src/gengraph_graph_molloy_optimized.cpp | 12 ++++----- src/prpack/prpack_solver.cpp | 3 +- src/uuid/gen_uuid.c | 25 ++++++++++++++----- 22 files changed, 221 insertions(+), 162 deletions(-)
Title: Whole Genome Average Interval Mapping for QTL Detection using
Mixed Models
Description: Integrates sophisticated mixed modelling methods with a whole genome approach to detecting significant QTL in linkage maps.
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, Simon Diffey <simon.diffey@dpi.nsw.gov.au>, Ari Verbyla <ari.verbyla@csiro.au> and Brian Cullis <bcullis@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between wgaim versions 1.4-8 dated 2015-05-06 and 1.4-10 dated 2015-06-26
DESCRIPTION | 8 +++--- MD5 | 10 ++++---- R/wgaim9.R | 65 +++++------------------------------------------------ R/zzz.R | 4 +-- inst/NEWS.Rd | 11 +++++++- inst/doc/wgaim.pdf |binary 6 files changed, 27 insertions(+), 71 deletions(-)
Title: Transcriptome Overlap Measure
Description: A new bioinformatic tool for comparing transcriptomes of two biological samples from the same or different species. The mapping is conducted based on the overlap of the associated genes of different samples. More examples and detailed explanations are available in the vignette.
Author: Jingyi Jessica Li <jli@stat.ucla.edu>, Wei Vivian Li <liw@ucla.edu>
Maintainer: Jingyi Jessica Li <jli@stat.ucla.edu>
Diff between TROM versions 1.0 dated 2015-04-08 and 1.1 dated 2015-06-26
TROM-1.0/TROM/inst/doc/Vignette.pdf |only TROM-1.1/TROM/DESCRIPTION | 19 + TROM-1.1/TROM/MD5 | 51 ++-- TROM-1.1/TROM/NAMESPACE | 1 TROM-1.1/TROM/R/TROM-internal.R | 250 +++++++++++------------ TROM-1.1/TROM/R/bs.trom.R | 16 + TROM-1.1/TROM/R/choose.z.R |only TROM-1.1/TROM/R/find.top.GO.slim.terms.R | 2 TROM-1.1/TROM/R/find.top.GO.terms.R | 1 TROM-1.1/TROM/R/select.associated.genes.R | 6 TROM-1.1/TROM/R/select.associated.orthologs.R | 9 TROM-1.1/TROM/R/sp.associated.idx.R | 4 TROM-1.1/TROM/R/ws.trom.R | 133 ++++++------ TROM-1.1/TROM/R/ws.trom.forZ.R |only TROM-1.1/TROM/R/ws.trom.orthologs.R | 178 ++++++++-------- TROM-1.1/TROM/R/ws.trom.three.R |only TROM-1.1/TROM/R/ws.trom.two.R |only TROM-1.1/TROM/data/GO_slim_id.rda |binary TROM-1.1/TROM/inst/dm_associated_orthologs.xlsx |binary TROM-1.1/TROM/inst/doc/TROM_Vignette.pdf |only TROM-1.1/TROM/man/TROM-package.Rd | 9 TROM-1.1/TROM/man/bs.trom.Rd | 17 - TROM-1.1/TROM/man/choose.z.Rd |only TROM-1.1/TROM/man/find.top.GO.slim.terms.Rd | 2 TROM-1.1/TROM/man/find.top.GO.terms.Rd | 2 TROM-1.1/TROM/man/heatmap.3.Rd | 4 TROM-1.1/TROM/man/select.associated.genes.Rd | 18 - TROM-1.1/TROM/man/select.associated.orthologs.Rd | 16 - TROM-1.1/TROM/man/ws.trom.Rd | 52 +++- TROM-1.1/TROM/man/ws.trom.orthologs.Rd | 66 +++--- 30 files changed, 465 insertions(+), 391 deletions(-)
Title: Datasets from Sen & Srivastava
Description: Collection of datasets from Sen & Srivastava: "Regression
Analysis, Theory, Methods and Applications", Springer. Sources
for individual data files are more fully documented in the
book.
Author: Kjetil B Halvorsen <kjetil1001@gmail.com>
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between SenSrivastava versions 2012-04-0 dated 2012-04-04 and 2015.6.25 dated 2015-06-26
SenSrivastava-2012-04-0/SenSrivastava/SenSrivastava-Ex.R |only SenSrivastava-2015.6.25/SenSrivastava/DESCRIPTION | 17 +++++++-------- SenSrivastava-2015.6.25/SenSrivastava/MD5 | 5 +--- SenSrivastava-2015.6.25/SenSrivastava/NEWS | 3 ++ 4 files changed, 14 insertions(+), 11 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.2.2 dated 2015-01-21 and 0.3.0 dated 2015-06-26
rvertnet-0.2.2/rvertnet/NEWS |only rvertnet-0.3.0/rvertnet/DESCRIPTION | 19 rvertnet-0.3.0/rvertnet/MD5 | 71 +- rvertnet-0.3.0/rvertnet/NAMESPACE | 5 rvertnet-0.3.0/rvertnet/R/bigsearch.R | 11 rvertnet-0.3.0/rvertnet/R/searchbyterm.R | 45 - rvertnet-0.3.0/rvertnet/R/vertmap.R | 25 rvertnet-0.3.0/rvertnet/R/vertsearch.R | 13 rvertnet-0.3.0/rvertnet/R/vertsummary.R | 2 rvertnet-0.3.0/rvertnet/R/yyy.R | 4 rvertnet-0.3.0/rvertnet/R/zzz.R | 163 +++-- rvertnet-0.3.0/rvertnet/README.md | 196 ++++-- rvertnet-0.3.0/rvertnet/build/vignette.rds |binary rvertnet-0.3.0/rvertnet/inst/doc/rvertnet_vignette.Rmd | 363 +++++++++--- rvertnet-0.3.0/rvertnet/inst/doc/rvertnet_vignette.html | 346 ++++++++--- rvertnet-0.3.0/rvertnet/inst/ignore |only rvertnet-0.3.0/rvertnet/inst/vign/figure |only rvertnet-0.3.0/rvertnet/inst/vign/rvertnet_vignette.Rmd | 79 ++ rvertnet-0.3.0/rvertnet/inst/vign/rvertnet_vignette.md | 361 +++++++++-- rvertnet-0.3.0/rvertnet/man/bigsearch.Rd | 11 rvertnet-0.3.0/rvertnet/man/rvertnet-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/rvertnet-package.Rd | 2 rvertnet-0.3.0/rvertnet/man/searchbyterm.Rd | 34 - rvertnet-0.3.0/rvertnet/man/spatialsearch.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertavailablemaps-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertlocations-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertmap.Rd | 16 rvertnet-0.3.0/rvertnet/man/vertoccurrence-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertoccurrencecount-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertproviders-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/man/vertsearch.Rd | 8 rvertnet-0.3.0/rvertnet/man/vertsummary.Rd | 4 rvertnet-0.3.0/rvertnet/man/verttaxa-defunct.Rd | 2 rvertnet-0.3.0/rvertnet/tests/testthat.R |only rvertnet-0.3.0/rvertnet/tests/testthat/test-bigsearch.R | 10 rvertnet-0.3.0/rvertnet/tests/testthat/test-searchbyterm.R | 65 +- rvertnet-0.3.0/rvertnet/tests/testthat/test-spatialsearch.R | 28 rvertnet-0.3.0/rvertnet/vignettes/rvertnet_vignette.Rmd | 363 +++++++++--- 38 files changed, 1646 insertions(+), 614 deletions(-)
Title: Japanese Utility Functions and Data
Description: Japan-specific data is sometimes too unhandy for R users to manage. The utility functions and data in this package disencumber us from such an unnecessary burden.
Author: Susumu Tanimura <aruminat@gmail.com>
Maintainer: Susumu Tanimura <aruminat@gmail.com>
Diff between Nippon versions 0.5.3 dated 2013-07-26 and 0.6.1 dated 2015-06-26
Nippon-0.5.3/Nippon/Nippon-Ex.R |only Nippon-0.5.3/Nippon/configure.ac.orig |only Nippon-0.5.3/Nippon/man/ja |only Nippon-0.5.3/Nippon/src/Makevars.in.orig |only Nippon-0.5.3/Nippon/src/Makevars.orig |only Nippon-0.6.1/Nippon/ChangeLog | 14 + Nippon-0.6.1/Nippon/DESCRIPTION | 14 - Nippon-0.6.1/Nippon/MD5 | 44 ++--- Nippon-0.6.1/Nippon/NAMESPACE | 1 Nippon-0.6.1/Nippon/R/JapanPrefecturesMap.R | 2 Nippon-0.6.1/Nippon/R/jholiday.R | 7 Nippon-0.6.1/Nippon/R/kakasi.R | 32 --- Nippon-0.6.1/Nippon/R/zen2han.R | 28 ++- Nippon-0.6.1/Nippon/TODO | 3 Nippon-0.6.1/Nippon/configure | 212 ++++++++++++------------- Nippon-0.6.1/Nippon/configure.ac | 4 Nippon-0.6.1/Nippon/man/JapanPrefecturesMap.Rd | 4 Nippon-0.6.1/Nippon/man/Nippon-package.Rd | 12 - Nippon-0.6.1/Nippon/man/jyear.Rd | 1 Nippon-0.6.1/Nippon/man/kakasi.Rd | 23 +- Nippon-0.6.1/Nippon/man/zen2han.Rd | 15 - Nippon-0.6.1/Nippon/src/kakasi/config.h.in | 10 - Nippon-0.6.1/Nippon/src/kakasi/libdict.c | 4 Nippon-0.6.1/Nippon/src/kakasi/libhh2.c | 132 ++++++++++----- Nippon-0.6.1/Nippon/src/kakasi/libhh2.c.new |only Nippon-0.6.1/Nippon/src/kakasi/libkanjiio.c | 10 - 26 files changed, 308 insertions(+), 264 deletions(-)
Title: Two Stage Least Squares with Model Implied Instrumental Variable
Search
Description: Functions for estimating structural equation models
using a model-implied instrumental variable (MIIV) search
and two stage least squares (2SLS) estimator (MIIV-2SLS).
Author: Zachary Fisher and Ken Bollen.
Maintainer: Zachary Fisher <fish.zachary@gmail.com>
Diff between MIIVsem versions 0.2 dated 2015-06-05 and 0.3 dated 2015-06-26
DESCRIPTION | 9 ++-- MD5 | 12 ++--- R/miive.R | 117 +++++++++++++++++++++++++++++++++----------------------- R/miivs.R | 82 +++++++++++++-------------------------- R/print.miivs.R | 10 ++++ man/miive.Rd | 2 man/miivs.Rd | 4 + 7 files changed, 123 insertions(+), 113 deletions(-)
Title: Data from the Book "Multivariate Statistical Modelling Based on
Generalized Linear Models", First Edition, by Ludwig Fahrmeir
and Gerhard Tutz
Description: Data and functions for the book "Multivariate Statistical
Modelling Based on Generalized Linear Models", first edition, by
Ludwig Fahrmeir and Gerhard Tutz. Useful when using the book.
Author: compiled by Kjetil B Halvorsen
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between Fahrmeir versions 2012.04-0 dated 2012-04-04 and 2015.6.25 dated 2015-06-26
DESCRIPTION | 23 ++++++++++++----------- MD5 | 4 ++-- NEWS | 5 +++++ 3 files changed, 19 insertions(+), 13 deletions(-)
Title: Empirical Bayesian Elastic Net
Description: Provides the Empirical Bayesian Elastic Net for handling multicollinearity in generalized linear regression models. As a special case of the 'EBglmnet'
package (also available on CRAN), this package encourages a grouping effects to select relevant variables and estimate the corresponding non-zero effects.
Author: Anhui Huang
Maintainer: Anhui Huang <a.huang1@umiami.edu>
Diff between EBEN versions 1.1.1 dated 2014-06-09 and 4.1 dated 2015-06-26
DESCRIPTION | 13 MD5 | 30 - R/EBelasticNet.Binomial.R |only R/EBelasticNet.BinomialCV.R |only R/EBelasticNet.Gaussian.R | 41 +- R/EBelasticNet.GaussianCV.R | 15 data/BASISbinomial.rda |only data/yBinomial.rda |only man/BASIS.Rd | 3 man/BASISbinomial.Rd |only man/EBEN-package.Rd | 34 + man/EBelasticNet.Binomial.Rd |only man/EBelasticNet.BinomialCV.Rd |only man/EBelasticNet.Gaussian.Rd | 41 -- man/EBelasticNet.GaussianCV.Rd | 33 - man/y.Rd | 3 man/yBinomial.Rd |only src/ElasticNetBinaryNEmainEff.c |only src/ElasticNetBinaryNeFull.c |only src/elasticNetLinearNeFull2.c | 629 +++++++++++++++++++------------ src/elasticNetLinearNeMainEff.c | 809 +++++++++++++++++++++++++++------------- 21 files changed, 1070 insertions(+), 581 deletions(-)
Title: Useful Functions for Box, Hunter and Hunter II
Description: Functions and data sets reproducing some examples in
Box, Hunter and Hunter II. Useful for statistical design
of experiments, especially factorial experiments.
Author: Ernesto Barrios
Maintainer: Kjetil B.Halvorsen <kjetil1001@gmail.com>
Diff between BHH2 versions 2012.04-0 dated 2012-04-04 and 2015.06.25 dated 2015-06-26
DESCRIPTION | 14 ++++++++------ MD5 | 26 ++++++++++++++------------ NEWS | 2 ++ build |only data/corrosion.data.rda |binary data/heads.data.rda |binary data/penicillin.data.rda |binary data/poison.data.rda |binary data/shoes.data.rda |binary data/tab03B1.rda |binary data/tab03B2.rda |binary data/tomato.data.rda |binary data/woolen.data.rda |binary inst/doc/BHH2.R |only inst/doc/BHH2.pdf |binary 15 files changed, 24 insertions(+), 18 deletions(-)
Title: Calculate Power Utilizing Asymptotic Likelihood Ratio Methods
Description: A set of routines written in the S language
that calculate power and related quantities utilizing asymptotic
likelihood ratio methods.
Author: S original by Barry W. Brown, James Lovato and Kathy Russel.
R port by Kjetil B Halvorsen <kjetil1001@gmail.com>
Maintainer: Kjetil B Halvorsen <kjetil1001@gmail.com>
Diff between asypow versions 2013.9-1 dated 2013-09-24 and 2015.6.25 dated 2015-06-26
asypow-2013.9-1/asypow/library.README |only asypow-2015.6.25/asypow/DESCRIPTION | 8 ++++---- asypow-2015.6.25/asypow/MD5 | 10 +++++----- asypow-2015.6.25/asypow/NEWS | 5 +++++ asypow-2015.6.25/asypow/README |only asypow-2015.6.25/asypow/inst/doc/asypow.pdf |binary asypow-2015.6.25/asypow/inst/doc/asypow.statlib.pdf |binary 7 files changed, 14 insertions(+), 9 deletions(-)
Title: Assertive Programming for R Analysis Pipelines
Description: Provides functionality to assert conditions
that have to be met so that errors in data used in
analysis pipelines can fail quickly. Similar to
'stopifnot()' but more powerful, friendly, and easier
for use in pipelines.
Author: Tony Fischetti [aut, cre]
Maintainer: Tony Fischetti <tony.fischetti@gmail.com>
Diff between assertr versions 0.4.1 dated 2015-03-24 and 1.0.0 dated 2015-06-26
DESCRIPTION | 10 - MD5 | 53 +++-- NAMESPACE | 11 + NEWS | 29 ++ R/assertions.R | 378 ++++++++++++++++++++++++++++++++++----- R/assertr.R | 27 ++ R/predicates.R | 129 ++++++++++--- R/row-redux.R |only R/utils.R | 56 +++++ README.md | 87 +++++++- build/vignette.rds |binary inst/doc/assertr.R | 7 inst/doc/assertr.Rmd | 295 +++++++++++++++++++++++++++--- inst/doc/assertr.html | 171 +++++++++++++++-- man/assert.Rd | 38 +++ man/assert_rows.Rd |only man/assertr.Rd | 29 ++ man/in_set.Rd | 2 man/insist.Rd | 28 ++ man/insist_rows.Rd |only man/maha_dist.Rd |only man/not_na.Rd | 16 - man/num_row_NAs.Rd |only man/verify.Rd | 7 man/within_bounds.Rd | 12 - man/within_n_mads.Rd |only man/within_n_sds.Rd | 7 tests/testthat/test-assertions.R | 367 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-predicates.R | 100 +++++++++- tests/testthat/test-row-redux.R |only vignettes/assertr.Rmd | 295 +++++++++++++++++++++++++++--- 31 files changed, 1908 insertions(+), 246 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<david.butler@daff.qld.gov.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 0.4-1 dated 2015-05-04 and 0.4-4 dated 2015-06-26
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- R/mstmap10.R | 56 +++++++++++++++++++++++++------------------- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++ inst/doc/asmapvignette.Rnw | 2 - vignettes/asmapvignette.Rnw | 2 - 7 files changed, 52 insertions(+), 35 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package arules with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.0-0 dated 2014-12-08 and 1.0-1 dated 2015-06-26
DESCRIPTION | 17 MD5 | 29 NAMESPACE | 7 R/graph.R | 1405 ++++++++++++++++++++++++------------------------ R/plot.R | 152 ++--- R/save.R | 2 R/scatterplot.R | 7 build/vignette.rds |binary inst/NEWS | 9 inst/doc/arulesViz.R | 7 inst/doc/arulesViz.Rnw | 22 inst/doc/arulesViz.pdf |binary inst/n.html |only man/plot.Rd | 20 man/save.Rd | 1 vignettes/arulesViz.Rnw | 22 16 files changed, 868 insertions(+), 832 deletions(-)