Wed, 22 Oct 2014

Package scrm updated to version 1.3-2 with previous version 1.3-1 dated 2014-10-21

Title: Simulating the Evolution of Biological Sequences
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution.
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab

Diff between scrm versions 1.3-1 dated 2014-10-21 and 1.3-2 dated 2014-10-22

 DESCRIPTION        |    8 ++++----
 MD5                |    8 ++++----
 NEWS               |    7 +++++++
 src/scrm/forest.cc |    5 ++++-
 src/scrm/param.h   |    1 +
 5 files changed, 20 insertions(+), 9 deletions(-)

More information about scrm at CRAN
Permanent link

New package lmenssp with initial version 1.0
Package: lmenssp
Type: Package
Title: Linear Mixed Effects Models with Non-stationary Stochastic Processes
Version: 1.0
Date: 2014-10-21
Author: Ozgur Asar, Peter J. Diggle
Maintainer: Ozgur Asar
Depends: MASS, nlme
Description: Fit, filter and smooth mixed models with non-stationary processes
License: GPL (>= 2)
Packaged: 2014-10-22 08:38:04 UTC; asar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 13:13:04

More information about lmenssp at CRAN
Permanent link

Package ParetoPosStable updated to version 1.0.3 with previous version 1.0.2 dated 2014-02-19

Title: Computing, fitting and validating the PPS distribution
Description: Statistical functions to describe a Pareto Positive Stable (PPS) distribution and fit it to real data. Graphical and statistical tools to validate the fits are included.
Author: Antonio Jose Saez-Castillo [aut, cre], Faustino Prieto [aut], Jose Maria Sarabia [aut]
Maintainer: Antonio Jose Saez-Castillo

Diff between ParetoPosStable versions 1.0.2 dated 2014-02-19 and 1.0.3 dated 2014-10-22

 ParetoPosStable-1.0.2/ParetoPosStable/man/GoF.PPSfit.Rd              |only
 ParetoPosStable-1.0.2/ParetoPosStable/man/hPPS.Rd                    |only
 ParetoPosStable-1.0.2/ParetoPosStable/man/pPPS.Rd                    |only
 ParetoPosStable-1.0.2/ParetoPosStable/man/qPPS.Rd                    |only
 ParetoPosStable-1.0.2/ParetoPosStable/man/rPPS.Rd                    |only
 ParetoPosStable-1.0.2/ParetoPosStable/man/se.PPSfit.Rd               |only
 ParetoPosStable-1.0.3/ParetoPosStable/DESCRIPTION                    |   26 -
 ParetoPosStable-1.0.3/ParetoPosStable/MD5                            |   32 +
 ParetoPosStable-1.0.3/ParetoPosStable/NAMESPACE                      |   20 +
 ParetoPosStable-1.0.3/ParetoPosStable/R/ParetoPosStable.R            |  165 +++++-----
 ParetoPosStable-1.0.3/ParetoPosStable/data                           |only
 ParetoPosStable-1.0.3/ParetoPosStable/inst                           |only
 ParetoPosStable-1.0.3/ParetoPosStable/man/GoF.Rd                     |only
 ParetoPosStable-1.0.3/ParetoPosStable/man/PPS.fit.Rd                 |   10 
 ParetoPosStable-1.0.3/ParetoPosStable/man/ParetoPosStable-package.Rd |   14 
 ParetoPosStable-1.0.3/ParetoPosStable/man/dPPS.Rd                    |   56 ++-
 ParetoPosStable-1.0.3/ParetoPosStable/man/forbes400.Rd               |only
 ParetoPosStable-1.0.3/ParetoPosStable/man/pareto.fit.Rd              |   16 
 ParetoPosStable-1.0.3/ParetoPosStable/man/plot.PPSfit.Rd             |    9 
 ParetoPosStable-1.0.3/ParetoPosStable/man/print.PPSfit.Rd            |    2 
 ParetoPosStable-1.0.3/ParetoPosStable/man/se.Rd                      |only
 ParetoPosStable-1.0.3/ParetoPosStable/man/turkey.Rd                  |only
 22 files changed, 190 insertions(+), 160 deletions(-)

More information about ParetoPosStable at CRAN
Permanent link

New package FDGcopulas with initial version 1.0
Package: FDGcopulas
Type: Package
Title: Multivariate Dependence with FDG Copulas
Version: 1.0
Date: 2014-09-19
Author: Gildas Mazo, Stephane Girard
Maintainer: Gildas Mazo
Description: FDG copulas are a class of copulas featuring an interesting balance between flexibility and tractability. This package provides tools to construct, calculate the pairwise dependence coefficients of, simulate from, and fit FDG copulas. The acronym FDG stands for 'one-Factor with Durante Generators', as an FDG copula is a one-factor copula -- that is, the variables are independent given a latent factor -- whose linking copulas belong to the Durante class of bivariate copulas (also referred to as exchangeable Marshall-Olkin or semilinear copulas).
License: GPL (>= 3)
Depends: Rcpp (>= 0.10.6), methods
LinkingTo: Rcpp
Imports: numDeriv, randtoolbox
Packaged: 2014-10-22 07:24:07 UTC; mazo
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-22 09:33:34

More information about FDGcopulas at CRAN
Permanent link

Package stepp updated to version 3.0-11 with previous version 2.3-2 dated 2011-05-23

Title: Subpopulation Treatment Effect Pattern Plot (STEPP)
Description: A method to explore the treatment-covariate interactions in survival or generalized linear model (GLM) for continuous, binomial and count data arising from two treatment arms of a clinical trial. A permutation distribution approach to inference is implemented, based on permuting the covariate values within each treatment group.
Author: Wai-ki Yip, with contributions from Ann Lazar, David Zahrieh, Chip Cole, Ann Lazar, Marco Bonetti, Victoria Wang, William Barcella and Richard Gelber
Maintainer: Wai-ki Yip

Diff between stepp versions 2.3-2 dated 2011-05-23 and 3.0-11 dated 2014-10-22

 stepp-2.3-2/stepp/CONTENTS                     |only
 stepp-2.3-2/stepp/man/steppCI.Rd               |only
 stepp-2.3-2/stepp/man/steppObj.Rd              |only
 stepp-3.0-11/stepp/DESCRIPTION                 |   26 
 stepp-3.0-11/stepp/MD5                         |   58 
 stepp-3.0-11/stepp/NAMESPACE                   |only
 stepp-3.0-11/stepp/R/stepp.R                   | 1474 +------------------------
 stepp-3.0-11/stepp/R/steppes.R                 |only
 stepp-3.0-11/stepp/R/stmodel.R                 |only
 stepp-3.0-11/stepp/R/stmodelCI.R               |only
 stepp-3.0-11/stepp/R/stmodelCOX.R              |only
 stepp-3.0-11/stepp/R/stmodelGLM.R              |only
 stepp-3.0-11/stepp/R/stmodelKM.R               |only
 stepp-3.0-11/stepp/R/stsubpop.R                |only
 stepp-3.0-11/stepp/R/stutil.R                  |only
 stepp-3.0-11/stepp/R/stwin.R                   |only
 stepp-3.0-11/stepp/data                        |only
 stepp-3.0-11/stepp/man/analyze.CumInc.stepp.Rd |only
 stepp-3.0-11/stepp/man/analyze.KM.stepp.Rd     |only
 stepp-3.0-11/stepp/man/aspirin.Rd              |only
 stepp-3.0-11/stepp/man/big.Rd                  |only
 stepp-3.0-11/stepp/man/estimate.Rd             |only
 stepp-3.0-11/stepp/man/generate.Rd             |only
 stepp-3.0-11/stepp/man/stepp.CI.Rd             |only
 stepp-3.0-11/stepp/man/stepp.COX.Rd            |only
 stepp-3.0-11/stepp/man/stepp.GLM.Rd            |only
 stepp-3.0-11/stepp/man/stepp.KM.Rd             |only
 stepp-3.0-11/stepp/man/stepp.Rd                |  229 ++-
 stepp-3.0-11/stepp/man/stepp.subpop.Rd         |only
 stepp-3.0-11/stepp/man/stepp.test.Rd           |only
 stepp-3.0-11/stepp/man/stepp.win.Rd            |only
 stepp-3.0-11/stepp/man/stepp_plot.Rd           |  115 +
 stepp-3.0-11/stepp/man/stepp_print.Rd          |   65 -
 stepp-3.0-11/stepp/man/stepp_summary.Rd        |   53 
 stepp-3.0-11/stepp/man/steppes-class.Rd        |only
 stepp-3.0-11/stepp/man/stmodel-class.Rd        |only
 stepp-3.0-11/stepp/man/stmodelCI-class.Rd      |only
 stepp-3.0-11/stepp/man/stmodelCOX-class.Rd     |only
 stepp-3.0-11/stepp/man/stmodelGLM-class.Rd     |only
 stepp-3.0-11/stepp/man/stmodelKM-class.Rd      |only
 stepp-3.0-11/stepp/man/stsubpop-class.Rd       |only
 stepp-3.0-11/stepp/man/stwin-class.Rd          |only
 stepp-3.0-11/stepp/man/test.Rd                 |only
 stepp-3.0-11/stepp/src                         |only
 44 files changed, 433 insertions(+), 1587 deletions(-)

More information about stepp at CRAN
Permanent link

New package indicoio with initial version 0.3
Package: indicoio
Title: A simple R Wrapper for the indico set of APIs - http://indico.io
Version: 0.3
Author: Alexander Gedranovich
Maintainer: Madison May
Description: R-based client for Machine Learning APIs at http://indico.io. Provides wrappers for following APIs: Positive/Negative Sentiment Analysis, Political Sentiment Analysis, Image Feature Extraction, Facial Emotion Recognition, Facial Feature Extraction, Language Detection
Depends: R (>= 3.0.2), httr, rjson, stringr, png
License: MIT + file LICENSE
LazyData: true
Suggests: testthat, jpeg
Packaged: 2014-10-22 00:37:34 UTC; mmay
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 08:58:17

More information about indicoio at CRAN
Permanent link

Package gramEvol updated to version 1.2-1 with previous version 1.1-1 dated 2014-06-23

Title: Grammatical Evolution For R
Description: Implementation of Context Free Grammar and Grammatical Evolution for R
Author: Farzad Noorian, Anthony Mihirana de Silva
Maintainer: Farzad Noorian

Diff between gramEvol versions 1.1-1 dated 2014-06-23 and 1.2-1 dated 2014-10-22

 gramEvol-1.1-1/gramEvol/README                            |only
 gramEvol-1.1-1/gramEvol/tests/regression.R                |only
 gramEvol-1.2-1/gramEvol/ChangeLog                         |    6 ++
 gramEvol-1.2-1/gramEvol/DESCRIPTION                       |    8 +--
 gramEvol-1.2-1/gramEvol/MD5                               |   30 +++++++-------
 gramEvol-1.2-1/gramEvol/NAMESPACE                         |   10 ++--
 gramEvol-1.2-1/gramEvol/NEWS                              |    5 ++
 gramEvol-1.2-1/gramEvol/R/CreateGrammar.R                 |   14 ++++++
 gramEvol-1.2-1/gramEvol/R/ReadBNFFile.R                   |only
 gramEvol-1.2-1/gramEvol/R/print.grammar.R                 |   12 ++---
 gramEvol-1.2-1/gramEvol/man/CreateGrammar.Rd              |   29 +++++++------
 gramEvol-1.2-1/gramEvol/man/EvalExpressions.Rd            |    3 -
 gramEvol-1.2-1/gramEvol/man/GeneticAlg.int.Rd             |    3 -
 gramEvol-1.2-1/gramEvol/man/GrammarGenotypeToPhenotype.Rd |   15 +++----
 gramEvol-1.2-1/gramEvol/man/GrammaticalEvolution.Rd       |   19 ++++----
 gramEvol-1.2-1/gramEvol/tests/bnf.R                       |only
 gramEvol-1.2-1/gramEvol/tests/ga.R                        |only
 gramEvol-1.2-1/gramEvol/tests/ge.R                        |only
 gramEvol-1.2-1/gramEvol/tests/grammar.R                   |only
 gramEvol-1.2-1/gramEvol/tests/test.bnf                    |only
 20 files changed, 93 insertions(+), 61 deletions(-)

More information about gramEvol at CRAN
Permanent link

Tue, 21 Oct 2014

Package pcaPP updated to version 1.9-60 with previous version 1.9-50 dated 2014-09-19

Title: Robust PCA by Projection Pursuit
Description: Robust PCA by Projection Pursuit
Author: Peter Filzmoser, Heinrich Fritz, Klaudius Kalcher
Maintainer: Valentin Todorov

Diff between pcaPP versions 1.9-50 dated 2014-09-19 and 1.9-60 dated 2014-10-21

 ChangeLog          |only
 DESCRIPTION        |   15 ++++++---------
 MD5                |    7 ++++---
 NAMESPACE          |    2 +-
 build/vignette.rds |binary
 5 files changed, 11 insertions(+), 13 deletions(-)

More information about pcaPP at CRAN
Permanent link

Package ore updated to version 1.0.1 with previous version 1.0.0 dated 2014-10-20

Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden

Diff between ore versions 1.0.0 dated 2014-10-20 and 1.0.1 dated 2014-10-21

 DESCRIPTION                    |    8 ++++----
 MD5                            |   12 +++++++-----
 NEWS                           |only
 R/ore.R                        |    6 +++---
 README.md                      |    2 ++
 man/ore.Rd                     |    6 +++---
 tests/testthat/drink.txt       |only
 tests/testthat/test-10-match.R |    2 +-
 8 files changed, 20 insertions(+), 16 deletions(-)

More information about ore at CRAN
Permanent link

Package PKfit updated to version 1.2.4 with previous version 1.2.3 dated 2014-08-21

Title: Data Analysis Tool for Pharmacokinetics
Description: PKfit is a nonlinear regression program which is designed to perform model/curve fitting and model simulations for pharmacokinetics.
Author: Chun-ying Lee, Yung-jin Lee
Maintainer: Yung-jin Lee

Diff between PKfit versions 1.2.3 dated 2014-08-21 and 1.2.4 dated 2014-10-21

 DESCRIPTION                      |   12 ++++-----
 MD5                              |   49 +++++++++++++++++++--------------------
 NAMESPACE                        |    1 
 NEWS                             |   13 +++++++++-
 R/description_version.r          |    3 +-
 R/fbolus1.R                      |   44 +++++++++++++++++------------------
 R/fbolus2.R                      |   32 ++++++++++++-------------
 R/fbolus3.R                      |   38 +++++++++++++++---------------
 R/fbolus3.mm.R                   |   38 +++++++++++++++---------------
 R/ffirst.lag.R                   |   48 +++++++++++++++++++-------------------
 R/ffirst.nolag.R                 |   48 +++++++++++++++++++-------------------
 R/ffirst2.R                      |   37 +++++++++++++++--------------
 R/finfu1.R                       |   44 +++++++++++++++++------------------
 R/finfu2.R                       |   34 +++++++++++++--------------
 R/fmacro.three.R                 |   39 +++++++++++++++----------------
 R/fmacro.two.R                   |   35 +++++++++++++--------------
 R/fzero.nolag.R                  |   48 +++++++++++++++++++-------------------
 R/iv.bolus.demo.R                |   16 +++++++-----
 R/mcsim.demo.R                   |    2 -
 R/mmpk.demo.R                    |   19 +++++++--------
 R/plotting.lin.R                 |    3 +-
 R/plotting.non.R                 |    2 -
 R/plotting.sim.R                 |    2 -
 R/zzz.R                          |    2 -
 inst/CITATION                    |only
 inst/UserDefinedModels/mymodel.R |   24 ++++++++++++-------
 26 files changed, 329 insertions(+), 304 deletions(-)

More information about PKfit at CRAN
Permanent link

Package MESS updated to version 0.3-2 with previous version 0.2-1 dated 2014-03-19

Title: Miscellaneous Esoteric Statistical Scripts
Description: A mixed collection of useful and semi-useful functions, some of which may even be referenced in The R Primer book.
Author: Claus Ekstrom
Maintainer: Claus Ekstrom

Diff between MESS versions 0.2-1 dated 2014-03-19 and 0.3-2 dated 2014-10-21

 DESCRIPTION               |   19 +--
 MD5                       |   48 +++++++--
 NAMESPACE                 |    8 +
 R/adaptive.weights.R      |only
 R/common.shared.R         |    6 -
 R/desctable.R             |only
 R/drop1.geeglm.R          |   68 +++++++------
 R/feature.test.R          |  232 +++++++++++++++++++++++++++++++++++++---------
 R/fitted.geese.R          |    3 
 R/gkgamma.R               |only
 R/power.binom.test.R      |only
 R/power.mcnemar.test.R    |only
 R/qic.R                   |   88 +++++++++++++++++
 R/scorefct.R              |only
 data/bees.rda             |only
 data/clotting.RData       |only
 data/datalist             |only
 data/greenland.rda        |only
 data/qpcr.rda             |only
 data/rainman.rda          |only
 data/soccer.rda           |binary
 data/superroot2.rda       |only
 man/QIC.Rd                |    2 
 man/adaptive.weights.Rd   |only
 man/bees.Rd               |only
 man/clotting.Rd           |only
 man/desctable.Rd          |only
 man/drop1.geeglm.Rd       |    2 
 man/feature.test.Rd       |   23 +++-
 man/gkgamma.Rd            |only
 man/greenland.Rd          |only
 man/power.binom.test.Rd   |only
 man/power.mcnemar.test.Rd |only
 man/qpcr.Rd               |only
 man/rainman.Rd            |only
 man/soccer.Rd             |   17 +--
 man/superroot2.Rd         |only
 37 files changed, 397 insertions(+), 119 deletions(-)

More information about MESS at CRAN
Permanent link

Package equate updated to version 2.0-3 with previous version 2.0-2 dated 2014-02-22

Title: Observed-Score Linking and Equating
Description: Contains methods for observed-score linking and equating under the single-group, equivalent-groups, and nonequivalent-groups with anchor test(s) designs. Equating types include identity, mean, linear, general linear, equipercentile, circle-arc, and composites of these. Equating methods include synthetic, nominal weights, Tucker, Levine observed score, Levine true score, Braun/Holland, frequency estimation, and chained equating. Plotting and summary methods, and methods for multivariate presmoothing and bootstrap error estimation are also provided.
Author: Anthony Albano
Maintainer: Anthony Albano

Diff between equate versions 2.0-2 dated 2014-02-22 and 2.0-3 dated 2014-10-21

 equate-2.0-2/equate/R/smoothing.r                |only
 equate-2.0-2/equate/man/equate-package.rd        |only
 equate-2.0-3/equate/DESCRIPTION                  |   30 -
 equate-2.0-3/equate/MD5                          |   59 +-
 equate-2.0-3/equate/NAMESPACE                    |   45 +
 equate-2.0-3/equate/NEWS                         |   41 +
 equate-2.0-3/equate/R/circlearc.R                |   25 -
 equate-2.0-3/equate/R/composite.R                |   13 
 equate-2.0-3/equate/R/equate.R                   |   68 +-
 equate-2.0-3/equate/R/equipercentile.R           |   94 +--
 equate-2.0-3/equate/R/error.R                    |  109 ++--
 equate-2.0-3/equate/R/freqtab.R                  |  553 ++++++++++++++++-------
 equate-2.0-3/equate/R/linear.R                   |   36 -
 equate-2.0-3/equate/R/smoothing.R                |only
 equate-2.0-3/equate/R/synthetic.R                |  121 ++---
 equate-2.0-3/equate/build/vignette.rds           |binary
 equate-2.0-3/equate/data/KBneat.rdata            |binary
 equate-2.0-3/equate/inst/doc/equatevignette.R    |  247 ++++++----
 equate-2.0-3/equate/inst/doc/equatevignette.Rnw  |  514 ++++++++++++++++-----
 equate-2.0-3/equate/inst/doc/equatevignette.pdf  |binary
 equate-2.0-3/equate/man/composite.Rd             |    7 
 equate-2.0-3/equate/man/descriptives.Rd          |   64 +-
 equate-2.0-3/equate/man/equate-package.Rd        |only
 equate-2.0-3/equate/man/equate.Rd                |   50 +-
 equate-2.0-3/equate/man/error.Rd                 |   34 +
 equate-2.0-3/equate/man/freqtab.Rd               |  115 +++-
 equate-2.0-3/equate/man/percentiles.Rd           |only
 equate-2.0-3/equate/man/plot.bootstrap.Rd        |   11 
 equate-2.0-3/equate/man/plot.equate.Rd           |   15 
 equate-2.0-3/equate/man/plot.freqtab.Rd          |   15 
 equate-2.0-3/equate/man/presmoothing.Rd          |  106 ++--
 equate-2.0-3/equate/vignettes/equatebibfile.bib  |   24 
 equate-2.0-3/equate/vignettes/equatevignette.Rnw |  514 ++++++++++++++++-----
 33 files changed, 1987 insertions(+), 923 deletions(-)

More information about equate at CRAN
Permanent link

Package EnvStats updated to version 1.0.3 with previous version 1.0.2 dated 2013-10-30

Title: Package for Environmental Statistics, including US EPA Guidance
Description: Functions and datasets to perform analyses of environmental data.
Author: Steven P. Millard
Maintainer: Steven P. Millard

Diff between EnvStats versions 1.0.2 dated 2013-10-30 and 1.0.3 dated 2014-10-21

 DESCRIPTION                                     |   10 
 MD5                                             |  386 ++++++++++++------------
 NAMESPACE                                       |    1 
 NEWS                                            |   89 +++++
 R/anovaPE.R                                     |   27 +
 R/calibrate.R                                   |  149 +++++++--
 R/cdfCompare.R                                  |    2 
 R/cdfPlot.R                                     |    8 
 R/check.distribution.args.R                     |   12 
 R/check.distribution.args.simulate.R            |   12 
 R/chisqGofTest.R                                |    2 
 R/ci.epoisCensored.profile.likelihood.R         |   34 +-
 R/ci.gammaAltCensored.profile.likelihood.R      |   37 +-
 R/detectionLimitCalibrate.R                     |   10 
 R/egammaAltCensored.R                           |   22 -
 R/egammaAltCensored.bootstrap.ci.R              |   43 +-
 R/egammaAltCensored.mle.R                       |    2 
 R/egammaCensored.R                              |   25 -
 R/elnormAltCensored.R                           |    7 
 R/elnormAltMultiplyCensored.R                   |   26 -
 R/elnormAltMultiplyCensored.bootstrap.ci.R      |   44 +-
 R/elnormAltMultiplyCensored.mle.R               |   35 +-
 R/elnormAltSinglyCensored.R                     |   22 -
 R/elnormAltSinglyCensored.bootstrap.ci.R        |   43 +-
 R/elnormAltSinglyCensored.mle.R                 |   35 +-
 R/elnormCensored.R                              |    8 
 R/elnormMultiplyCensored.R                      |   18 -
 R/elnormSinglyCensored.R                        |   18 -
 R/enorm.R                                       |    7 
 R/enormCensored.R                               |    8 
 R/enormMultiplyCensored.R                       |   24 -
 R/enormMultiplyCensored.bootstrap.ci.R          |   44 +-
 R/enormMultiplyCensored.mle.R                   |   40 +-
 R/enormSinglyCensored.R                         |   24 -
 R/enormSinglyCensored.bootstrap.ci.R            |   43 +-
 R/enormSinglyCensored.mle.R                     |   34 +-
 R/enparCensored.R                               |   25 -
 R/enparCensored.bootstrap.ci.R                  |   82 +++--
 R/enparCensored.jackknife.R                     |    9 
 R/epoisCensored.R                               |    7 
 R/epoisMultiplyCensored.R                       |   24 -
 R/epoisMultiplyCensored.bootstrap.ci.R          |   45 +-
 R/epoisMultiplyCensored.mle.R                   |    2 
 R/epoisSinglyCensored.R                         |   24 -
 R/epoisSinglyCensored.bootstrap.ci.R            |   45 +-
 R/epoisSinglyCensored.mle.R                     |    2 
 R/gofTest.default.R                             |    3 
 R/kendallSeasonalTrendTest.default.R            |   52 ---
 R/ksGofTest.R                                   |    2 
 R/oneSamplePermutationTest.R                    |    8 
 R/pdfPlot.R                                     |    8 
 R/ppccGeneralGofTest.R                          |    3 
 R/print.gofOutlier.R                            |only
 R/print.intervalEstimateCensored.R              |   19 -
 R/qqPlot.R                                      |    2 
 R/qqPlotGestalt.R                               |    2 
 R/rosnerTest.R                                  |only
 R/rosnerTestLambda.R                            |only
 R/sfGeneralGofTest.R                            |    3 
 R/sfMultiplyCensoredGofTest.R                   |    4 
 R/signTest.R                                    |   17 -
 R/simulateMvMatrix.R                            |    4 
 R/simulateVector.R                              |    4 
 R/stripChart.default.R                          |  212 +++++++------
 R/swGeneralGofTest.R                            |    3 
 R/twoSamplePermutationTestLocation.R            |   11 
 data/Air.df.rda                                 |binary
 data/Benthic.df.rda                             |binary
 data/Distribution.df.rda                        |binary
 data/EPA.02d.Ex.2.ug.per.L.vec.rda              |binary
 data/EPA.02d.Ex.4.mg.per.kg.vec.rda             |binary
 data/EPA.02d.Ex.6.mg.per.kg.vec.rda             |binary
 data/EPA.02d.Ex.9.mg.per.L.vec.rda              |binary
 data/EPA.09.Ex.10.1.nickel.df.rda               |binary
 data/EPA.09.Ex.11.1.arsenic.df.rda              |binary
 data/EPA.09.Ex.12.1.ccl4.df.rda                 |binary
 data/EPA.09.Ex.12.4.naphthalene.df.rda          |binary
 data/EPA.09.Ex.13.1.iron.df.rda                 |binary
 data/EPA.09.Ex.14.1.manganese.df.rda            |binary
 data/EPA.09.Ex.14.3.alkalinity.df.rda           |binary
 data/EPA.09.Ex.14.4.arsenic.df.rda              |binary
 data/EPA.09.Ex.14.8.df.rda                      |binary
 data/EPA.09.Ex.15.1.manganese.df.rda            |binary
 data/EPA.09.Ex.16.1.sulfate.df.rda              |binary
 data/EPA.09.Ex.16.2.benzene.df.rda              |binary
 data/EPA.09.Ex.16.4.copper.df.rda               |binary
 data/EPA.09.Ex.16.5.PCE.df.rda                  |binary
 data/EPA.09.Ex.17.1.loglead.df.rda              |binary
 data/EPA.09.Ex.17.2.toluene.df.rda              |binary
 data/EPA.09.Ex.17.3.chrysene.df.rda             |binary
 data/EPA.09.Ex.17.3.log.chrysene.df.rda         |binary
 data/EPA.09.Ex.17.4.copper.df.rda               |binary
 data/EPA.09.Ex.17.5.chloride.df.rda             |binary
 data/EPA.09.Ex.17.6.sulfate.df.rda              |binary
 data/EPA.09.Ex.17.7.sodium.df.rda               |binary
 data/EPA.09.Ex.18.1.arsenic.df.rda              |binary
 data/EPA.09.Ex.18.2.chrysene.df.rda             |binary
 data/EPA.09.Ex.18.3.TCE.df.rda                  |binary
 data/EPA.09.Ex.18.4.xylene.df.rda               |binary
 data/EPA.09.Ex.19.1.sulfate.df.rda              |binary
 data/EPA.09.Ex.19.2.chloride.df.rda             |binary
 data/EPA.09.Ex.19.5.mercury.df.rda              |binary
 data/EPA.09.Ex.20.1.nickel.df.rda               |binary
 data/EPA.09.Ex.21.1.aldicarb.df.rda             |binary
 data/EPA.09.Ex.21.2.benzene.df.rda              |binary
 data/EPA.09.Ex.21.5.beryllium.df.rda            |binary
 data/EPA.09.Ex.21.6.nitrate.df.rda              |binary
 data/EPA.09.Ex.21.7.TCE.df.rda                  |binary
 data/EPA.09.Ex.22.1.VC.df.rda                   |binary
 data/EPA.09.Ex.22.2.Specific.Conductance.df.rda |binary
 data/EPA.09.Ex.6.3.sulfate.df.rda               |binary
 data/EPA.09.Ex.7.1.arsenic.df.rda               |binary
 data/EPA.09.Table.9.1.TCE.df.rda                |binary
 data/EPA.09.Table.9.3.df.rda                    |binary
 data/EPA.09.Table.9.4.nickel.vec.rda            |binary
 data/EPA.89b.aldicarb1.df.rda                   |binary
 data/EPA.89b.aldicarb2.df.rda                   |binary
 data/EPA.89b.benzene.df.rda                     |binary
 data/EPA.89b.cadmium.df.rda                     |binary
 data/EPA.89b.chlordane1.df.rda                  |binary
 data/EPA.89b.chlordane2.df.rda                  |binary
 data/EPA.89b.edb.df.rda                         |binary
 data/EPA.89b.lead.df.rda                        |binary
 data/EPA.89b.loglead.df.rda                     |binary
 data/EPA.89b.manganese.df.rda                   |binary
 data/EPA.89b.sulfate.df.rda                     |binary
 data/EPA.89b.t29.df.rda                         |binary
 data/EPA.89b.toc.vec.rda                        |binary
 data/EPA.92c.arsenic1.df.rda                    |binary
 data/EPA.92c.arsenic2.df.rda                    |binary
 data/EPA.92c.arsenic3.df.rda                    |binary
 data/EPA.92c.benzene1.df.rda                    |binary
 data/EPA.92c.benzene2.df.rda                    |binary
 data/EPA.92c.ccl4.df.rda                        |binary
 data/EPA.92c.chrysene.df.rda                    |binary
 data/EPA.92c.copper1.df.rda                     |binary
 data/EPA.92c.copper2.df.rda                     |binary
 data/EPA.92c.lognickel1.df.rda                  |binary
 data/EPA.92c.nickel1.df.rda                     |binary
 data/EPA.92c.nickel2.df.rda                     |binary
 data/EPA.92c.toluene.df.rda                     |binary
 data/EPA.92c.zinc.df.rda                        |binary
 data/EPA.92d.chromium.df.rda                    |binary
 data/EPA.92d.chromium.vec.rda                   |binary
 data/EPA.94b.lead.df.rda                        |binary
 data/EPA.94b.tccb.df.rda                        |binary
 data/EPA.97.cadmium.111.df.rda                  |binary
 data/Environmental.df.rda                       |binary
 data/Gibbons.et.al.09.Alkilinity.vec.rda        |binary
 data/Gibbons.et.al.09.Vinyl.Chloride.vec.rda    |binary
 data/Graham.et.al.75.etu.df.rda                 |binary
 data/Helsel.Cohn.88.app.b.df.rda                |binary
 data/Helsel.Cohn.88.silver.df.rda               |binary
 data/Lin.Evans.80.df.rda                        |binary
 data/Millard.Deverel.88.df.rda                  |binary
 data/Modified.TcCB.df.rda                       |binary
 data/NIOSH.89.air.lead.vec.rda                  |binary
 data/Olympic.NH4.df.rda                         |binary
 data/Ozone.NE.df.rda                            |binary
 data/Refinery.CO.df.rda                         |binary
 data/Skagit.NH3_N.df.rda                        |binary
 data/Total.P.df.rda                             |binary
 inst/doc/EnvStats-manual.pdf                    |binary
 man/EnvStats-package.Rd                         |   12 
 man/FcnsByCatGOFTests.Rd                        |   12 
 man/FcnsByCatPower.Rd                           |    2 
 man/anovaPE.Rd                                  |   69 +++-
 man/aovPower.Rd                                 |    3 
 man/boxcox.Rd                                   |   24 +
 man/boxcox.object.Rd                            |    3 
 man/calibrate.Rd                                |  115 ++++---
 man/ciBinomN.Rd                                 |    2 
 man/detectionLimitCalibrate.Rd                  |   61 +--
 man/egammaAltCensored.Rd                        |   65 ++--
 man/egammaCensored.Rd                           |   63 ++-
 man/elnormAltCensored.Rd                        |   61 ++-
 man/elnormCensored.Rd                           |   11 
 man/enorm.Rd                                    |    4 
 man/enormCensored.Rd                            |   59 +--
 man/enparCensored.Rd                            |   89 +++--
 man/epoisCensored.Rd                            |   57 +--
 man/gof.object.Rd                               |    4 
 man/gofOutlier.object.Rd                        |only
 man/gofTest.Rd                                  |    3 
 man/kendallSeasonalTrendTest.Rd                 |    4 
 man/oneSamplePermutationTest.Rd                 |    6 
 man/plotPredIntLnormAltTestPowerCurve.Rd        |   46 +-
 man/predIntNparSimultaneousTestPower.Rd         |    2 
 man/print.gofOutlier.Rd                         |only
 man/propTestN.Rd                                |    6 
 man/propTestPower.Rd                            |    8 
 man/qqPlotGestalt.Rd                            |    6 
 man/rosnerTest.Rd                               |only
 man/skewness.Rd                                 |   10 
 man/stripChart.Rd                               |   49 +--
 man/tTestPower.Rd                               |    6 
 man/twoSamplePermutationTestLocation.Rd         |    6 
 197 files changed, 1685 insertions(+), 1156 deletions(-)

More information about EnvStats at CRAN
Permanent link

New package DetMCD with initial version 0.0.1
Package: DetMCD
Type: Package
Title: DetMCD Algorithm (Robust and Deterministic Estimation of Location and Scatter)
Version: 0.0.1
Date: 2013-01-13
Depends: matrixStats, pcaPP (>= 1.8-1), robustbase, MASS
Suggests: mvtnorm
LinkingTo: Rcpp, RcppEigen
Description: DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),"A deterministic algorithm for robust location and scatter", Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637.
License: GPL (>= 2)
LazyLoad: yes
Authors@R: c(person("Vakili", "Kaveh", role = c("aut", "cre"), email = "vakili.kaveh.email@gmail.com"), person("Mia", "Hubert", role = "ths", email = "mia.hubert@wis.kuleuven.be"))
Maintainer: Vakili Kaveh
Author: Vakili Kaveh [aut, cre], Mia Hubert [ths]
Packaged: 2014-10-21 16:15:15 UTC; kaveh
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 20:01:49

More information about DetMCD at CRAN
Permanent link

New package scrm with initial version 1.3-1
Package: scrm
Type: Package
Title: Simulating the Evolution of Biological Sequences
Version: 1.3-1
Date: 2014-10-21
Authors@R: c( person('Paul', 'Staab', , 'develop@paulstaab.de', role=c('aut', 'cre', 'cph')), person('Zhu', 'Sha', role=c('aut', 'cph')), person('Dirk', 'Metzler', role='ths'), person('Gerton', 'Lunter', role=c('aut', 'cph', 'ths')) )
Description: A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution.
URL: https://github.com/scrm/scrm-r
License: GPL (>= 3)
Suggests: testthat (>= 0.9.0), knitr, ape
Imports: Rcpp (>= 0.11.2)
SystemRequirements: C++11
VignetteBuilder: knitr
LinkingTo: Rcpp
Packaged: 2014-10-21 11:42:11 UTC; paul
Author: Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [ths], Gerton Lunter [aut, cph, ths]
Maintainer: Paul Staab
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 17:48:23

More information about scrm at CRAN
Permanent link

Package prevalence updated to version 0.3.0 with previous version 0.2.0 dated 2013-09-22

Title: The prevalence package
Description: Tools for prevalence assessment studies. IMPORTANT: the truePrev functions in the prevalence package call on JAGS (Just Another Gibbs Sampler), which therefore has to be available on the user's system. JAGS can be downloaded from http://sourceforge.net/projects/mcmc-jags/files/
Author: Brecht Devleesschauwer [aut, cre], Paul Torgerson [aut], Johannes Charlier [aut], Bruno Levecke [aut], Nicolas Praet [aut], Sophie Roelandt [aut], Suzanne Smit [aut], Pierre Dorny [aut], Dirk Berkvens [aut], Niko Speybroeck [aut]
Maintainer: Brecht Devleesschauwer

Diff between prevalence versions 0.2.0 dated 2013-09-22 and 0.3.0 dated 2014-10-21

 prevalence-0.2.0/prevalence/R/checkMultiPrior.R       |only
 prevalence-0.2.0/prevalence/R/definitions.R           |only
 prevalence-0.2.0/prevalence/R/explode.R               |only
 prevalence-0.2.0/prevalence/R/multiModel_SeSp.R       |only
 prevalence-0.2.0/prevalence/R/multiModel_probs.R      |only
 prevalence-0.2.0/prevalence/R/multiModel_select.R     |only
 prevalence-0.2.0/prevalence/R/plot_methods.R          |only
 prevalence-0.2.0/prevalence/R/plot_methods_coda.R     |only
 prevalence-0.2.0/prevalence/R/print_methods.R         |only
 prevalence-0.2.0/prevalence/R/truePrevMulti.R         |only
 prevalence-0.2.0/prevalence/R/truePrevMultinom.R      |only
 prevalence-0.2.0/prevalence/man/definition.Rd         |only
 prevalence-0.3.0/prevalence/DESCRIPTION               |   31 +--
 prevalence-0.3.0/prevalence/MD5                       |   63 +++---
 prevalence-0.3.0/prevalence/NAMESPACE                 |    5 
 prevalence-0.3.0/prevalence/NEWS                      |only
 prevalence-0.3.0/prevalence/R/betaPERT.R              |   14 -
 prevalence-0.3.0/prevalence/R/checkBinPrior.R         |    2 
 prevalence-0.3.0/prevalence/R/checkSeSp.R             |  109 +++++++---
 prevalence-0.3.0/prevalence/R/define-functions.R      |only
 prevalence-0.3.0/prevalence/R/dist2list.R             |   13 -
 prevalence-0.3.0/prevalence/R/plot-methods-coda.R     |only
 prevalence-0.3.0/prevalence/R/plot-methods.R          |only
 prevalence-0.3.0/prevalence/R/print-methods.R         |only
 prevalence-0.3.0/prevalence/R/truePrev.R              |   13 -
 prevalence-0.3.0/prevalence/R/truePrevBinom.R         |    6 
 prevalence-0.3.0/prevalence/R/truePrevMulti-helper.R  |only
 prevalence-0.3.0/prevalence/R/truePrevMulti-main.R    |only
 prevalence-0.3.0/prevalence/R/truePrevPools.R         |   23 +-
 prevalence-0.3.0/prevalence/R/writeSeSp.R             |   28 +-
 prevalence-0.3.0/prevalence/R/zzz.R                   |   97 +++++----
 prevalence-0.3.0/prevalence/inst/CITATION             |   22 +-
 prevalence-0.3.0/prevalence/man/betaExpert.Rd         |   21 --
 prevalence-0.3.0/prevalence/man/betaPERT.Rd           |   32 +--
 prevalence-0.3.0/prevalence/man/define.Rd             |only
 prevalence-0.3.0/prevalence/man/prev-class.Rd         |   23 --
 prevalence-0.3.0/prevalence/man/prevalence-package.Rd |   22 +-
 prevalence-0.3.0/prevalence/man/print-methods.Rd      |   14 -
 prevalence-0.3.0/prevalence/man/show-methods.Rd       |    2 
 prevalence-0.3.0/prevalence/man/truePrev.Rd           |   53 +----
 prevalence-0.3.0/prevalence/man/truePrevMulti.Rd      |  180 +++++-------------
 prevalence-0.3.0/prevalence/man/truePrevMulti2.Rd     |only
 prevalence-0.3.0/prevalence/man/truePrevPools.Rd      |   69 ++----
 43 files changed, 373 insertions(+), 469 deletions(-)

More information about prevalence at CRAN
Permanent link

New package rtkpp with initial version 0.8.2
Package: rtkpp
Type: Package
Title: STK++ integration to R using Rcpp.
Version: 0.8.2
Encoding: UTF-8
Date: 2014-02-08
Authors@R: c(person("Serge", "Iovleff", role=c("aut","cre"), email="serge.iovleff@stkpp.org"), person("Vincent", "Kubicki", role="ctb", email="Vincent.Kubicki@inria.fr"), person("Quentin", "Grimonprez", role="ctb", email="Quentin.Grimonprez@inria.fr"), person("Parmeet", "Bhatia", role="ctb", email="bhatia.parmeet@gmail.com"))
Copyright: Inria, and specifically inst/COPYRIGHTS for the STK++ library
Maintainer: Serge Iovleff
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later.
License: GPL (>= 2) | LGPL (>= 2) | file LICENSE
BugReports: https://www.stkpp.org
LazyLoad: yes
Depends: R (>= 3.0.2), Rcpp
LinkingTo: Rcpp
Imports: methods
URL: http://www.stkpp.org
NeedsCompilation: yes
SystemRequirements: GNU make
Collate: 'ClusterAlgo.R' 'ClusterInit.R' 'ClusterStrategy.R' 'IClusterModel.R' 'ClusterCategorical.R' 'ClusterDiagGaussian.R' 'ClusterGamma.R' 'ClusterModelNames.R' 'ClusterPlot.R' 'global.R' 'rtkpp.R' 'rtkppFlags.R' 'inlineCxxPlugin.R'
Packaged: 2014-10-21 12:37:40 UTC; iovleff
Author: Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb]
Repository: CRAN
Date/Publication: 2014-10-21 17:48:19

More information about rtkpp at CRAN
Permanent link

Package nhlscrapr updated to version 1.8 with previous version 1.5.1 dated 2014-06-10

Title: Compiling the NHL Real Time Scoring System Database for easy use in R
Description: Compiling the NHL Real Time Scoring System Database for easy use in R
Author: A.C. Thomas, Samuel L. Ventura
Maintainer: A.C. Thomas

Diff between nhlscrapr versions 1.5.1 dated 2014-06-10 and 1.8 dated 2014-10-21

 nhlscrapr-1.5.1/nhlscrapr/R/capgeek.R                 |only
 nhlscrapr-1.5.1/nhlscrapr/man/capgeek.Rd              |only
 nhlscrapr-1.8/nhlscrapr/DESCRIPTION                   |    8 
 nhlscrapr-1.8/nhlscrapr/MD5                           |   24 -
 nhlscrapr-1.8/nhlscrapr/NAMESPACE                     |    4 
 nhlscrapr-1.8/nhlscrapr/R/convert-html.R              |   28 -
 nhlscrapr-1.8/nhlscrapr/R/integrate.R                 |  421 ++++++++++--------
 nhlscrapr-1.8/nhlscrapr/R/manual-name-fixes.R         |   35 +
 nhlscrapr-1.8/nhlscrapr/R/operations.R                |  133 ++++-
 nhlscrapr-1.8/nhlscrapr/R/subzone-adjustments.R       |only
 nhlscrapr-1.8/nhlscrapr/data/date201415.RData         |only
 nhlscrapr-1.8/nhlscrapr/data/pushpull.RData           |only
 nhlscrapr-1.8/nhlscrapr/data/zone-adjust-prefab.RData |only
 nhlscrapr-1.8/nhlscrapr/man/full.game.database.Rd     |   15 
 nhlscrapr-1.8/nhlscrapr/man/process-games.Rd          |   32 -
 nhlscrapr-1.8/nhlscrapr/man/quadsarray.Rd             |   20 
 16 files changed, 464 insertions(+), 256 deletions(-)

More information about nhlscrapr at CRAN
Permanent link

Package MPTinR updated to version 1.6.3 with previous version 1.5.1 dated 2014-08-07

Title: Analyze Multinomial Processing Tree Models
Description: MPTinR provides a user-friendly way for the analysis of multinomial processing tree (MPT) models (e.g., Riefer, D. M., and Batchelder, W. H. [1988]. Multinomial modeling and the measurement of cognitive processes. Psychological Review, 95, 318-339) for single and multiple datasets. The main functions perform model fitting and model selection. Model selection can be done using AIC, BIC, or the Fisher Information Approximation (FIA) a measure based on the Minimum Description Length (MDL) framework. The model and restrictions can be specified in external files or within an R script in an intuitive syntax or using the context-free language for MPTs. The 'classical' .EQN file format for model files is also supported. Besides MPTs, MPTinR can fit a wide variety of other cognitive models such as SDT models (see fit.model). MPTinR supports multicore fitting and FIA calculation using the snowfall package. MPTinR can generate data from a model for e.g., simulation or parametric bootstrap and plot predicted versus observed data.
Author: Henrik Singmann [aut, cre], David Kellen [aut], Quentin Gronau [aut], Christian Mueller [ctb], Akhil S Bhel [ctb]
Maintainer: Henrik Singmann

Diff between MPTinR versions 1.5.1 dated 2014-08-07 and 1.6.3 dated 2014-10-21

 MPTinR-1.5.1/MPTinR/ChangeLog             |only
 MPTinR-1.5.1/MPTinR/src/Makevars          |only
 MPTinR-1.5.1/MPTinR/src/Makevars.win      |only
 MPTinR-1.6.3/MPTinR/DESCRIPTION           |   24 ++++----
 MPTinR-1.6.3/MPTinR/MD5                   |   45 +++++++--------
 MPTinR-1.6.3/MPTinR/NAMESPACE             |    1 
 MPTinR-1.6.3/MPTinR/NEWS                  |   36 +++++++++++-
 MPTinR-1.6.3/MPTinR/R/RcppExports.R       |only
 MPTinR-1.6.3/MPTinR/R/bmpt.fia.R          |   16 ++---
 MPTinR-1.6.3/MPTinR/R/fit.model.R         |    2 
 MPTinR-1.6.3/MPTinR/R/fit.mpt.old.R       |    8 +-
 MPTinR-1.6.3/MPTinR/R/fit.mptinr.R        |    8 +-
 MPTinR-1.6.3/MPTinR/R/select.mpt.R        |    7 +-
 MPTinR-1.6.3/MPTinR/man/MPTinR-package.Rd |   10 +--
 MPTinR-1.6.3/MPTinR/man/bmpt.fia.Rd       |    4 -
 MPTinR-1.6.3/MPTinR/man/check.mpt.Rd      |    8 +-
 MPTinR-1.6.3/MPTinR/man/fit.model.Rd      |    8 +-
 MPTinR-1.6.3/MPTinR/man/fit.mpt.Rd        |   23 +++----
 MPTinR-1.6.3/MPTinR/man/fit.mpt.old.Rd    |   18 +++---
 MPTinR-1.6.3/MPTinR/man/fit.mptinr.Rd     |   18 +++---
 MPTinR-1.6.3/MPTinR/man/get.mpt.fia.Rd    |   12 ++--
 MPTinR-1.6.3/MPTinR/man/make.mpt.cf.Rd    |    6 +-
 MPTinR-1.6.3/MPTinR/man/select.mpt.Rd     |    8 +-
 MPTinR-1.6.3/MPTinR/src/RcppExports.cpp   |only
 MPTinR-1.6.3/MPTinR/src/determinant.cpp   |   85 ++++++++--------------------
 MPTinR-1.6.3/MPTinR/src/determinant_c.cpp |   88 ++++++++----------------------
 26 files changed, 202 insertions(+), 233 deletions(-)

More information about MPTinR at CRAN
Permanent link

Package GGIR updated to version 1.1-3 with previous version 1.0-6 dated 2014-09-01

Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb], Severine Sabia [ctb]
Maintainer: Vincent T van Hees

Diff between GGIR versions 1.0-6 dated 2014-09-01 and 1.1-3 dated 2014-10-21

 DESCRIPTION             |   29 ++--
 MD5                     |   37 +++--
 NAMESPACE               |    3 
 R/g.analyse.R           |  141 +++++++++++++++----
 R/g.calibrate.R         |   99 ++-----------
 R/g.convert.day.names.R |only
 R/g.detecmidnight.R     |   33 ++--
 R/g.dotorcomma.R        |    2 
 R/g.getmeta.R           |  248 +++++++++++++++++++++-------------
 R/g.impute.R            |   53 +++++++
 R/g.inspectfile.R       |  347 ++++++++++++++++++++++++------------------------
 R/g.metric.R            |  291 +++++++++++++++++++++-------------------
 R/g.part1.R             |only
 R/g.part2.R             |only
 R/g.shell.GGIR.R        |only
 inst/NEWS.Rd            |   14 +
 man/GGIR-package.Rd     |   74 +++++++---
 man/g.calibrate.Rd      |    7 
 man/g.getmeta.Rd        |   36 ++++
 man/g.impute.Rd         |   10 +
 man/g.part1.Rd          |only
 man/g.part2.Rd          |only
 man/g.shell.GGIR.Rd     |only
 23 files changed, 834 insertions(+), 590 deletions(-)

More information about GGIR at CRAN
Permanent link

New package cdcsis with initial version 1.0
Package: cdcsis
Type: Package
Title: Conditional Distance Correlation and Its Related Feature Screening Method
Version: 1.0
Date: 2014-09-01
Author: Canhong Wen, Wenliang Pan, Mian Huang, and Xueqin Wang
Depends: R(>= 3.0.1), stats
Imports: ks
Suggests: MASS, energy
Maintainer: Canhong Wen
Description: Gives conditional distance correlation and performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data. The conditional distance correlation is a novel conditional dependence measurement of two random variables given a third variable. The conditional distance correlation sure independence screening is used for screening variables in ultrahigh dimensional setting.
License: GPL (>= 2)
Packaged: 2014-10-21 14:47:45 UTC; wencanh
Repository: CRAN
Collate: 'cdcov.R' 'cdcor.R' 'cdcor.ada.R' 'bw.R' 'cdcsis.R'
NeedsCompilation: yes
Date/Publication: 2014-10-21 17:48:22

More information about cdcsis at CRAN
Permanent link

Package bio3d updated to version 2.1-2 with previous version 2.1-1 dated 2014-10-15

Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Author: Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide
Maintainer: Barry Grant

Diff between bio3d versions 2.1-1 dated 2014-10-15 and 2.1-2 dated 2014-10-21

 DESCRIPTION                        |   19 +---
 MD5                                |  144 ++++++++++++++++++-------------------
 R/read.dcd.R                       |    7 +
 inst/examples/1dpx.pdb             |only
 inst/examples/1hel.pdb             |only
 man/aa.mass.Rd                     |    3 
 man/angle.xyz.Rd                   |    2 
 man/atom.select.Rd                 |   10 +-
 man/atom2ele.Rd                    |    2 
 man/atom2mass.Rd                   |    3 
 man/bio3d.package.Rd               |   53 +++++++------
 man/bwr.colors.Rd                  |    2 
 man/chain.pdb.Rd                   |    2 
 man/cna.Rd                         |    2 
 man/com.Rd                         |    3 
 man/combine.sel.Rd                 |   12 +--
 man/community.tree.Rd              |    3 
 man/convert.pdb.Rd                 |    3 
 man/dccm.nma.Rd                    |    2 
 man/deformation.nma.Rd             |    4 -
 man/dm.Rd                          |    2 
 man/fluct.nma.Rd                   |    2 
 man/get.pdb.Rd                     |    3 
 man/identify.cna.Rd                |   17 ----
 man/inner.prod.Rd                  |    2 
 man/is.pdb.Rd                      |    2 
 man/is.select.Rd                   |    6 -
 man/is.xyz.Rd                      |    2 
 man/load.enmff.Rd                  |    4 -
 man/mktrj.nma.Rd                   |    2 
 man/motif.find.Rd                  |    2 
 man/nma.pdb.Rd                     |    2 
 man/normalize.vector.Rd            |    2 
 man/orient.pdb.Rd                  |    2 
 man/pca.xyz.Rd                     |    5 -
 man/pdb.annotate.Rd                |    4 -
 man/plot.bio3d.Rd                  |    3 
 man/plot.cna.Rd                    |    3 
 man/plot.dmat.Rd                   |    4 -
 man/plot.nma.Rd                    |    2 
 man/plot.rmsip.Rd                  |    2 
 man/print.xyz.Rd                   |    2 
 man/read.mol2.Rd                   |    2 
 man/read.pdb.Rd                    |    4 -
 man/read.pdcBD.Rd                  |    3 
 man/read.pqr.Rd                    |    3 
 man/rgyr.Rd                        |    2 
 man/sdENM.Rd                       |    2 
 man/sip.Rd                         |    2 
 man/sse.bridges.Rd                 |    4 -
 man/torsion.pdb.Rd                 |    2 
 man/uniprot.Rd                     |    2 
 man/view.cna.Rd                    |   19 ----
 man/view.dccm.Rd                   |    2 
 man/view.modes.Rd                  |    2 
 man/write.fasta.Rd                 |    3 
 man/write.pdb.Rd                   |    3 
 man/write.pqr.Rd                   |    2 
 tests/testthat/test-aa2mass.R      |    3 
 tests/testthat/test-atom2mass.R    |   31 +++----
 tests/testthat/test-cmap.R         |   10 +-
 tests/testthat/test-core.find.R    |   31 ++++---
 tests/testthat/test-dccm.R         |   13 +--
 tests/testthat/test-deformation.R  |   32 ++++----
 tests/testthat/test-fitting.R      |   62 +++++++++------
 tests/testthat/test-get.pdb.R      |    4 +
 tests/testthat/test-nma.R          |   22 -----
 tests/testthat/test-nma.pdbs.R     |  109 ++++++++++------------------
 tests/testthat/test-overlap.R      |    8 +-
 tests/testthat/test-pca.R          |   34 +++-----
 tests/testthat/test-pdb.annotate.R |    1 
 tests/testthat/test-pdbsplit.R     |    3 
 tests/testthat/test-read.pdb.R     |   46 ++++++++---
 tests/testthat/test-rmsd.R         |   50 +++++++-----
 74 files changed, 451 insertions(+), 416 deletions(-)

More information about bio3d at CRAN
Permanent link

Package vcf2geno (with last version 2.3) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-01-23 2.3
2013-03-15 2.0
2013-03-05 1.9
2013-02-01 1.8
2013-01-20 1.7
2013-01-02 1.6
2012-10-25 1.5
2012-09-07 1.4
2012-08-29 1.3
2012-08-22 1.0

Permanent link
Package STARSEQ updated to version 1.2.1 with previous version 1.02 dated 2012-08-24

Title: Secondary Trait Association analysis for Rare variants via SEQuence data
Description: STARSEQ is an R-package for detecting associations with rare variants using selected samples in sequence-based association studies. It corrects for the bias in the secondary trait distribution induced by selective sampling on the primary trait. The corrected secondary trait can be analyzed by standard rare variant tests. In the STARSEQ package, several popular rare variant tests were implemented, which include 1.) combined multivariate and collapsing 2.) weighted sum statistics, 3.) kernel based adaptive cluster, 4.) variable threshold test 5.) sequence kernel association test.
Author: Dajiang Liu
Maintainer: Dajiang Liu

Diff between STARSEQ versions 1.02 dated 2012-08-24 and 1.2.1 dated 2014-10-21

 DESCRIPTION |    9 +++++----
 MD5         |    2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

More information about STARSEQ at CRAN
Permanent link

Package RcppParallel updated to version 4.3.3 with previous version 4.2.5.3 dated 2014-08-17

Title: Parallel programming tools for Rcpp
Description: High level functions for doing parallel programming with Rcpp. For example, the parallelFor function can be used to convert the work of a standard serial "for" loop into a parallel one and the parallelReduce function can be used for accumulating aggregate or other values.
Author: JJ Allaire; Romain Francois; Intel, Inc.; Marcus Geelnard
Maintainer: JJ Allaire

Diff between RcppParallel versions 4.2.5.3 dated 2014-08-17 and 4.3.3 dated 2014-10-21

 RcppParallel-4.2.5.3/src/tbb/build/vs2008                                        |only
 RcppParallel-4.2.5.3/src/tbb/src/test/test_concurrent_unordered.cpp              |only
 RcppParallel-4.3.3/DESCRIPTION                                                   |    8 
 RcppParallel-4.3.3/MD5                                                           | 1147 ++++----
 RcppParallel-4.3.3/NEWS                                                          |    6 
 RcppParallel-4.3.3/inst/include/tbb/aggregator.h                                 |   38 
 RcppParallel-4.3.3/inst/include/tbb/aligned_space.h                              |   38 
 RcppParallel-4.3.3/inst/include/tbb/atomic.h                                     |   40 
 RcppParallel-4.3.3/inst/include/tbb/blocked_range.h                              |   46 
 RcppParallel-4.3.3/inst/include/tbb/blocked_range2d.h                            |   42 
 RcppParallel-4.3.3/inst/include/tbb/blocked_range3d.h                            |   42 
 RcppParallel-4.3.3/inst/include/tbb/cache_aligned_allocator.h                    |   47 
 RcppParallel-4.3.3/inst/include/tbb/combinable.h                                 |   38 
 RcppParallel-4.3.3/inst/include/tbb/compat/condition_variable                    |   38 
 RcppParallel-4.3.3/inst/include/tbb/compat/ppl.h                                 |   38 
 RcppParallel-4.3.3/inst/include/tbb/compat/thread                                |   38 
 RcppParallel-4.3.3/inst/include/tbb/compat/tuple                                 |   38 
 RcppParallel-4.3.3/inst/include/tbb/concurrent_hash_map.h                        |  203 -
 RcppParallel-4.3.3/inst/include/tbb/concurrent_lru_cache.h                       |   38 
 RcppParallel-4.3.3/inst/include/tbb/concurrent_priority_queue.h                  |  175 -
 RcppParallel-4.3.3/inst/include/tbb/concurrent_queue.h                           |  268 +
 RcppParallel-4.3.3/inst/include/tbb/concurrent_unordered_map.h                   |  166 -
 RcppParallel-4.3.3/inst/include/tbb/concurrent_unordered_set.h                   |  193 -
 RcppParallel-4.3.3/inst/include/tbb/concurrent_vector.h                          |  263 +
 RcppParallel-4.3.3/inst/include/tbb/critical_section.h                           |   38 
 RcppParallel-4.3.3/inst/include/tbb/enumerable_thread_specific.h                 |   46 
 RcppParallel-4.3.3/inst/include/tbb/flow_graph.h                                 | 1088 +++++--
 RcppParallel-4.3.3/inst/include/tbb/internal/_aggregator_impl.h                  |   38 
 RcppParallel-4.3.3/inst/include/tbb/internal/_concurrent_queue_impl.h            |  176 -
 RcppParallel-4.3.3/inst/include/tbb/internal/_concurrent_unordered_impl.h        |  185 +
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_impl.h                  |  480 ++-
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_indexer_impl.h          |  154 -
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_item_buffer_impl.h      |  244 +
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_join_impl.h             |  343 +-
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_node_impl.h             |  200 +
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_tagged_buffer_impl.h    |  259 +
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_trace_impl.h            |   38 
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_types_impl.h            |   81 
 RcppParallel-4.3.3/inst/include/tbb/internal/_mutex_padding.h                    |   42 
 RcppParallel-4.3.3/inst/include/tbb/internal/_range_iterator.h                   |only
 RcppParallel-4.3.3/inst/include/tbb/internal/_tbb_strings.h                      |   38 
 RcppParallel-4.3.3/inst/include/tbb/internal/_tbb_windef.h                       |   38 
 RcppParallel-4.3.3/inst/include/tbb/internal/_x86_eliding_mutex_impl.h           |   41 
 RcppParallel-4.3.3/inst/include/tbb/internal/_x86_rtm_rw_mutex_impl.h            |  102 
 RcppParallel-4.3.3/inst/include/tbb/machine/gcc_armv7.h                          |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/gcc_generic.h                        |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/gcc_ia32_common.h                    |   45 
 RcppParallel-4.3.3/inst/include/tbb/machine/gcc_itsx.h                           |   53 
 RcppParallel-4.3.3/inst/include/tbb/machine/ibm_aix51.h                          |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/icc_generic.h                        |   49 
 RcppParallel-4.3.3/inst/include/tbb/machine/linux_common.h                       |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/linux_ia32.h                         |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/linux_ia64.h                         |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/linux_intel64.h                      |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/mac_ppc.h                            |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/macos_common.h                       |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/mic_common.h                         |   42 
 RcppParallel-4.3.3/inst/include/tbb/machine/msvc_armv7.h                         |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/msvc_ia32_common.h                   |   57 
 RcppParallel-4.3.3/inst/include/tbb/machine/sunos_sparc.h                        |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/windows_api.h                        |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/windows_ia32.h                       |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/windows_intel64.h                    |   38 
 RcppParallel-4.3.3/inst/include/tbb/machine/xbox360_ppc.h                        |   38 
 RcppParallel-4.3.3/inst/include/tbb/memory_pool.h                                |   47 
 RcppParallel-4.3.3/inst/include/tbb/mutex.h                                      |   44 
 RcppParallel-4.3.3/inst/include/tbb/null_mutex.h                                 |   47 
 RcppParallel-4.3.3/inst/include/tbb/null_rw_mutex.h                              |   47 
 RcppParallel-4.3.3/inst/include/tbb/parallel_do.h                                |   60 
 RcppParallel-4.3.3/inst/include/tbb/parallel_for.h                               |   38 
 RcppParallel-4.3.3/inst/include/tbb/parallel_for_each.h                          |   64 
 RcppParallel-4.3.3/inst/include/tbb/parallel_invoke.h                            |  147 -
 RcppParallel-4.3.3/inst/include/tbb/parallel_reduce.h                            |   38 
 RcppParallel-4.3.3/inst/include/tbb/parallel_scan.h                              |   38 
 RcppParallel-4.3.3/inst/include/tbb/parallel_sort.h                              |   67 
 RcppParallel-4.3.3/inst/include/tbb/parallel_while.h                             |   38 
 RcppParallel-4.3.3/inst/include/tbb/partitioner.h                                |   38 
 RcppParallel-4.3.3/inst/include/tbb/pipeline.h                                   |   59 
 RcppParallel-4.3.3/inst/include/tbb/queuing_mutex.h                              |   40 
 RcppParallel-4.3.3/inst/include/tbb/queuing_rw_mutex.h                           |   40 
 RcppParallel-4.3.3/inst/include/tbb/reader_writer_lock.h                         |   38 
 RcppParallel-4.3.3/inst/include/tbb/recursive_mutex.h                            |   44 
 RcppParallel-4.3.3/inst/include/tbb/runtime_loader.h                             |   38 
 RcppParallel-4.3.3/inst/include/tbb/scalable_allocator.h                         |   47 
 RcppParallel-4.3.3/inst/include/tbb/spin_mutex.h                                 |   40 
 RcppParallel-4.3.3/inst/include/tbb/spin_rw_mutex.h                              |   79 
 RcppParallel-4.3.3/inst/include/tbb/task.h                                       |   60 
 RcppParallel-4.3.3/inst/include/tbb/task_arena.h                                 |   38 
 RcppParallel-4.3.3/inst/include/tbb/task_group.h                                 |   53 
 RcppParallel-4.3.3/inst/include/tbb/task_scheduler_init.h                        |   38 
 RcppParallel-4.3.3/inst/include/tbb/task_scheduler_observer.h                    |   38 
 RcppParallel-4.3.3/inst/include/tbb/tbb.h                                        |   48 
 RcppParallel-4.3.3/inst/include/tbb/tbb_allocator.h                              |   47 
 RcppParallel-4.3.3/inst/include/tbb/tbb_config.h                                 |  205 -
 RcppParallel-4.3.3/inst/include/tbb/tbb_exception.h                              |   38 
 RcppParallel-4.3.3/inst/include/tbb/tbb_machine.h                                |   38 
 RcppParallel-4.3.3/inst/include/tbb/tbb_profiling.h                              |   38 
 RcppParallel-4.3.3/inst/include/tbb/tbb_stddef.h                                 |  139 
 RcppParallel-4.3.3/inst/include/tbb/tbb_thread.h                                 |  130 
 RcppParallel-4.3.3/inst/include/tbb/tbbmalloc_proxy.h                            |   38 
 RcppParallel-4.3.3/inst/include/tbb/tick_count.h                                 |   38 
 RcppParallel-4.3.3/src/Makevars                                                  |    6 
 RcppParallel-4.3.3/src/tbb/CHANGES                                               |   80 
 RcppParallel-4.3.3/src/tbb/Makefile                                              |   36 
 RcppParallel-4.3.3/src/tbb/build/AIX.gcc.inc                                     |   38 
 RcppParallel-4.3.3/src/tbb/build/AIX.inc                                         |   36 
 RcppParallel-4.3.3/src/tbb/build/FreeBSD.gcc.inc                                 |   40 
 RcppParallel-4.3.3/src/tbb/build/FreeBSD.inc                                     |   36 
 RcppParallel-4.3.3/src/tbb/build/Makefile.rml                                    |   40 
 RcppParallel-4.3.3/src/tbb/build/Makefile.tbb                                    |   40 
 RcppParallel-4.3.3/src/tbb/build/Makefile.tbbmalloc                              |   64 
 RcppParallel-4.3.3/src/tbb/build/Makefile.tbbproxy                               |   36 
 RcppParallel-4.3.3/src/tbb/build/Makefile.test                                   |   58 
 RcppParallel-4.3.3/src/tbb/build/SunOS.gcc.inc                                   |   40 
 RcppParallel-4.3.3/src/tbb/build/SunOS.inc                                       |   36 
 RcppParallel-4.3.3/src/tbb/build/SunOS.suncc.inc                                 |   38 
 RcppParallel-4.3.3/src/tbb/build/android.gcc.inc                                 |   38 
 RcppParallel-4.3.3/src/tbb/build/android.inc                                     |   38 
 RcppParallel-4.3.3/src/tbb/build/android.linux.inc                               |   36 
 RcppParallel-4.3.3/src/tbb/build/android.linux.launcher.sh                       |   38 
 RcppParallel-4.3.3/src/tbb/build/android.macos.inc                               |   36 
 RcppParallel-4.3.3/src/tbb/build/android.windows.inc                             |   36 
 RcppParallel-4.3.3/src/tbb/build/big_iron.inc                                    |   36 
 RcppParallel-4.3.3/src/tbb/build/common.inc                                      |   36 
 RcppParallel-4.3.3/src/tbb/build/common_rules.inc                                |   36 
 RcppParallel-4.3.3/src/tbb/build/detect.js                                       |   36 
 RcppParallel-4.3.3/src/tbb/build/generate_tbbvars.bat                            |   38 
 RcppParallel-4.3.3/src/tbb/build/generate_tbbvars.sh                             |   38 
 RcppParallel-4.3.3/src/tbb/build/linux.clang.inc                                 |   41 
 RcppParallel-4.3.3/src/tbb/build/linux.gcc.inc                                   |   46 
 RcppParallel-4.3.3/src/tbb/build/linux.icc.inc                                   |   36 
 RcppParallel-4.3.3/src/tbb/build/linux.inc                                       |   36 
 RcppParallel-4.3.3/src/tbb/build/linux.xl.inc                                    |   36 
 RcppParallel-4.3.3/src/tbb/build/macos.clang.inc                                 |   49 
 RcppParallel-4.3.3/src/tbb/build/macos.gcc.inc                                   |   40 
 RcppParallel-4.3.3/src/tbb/build/macos.icc.inc                                   |   38 
 RcppParallel-4.3.3/src/tbb/build/macos.inc                                       |   40 
 RcppParallel-4.3.3/src/tbb/build/mic.icc.inc                                     |   36 
 RcppParallel-4.3.3/src/tbb/build/mic.linux.inc                                   |   36 
 RcppParallel-4.3.3/src/tbb/build/mic.linux.launcher.sh                           |   38 
 RcppParallel-4.3.3/src/tbb/build/mic.offload.inc                                 |   36 
 RcppParallel-4.3.3/src/tbb/build/test_launcher.bat                               |   38 
 RcppParallel-4.3.3/src/tbb/build/test_launcher.sh                                |   55 
 RcppParallel-4.3.3/src/tbb/build/version_info_aix.sh                             |   38 
 RcppParallel-4.3.3/src/tbb/build/version_info_android.sh                         |   38 
 RcppParallel-4.3.3/src/tbb/build/version_info_linux.sh                           |   38 
 RcppParallel-4.3.3/src/tbb/build/version_info_macos.sh                           |   38 
 RcppParallel-4.3.3/src/tbb/build/version_info_sunos.sh                           |   38 
 RcppParallel-4.3.3/src/tbb/build/version_info_windows.js                         |   36 
 RcppParallel-4.3.3/src/tbb/build/vs2010/tbb.vcxproj                              | 1423 +++++-----
 RcppParallel-4.3.3/src/tbb/build/vs2010/tbbmalloc.vcxproj                        | 1168 ++++----
 RcppParallel-4.3.3/src/tbb/build/vs2010/tbbmalloc_proxy.vcxproj                  |  842 ++---
 RcppParallel-4.3.3/src/tbb/build/windows.cl.inc                                  |   36 
 RcppParallel-4.3.3/src/tbb/build/windows.gcc.inc                                 |   47 
 RcppParallel-4.3.3/src/tbb/build/windows.icl.inc                                 |   36 
 RcppParallel-4.3.3/src/tbb/build/windows.inc                                     |   36 
 RcppParallel-4.3.3/src/tbb/build/xbox360.cl.inc                                  |   36 
 RcppParallel-4.3.3/src/tbb/build/xbox360.inc                                     |   36 
 RcppParallel-4.3.3/src/tbb/include/serial/tbb/parallel_for.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/serial/tbb/tbb_annotate.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/aggregator.h                              |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/aligned_space.h                           |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/atomic.h                                  |   40 
 RcppParallel-4.3.3/src/tbb/include/tbb/blocked_range.h                           |   46 
 RcppParallel-4.3.3/src/tbb/include/tbb/blocked_range2d.h                         |   42 
 RcppParallel-4.3.3/src/tbb/include/tbb/blocked_range3d.h                         |   42 
 RcppParallel-4.3.3/src/tbb/include/tbb/cache_aligned_allocator.h                 |   47 
 RcppParallel-4.3.3/src/tbb/include/tbb/combinable.h                              |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/compat/condition_variable                 |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/compat/ppl.h                              |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/compat/thread                             |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/compat/tuple                              |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_hash_map.h                     |  203 -
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_lru_cache.h                    |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_priority_queue.h               |  175 -
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_queue.h                        |  268 +
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_unordered_map.h                |  166 -
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_unordered_set.h                |  193 -
 RcppParallel-4.3.3/src/tbb/include/tbb/concurrent_vector.h                       |  263 +
 RcppParallel-4.3.3/src/tbb/include/tbb/critical_section.h                        |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/enumerable_thread_specific.h              |   46 
 RcppParallel-4.3.3/src/tbb/include/tbb/flow_graph.h                              | 1088 +++++--
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_aggregator_impl.h               |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_concurrent_queue_impl.h         |  176 -
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_concurrent_unordered_impl.h     |  185 +
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_impl.h               |  480 ++-
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_indexer_impl.h       |  154 -
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_item_buffer_impl.h   |  244 +
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_join_impl.h          |  343 +-
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_node_impl.h          |  200 +
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_tagged_buffer_impl.h |  259 +
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_trace_impl.h         |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_flow_graph_types_impl.h         |   81 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_mutex_padding.h                 |   42 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_range_iterator.h                |only
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_tbb_strings.h                   |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_tbb_windef.h                    |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_x86_eliding_mutex_impl.h        |   41 
 RcppParallel-4.3.3/src/tbb/include/tbb/internal/_x86_rtm_rw_mutex_impl.h         |  102 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/gcc_armv7.h                       |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/gcc_generic.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/gcc_ia32_common.h                 |   45 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/gcc_itsx.h                        |   53 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/ibm_aix51.h                       |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/icc_generic.h                     |   49 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/linux_common.h                    |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/linux_ia32.h                      |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/linux_ia64.h                      |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/linux_intel64.h                   |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/mac_ppc.h                         |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/macos_common.h                    |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/mic_common.h                      |   42 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/msvc_armv7.h                      |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/msvc_ia32_common.h                |   57 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/sunos_sparc.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/windows_api.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/windows_ia32.h                    |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/windows_intel64.h                 |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/machine/xbox360_ppc.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/memory_pool.h                             |   47 
 RcppParallel-4.3.3/src/tbb/include/tbb/mutex.h                                   |   44 
 RcppParallel-4.3.3/src/tbb/include/tbb/null_mutex.h                              |   47 
 RcppParallel-4.3.3/src/tbb/include/tbb/null_rw_mutex.h                           |   47 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_do.h                             |   60 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_for.h                            |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_for_each.h                       |   64 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_invoke.h                         |  147 -
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_reduce.h                         |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_scan.h                           |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_sort.h                           |   67 
 RcppParallel-4.3.3/src/tbb/include/tbb/parallel_while.h                          |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/partitioner.h                             |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/pipeline.h                                |   59 
 RcppParallel-4.3.3/src/tbb/include/tbb/queuing_mutex.h                           |   40 
 RcppParallel-4.3.3/src/tbb/include/tbb/queuing_rw_mutex.h                        |   40 
 RcppParallel-4.3.3/src/tbb/include/tbb/reader_writer_lock.h                      |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/recursive_mutex.h                         |   44 
 RcppParallel-4.3.3/src/tbb/include/tbb/runtime_loader.h                          |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/scalable_allocator.h                      |   47 
 RcppParallel-4.3.3/src/tbb/include/tbb/spin_mutex.h                              |   40 
 RcppParallel-4.3.3/src/tbb/include/tbb/spin_rw_mutex.h                           |   79 
 RcppParallel-4.3.3/src/tbb/include/tbb/task.h                                    |   60 
 RcppParallel-4.3.3/src/tbb/include/tbb/task_arena.h                              |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/task_group.h                              |   53 
 RcppParallel-4.3.3/src/tbb/include/tbb/task_scheduler_init.h                     |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/task_scheduler_observer.h                 |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb.h                                     |   48 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_allocator.h                           |   47 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_config.h                              |  205 -
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_exception.h                           |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_machine.h                             |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_profiling.h                           |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_stddef.h                              |  139 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbb_thread.h                              |  130 
 RcppParallel-4.3.3/src/tbb/include/tbb/tbbmalloc_proxy.h                         |   38 
 RcppParallel-4.3.3/src/tbb/include/tbb/tick_count.h                              |   38 
 RcppParallel-4.3.3/src/tbb/src/Makefile                                          |   40 
 RcppParallel-4.3.3/src/tbb/src/perf/coarse_grained_raii_lru_cache.h              |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/cpq_pdes.cpp                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/cpq_throughput_test.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/fibonacci_impl_tbb.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/perf.cpp                                     |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/perf.h                                       |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/perf_sched.cpp                               |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/run_statistics.sh                            |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/statistics.cpp                               |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/statistics.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/statistics_xml.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_fibonacci_cutoff.cpp                    |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_framework.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_hash_map.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_hash_map_fill.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_locked_work.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_lru_cache_throughput.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_sandbox.h                               |   38 
 RcppParallel-4.3.3/src/tbb/src/perf/time_vector.cpp                              |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/client/library_assert.h                       |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/client/omp_dynamic_link.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/client/omp_dynamic_link.h                     |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/client/rml_factory.h                          |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/client/rml_omp.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/client/rml_tbb.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/include/rml_base.h                            |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/include/rml_omp.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/include/rml_tbb.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/perfor/omp_nested.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/perfor/omp_simple.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/perfor/tbb_multi_omp.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/perfor/tbb_simple.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/perfor/thread_level.h                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/server/irml.rc                                |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/server/job_automaton.h                        |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/server/lin-rml-export.def                     |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/server/rml_server.cpp                         |   42 
 RcppParallel-4.3.3/src/tbb/src/rml/server/thread_monitor.h                       |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/server/wait_counter.h                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/server/win32-rml-export.def                   |   36 
 RcppParallel-4.3.3/src/tbb/src/rml/server/win64-rml-export.def                   |   36 
 RcppParallel-4.3.3/src/tbb/src/rml/test/rml_omp_stub.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_job_automaton.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_rml_mixed.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_rml_omp.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_rml_omp_c_linkage.c                 |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_rml_tbb.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_server.h                            |   38 
 RcppParallel-4.3.3/src/tbb/src/rml/test/test_thread_monitor.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/arena.cpp                                     |  171 -
 RcppParallel-4.3.3/src/tbb/src/tbb/arena.h                                       |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/cache_aligned_allocator.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/cilk-tbb-interop.h                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/concurrent_hash_map.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/concurrent_monitor.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/concurrent_monitor.h                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/concurrent_queue.cpp                          |  120 
 RcppParallel-4.3.3/src/tbb/src/tbb/concurrent_vector.cpp                         |   50 
 RcppParallel-4.3.3/src/tbb/src/tbb/condition_variable.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/critical_section.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/custom_scheduler.h                            |   47 
 RcppParallel-4.3.3/src/tbb/src/tbb/dynamic_link.cpp                              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/dynamic_link.h                                |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/governor.cpp                                  |   40 
 RcppParallel-4.3.3/src/tbb/src/tbb/governor.h                                    |   42 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia32-masm/atomic_support.asm                  |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia32-masm/itsx.asm                            |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia32-masm/lock_byte.asm                       |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia64-gas/atomic_support.s                     |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia64-gas/ia64_misc.s                          |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia64-gas/lock_byte.s                          |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia64-gas/log2.s                               |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ia64-gas/pause.s                              |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/ibm_aix51/atomic_support.c                    |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/intel64-masm/atomic_support.asm               |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/intel64-masm/intel64_misc.asm                 |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/intel64-masm/itsx.asm                         |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/intrusive_list.h                              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/itt_notify.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/itt_notify.h                                  |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/lin32-tbb-export.def                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/lin32-tbb-export.lst                          |   58 
 RcppParallel-4.3.3/src/tbb/src/tbb/lin64-tbb-export.def                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/lin64-tbb-export.lst                          |   58 
 RcppParallel-4.3.3/src/tbb/src/tbb/lin64ipf-tbb-export.def                       |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/lin64ipf-tbb-export.lst                       |   41 
 RcppParallel-4.3.3/src/tbb/src/tbb/mac32-tbb-export.def                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/mac32-tbb-export.lst                          |   57 
 RcppParallel-4.3.3/src/tbb/src/tbb/mac64-tbb-export.def                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/mac64-tbb-export.lst                          |   57 
 RcppParallel-4.3.3/src/tbb/src/tbb/mailbox.h                                     |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/market.cpp                                    |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/market.h                                      |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/mutex.cpp                                     |   55 
 RcppParallel-4.3.3/src/tbb/src/tbb/observer_proxy.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/observer_proxy.h                              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/pipeline.cpp                                  |   64 
 RcppParallel-4.3.3/src/tbb/src/tbb/private_server.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/queuing_mutex.cpp                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/queuing_rw_mutex.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/reader_writer_lock.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/recursive_mutex.cpp                           |   53 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler.cpp                                 |   50 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler.h                                   |   83 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler_common.h                            |   84 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler_utility.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/semaphore.cpp                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/semaphore.h                                   |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/spin_mutex.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/spin_rw_mutex.cpp                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/task.cpp                                      |   44 
 RcppParallel-4.3.3/src/tbb/src/tbb/task_group_context.cpp                        |   58 
 RcppParallel-4.3.3/src/tbb/src/tbb/task_stream.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_assert_impl.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_main.cpp                                  |   40 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_main.h                                    |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_misc.cpp                                  |   71 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_misc.h                                    |   46 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_misc_ex.cpp                               |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_resource.rc                               |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_statistics.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_statistics.h                              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_thread.cpp                                |   49 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_version.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tls.h                                         |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/disable_warnings.h                  |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/internal/ittnotify.h                |  659 ----
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify.h                         |  560 +++
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_config.h                  |  169 -
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_static.c                  |  371 +-
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_static.h                  |   89 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_types.h                   |   42 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/legacy/ittnotify.h                  |   74 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/prototype/ittnotify.h               |  143 -
 RcppParallel-4.3.3/src/tbb/src/tbb/win32-tbb-export.def                          |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/win32-tbb-export.lst                          |   55 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-gcc-tbb-export.def                      |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-gcc-tbb-export.lst                      |   51 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-tbb-export.def                          |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-tbb-export.lst                          |   55 
 RcppParallel-4.3.3/src/tbb/src/tbb/winrt-tbb-export.lst                          |   39 
 RcppParallel-4.3.3/src/tbb/src/tbb/x86_rtm_rw_mutex.cpp                          |   91 
 RcppParallel-4.3.3/src/tbb/src/tbb/xbox360-tbb-export.def                        |   36 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/Customize.h                             |   43 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/MapMemory.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/Statistics.h                            |   40 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/TypeDefinitions.h                       |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/backend.cpp                             |  235 -
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/backref.cpp                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/frontend.cpp                            |  117 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/large_objects.cpp                       |  153 -
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin32-proxy-export.def                  |   39 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin32-tbbmalloc-export.def              |   49 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64-proxy-export.def                  |   39 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64-tbbmalloc-export.def              |   49 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64ipf-proxy-export.def               |   39 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64ipf-tbbmalloc-export.def           |   49 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/mac32-tbbmalloc-export.def              |   44 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/mac64-tbbmalloc-export.def              |   44 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/proxy.cpp                               |  308 +-
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/proxy.h                                 |   67 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/proxy_overload_osx.h                    |only
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/shared_utils.h                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbb_function_replacement.cpp            |   48 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbb_function_replacement.h              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc.cpp                           |  142 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc.rc                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc_internal.h                    |  179 -
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc_internal_api.h                |   40 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win32-gcc-tbbmalloc-export.def          |   48 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win32-tbbmalloc-export.def              |   46 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win64-gcc-tbbmalloc-export.def          |   48 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win64-tbbmalloc-export.def              |   46 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/xbox360-tbbmalloc-export.def            |   46 
 RcppParallel-4.3.3/src/tbb/src/tbbproxy/tbbproxy-windows.asm                     |   36 
 RcppParallel-4.3.3/src/tbb/src/tbbproxy/tbbproxy.cpp                             |   42 
 RcppParallel-4.3.3/src/tbb/src/test/harness.h                                    |   62 
 RcppParallel-4.3.3/src/tbb/src/test/harness_allocator.h                          |  397 ++
 RcppParallel-4.3.3/src/tbb/src/test/harness_assert.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_bad_expr.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_barrier.h                            |   47 
 RcppParallel-4.3.3/src/tbb/src/test/harness_checktype.h                          |   39 
 RcppParallel-4.3.3/src/tbb/src/test/harness_concurrency.h                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_concurrency_tracker.h                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_cpu.h                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_defs.h                               |   80 
 RcppParallel-4.3.3/src/tbb/src/test/harness_dynamic_libs.h                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_eh.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_fp.h                                 |only
 RcppParallel-4.3.3/src/tbb/src/test/harness_graph.h                              |  585 +++-
 RcppParallel-4.3.3/src/tbb/src/test/harness_inject_scheduler.h                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_iterator.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_m128.h                               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_memory.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_mic.h                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_report.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_runtime_loader.h                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_task.h                               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_tbb_independence.h                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_test_cases_framework.h               |   39 
 RcppParallel-4.3.3/src/tbb/src/test/harness_tsx.h                                |   63 
 RcppParallel-4.3.3/src/tbb/src/test/test_ScalableAllocator.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_ScalableAllocator_STL.cpp               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_aggregator.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_aligned_space.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_allocator.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_allocator_STL.h                         |   74 
 RcppParallel-4.3.3/src/tbb/src/test/test_assembly.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_atomic.cpp                              |  165 -
 RcppParallel-4.3.3/src/tbb/src/test/test_blocked_range.cpp                       |   46 
 RcppParallel-4.3.3/src/tbb/src/test/test_blocked_range2d.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_blocked_range3d.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_broadcast_node.cpp                      |  208 +
 RcppParallel-4.3.3/src/tbb/src/test/test_buffer_node.cpp                         |   62 
 RcppParallel-4.3.3/src/tbb/src/test/test_cache_aligned_allocator.cpp             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cache_aligned_allocator_STL.cpp         |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cilk_common.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cilk_dynamic_load.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cilk_interop.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_combinable.cpp                          |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_hash_map.cpp                 |  489 +++
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_lru_cache.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_monitor.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_priority_queue.cpp           |  622 +++-
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_queue.cpp                    |  803 ++++-
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_queue.h                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_queue_whitebox.cpp           |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_unordered_common.h           |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_unordered_map.cpp            |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_unordered_set.cpp            |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_vector.cpp                   | 1143 +++++---
 RcppParallel-4.3.3/src/tbb/src/test/test_condition_variable.h                    |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_container_move_support.h                |only
 RcppParallel-4.3.3/src/tbb/src/test/test_continue_node.cpp                       |  168 +
 RcppParallel-4.3.3/src/tbb/src/test/test_critical_section.cpp                    |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_dynamic_link.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_eh_algorithms.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_eh_flow_graph.cpp                       |   49 
 RcppParallel-4.3.3/src/tbb/src/test/test_eh_tasks.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_enumerable_thread_specific.cpp          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_examples_common_utility.cpp             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_fast_random.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_flow_graph.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_flow_graph_whitebox.cpp                 |only
 RcppParallel-4.3.3/src/tbb/src/test/test_fp.cpp                                  |  174 -
 RcppParallel-4.3.3/src/tbb/src/test/test_function_node.cpp                       |  178 +
 RcppParallel-4.3.3/src/tbb/src/test/test_halt.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_handle_perror.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_hw_concurrency.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_indexer_node.cpp                        |  376 ++
 RcppParallel-4.3.3/src/tbb/src/test/test_initializer_list.h                      |  105 
 RcppParallel-4.3.3/src/tbb/src/test/test_inits_loop.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_intrusive_list.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_ittnotify.cpp                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_join_node.cpp                           |  663 +++-
 RcppParallel-4.3.3/src/tbb/src/test/test_lambda.cpp                              |   56 
 RcppParallel-4.3.3/src/tbb/src/test/test_limiter_node.cpp                        |  198 +
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_atexit.cpp                       |  185 -
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_compliance.cpp                   |   44 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_init_shutdown.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_lib_unload.cpp                   |   58 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_overload.cpp                     |  150 -
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_pools.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_pure_c.c                         |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_regression.cpp                   |   76 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_used_by_lib.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_whitebox.cpp                     |   48 
 RcppParallel-4.3.3/src/tbb/src/test/test_model_plugin.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_multifunction_node.cpp                  |  243 +
 RcppParallel-4.3.3/src/tbb/src/test/test_mutex.cpp                               |   77 
 RcppParallel-4.3.3/src/tbb/src/test/test_mutex_native_threads.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_openmp.cpp                              |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_overwrite_node.cpp                      |   52 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_do.cpp                         |   93 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_for.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_for_each.cpp                   |   96 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_for_vectorization.cpp          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_invoke.cpp                     |   42 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_pipeline.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_reduce.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_scan.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_sort.cpp                       |   92 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_while.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_partitioner.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_partitioner_whitebox.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_pipeline.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_pipeline_with_tbf.cpp                   |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_priority_queue_node.cpp                 |   49 
 RcppParallel-4.3.3/src/tbb/src/test/test_queue_node.cpp                          |  360 +-
 RcppParallel-4.3.3/src/tbb/src/test/test_range_based_for.h                       |   44 
 RcppParallel-4.3.3/src/tbb/src/test/test_reader_writer_lock.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_runtime_loader.cpp                      |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_rwm_upgrade_downgrade.cpp               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_semaphore.cpp                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_sequencer_node.cpp                      |   46 
 RcppParallel-4.3.3/src/tbb/src/test/test_source_node.cpp                         |  213 +
 RcppParallel-4.3.3/src/tbb/src/test/test_split_node.cpp                          |   43 
 RcppParallel-4.3.3/src/tbb/src/test/test_static_assert.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_std_thread.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tagged_msg.cpp                          |   45 
 RcppParallel-4.3.3/src/tbb/src/test/test_task.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_arena.cpp                          |  236 +
 RcppParallel-4.3.3/src/tbb/src/test/test_task_assertions.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_auto_init.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_enqueue.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_group.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_leaks.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_priority.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_scheduler_init.cpp                 |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_scheduler_observer.cpp             |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_steal_limit.cpp                    |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_condition_variable.cpp              |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_fork.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_header.cpp                          |   92 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_thread.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_version.cpp                         |   42 
 RcppParallel-4.3.3/src/tbb/src/test/test_thread.h                                |   87 
 RcppParallel-4.3.3/src/tbb/src/test/test_tick_count.cpp                          |   67 
 RcppParallel-4.3.3/src/tbb/src/test/test_tuple.cpp                               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_write_once_node.cpp                     |   41 
 RcppParallel-4.3.3/src/tbb/src/test/test_yield.cpp                               |   38 
 578 files changed, 25737 insertions(+), 20735 deletions(-)

More information about RcppParallel at CRAN
Permanent link

Package SamplingStrata updated to version 1.0-3 with previous version 1.0-2 dated 2014-03-03

Title: Optimal stratification of sampling frames for multipurpose sampling surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package.
Author: Giulio Barcaroli, Daniela Pagliuca and Egon Willighagen
Maintainer: Giulio Barcaroli

Diff between SamplingStrata versions 1.0-2 dated 2014-03-03 and 1.0-3 dated 2014-10-21

 DESCRIPTION                          |    8 ++++----
 MD5                                  |   21 +++++++++++----------
 NEWS                                 |    9 +++++++++
 R/optimizeStrata.R                   |    6 +++---
 R/strataGenalg.R                     |   10 ++++++----
 build/vignette.rds                   |binary
 inst/CITATION                        |only
 inst/doc/SamplingStrataVignette.Rnw  |    3 ++-
 inst/doc/SamplingStrataVignette.pdf  |binary
 man/optimizeStrata.Rd                |   13 ++++++++++---
 vignettes/SamplingStrata.bib         |   23 ++++++++++++++++-------
 vignettes/SamplingStrataVignette.Rnw |    3 ++-
 12 files changed, 63 insertions(+), 33 deletions(-)

More information about SamplingStrata at CRAN
Permanent link

Package RnavGraph updated to version 0.1.7 with previous version 0.1.6 dated 2013-05-01

Title: Using Graphs as a Navigational Infrastructure.
Description: GUI to explore high dimensional data (including image data) using graphs as navigational infrastructure.
Author: Adrian R. Waddell and R. Wayne Oldford
Maintainer: Adrian Waddell

Diff between RnavGraph versions 0.1.6 dated 2013-05-01 and 0.1.7 dated 2014-10-21

 DESCRIPTION            |   19 +-
 MD5                    |   15 -
 NAMESPACE              |    3 
 NEWS                   |    5 
 R/scagNav.R            |  434 ++++++++++++++++++++++++-------------------------
 R/zzz.R                |   24 +-
 build                  |only
 inst/doc/RnavGraph.pdf |binary
 man/scagEdgeWeights.Rd |   12 -
 9 files changed, 260 insertions(+), 252 deletions(-)

More information about RnavGraph at CRAN
Permanent link

Package jackknifeKME updated to version 1.1 with previous version 1.0 dated 2013-02-24

Title: Jackknife Estimates of Kaplan-Meier Estimators or Integrals
Description: The package is for computing both the original and modified jackknife estimates of Kaplan-Meier estimators.
Author: Hasinur Rahaman Khan and Ewart Shaw
Maintainer: Hasinur Rahaman Khan

Diff between jackknifeKME versions 1.0 dated 2013-02-24 and 1.1 dated 2014-10-21

 DESCRIPTION                 |   15 +++++++--------
 MD5                         |   14 +++++++-------
 NAMESPACE                   |    1 +
 man/jackknifeKME-package.Rd |   19 ++++++++++++-------
 man/jackknifeKME.Rd         |   11 ++++++++---
 man/kmweight.Rd             |    2 +-
 man/kmweight.corr.Rd        |    4 ++--
 man/simdata.Rd              |    2 +-
 8 files changed, 39 insertions(+), 29 deletions(-)

More information about jackknifeKME at CRAN
Permanent link

Package extracat updated to version 1.7-1 with previous version 1.7-0 dated 2014-05-20

Title: Categorical Data Analysis and Visualization
Description: Categorical Data Analysis and Visualization
Author: Alexander Pilhoefer
Maintainer: Alexander Pilhoefer

Diff between extracat versions 1.7-0 dated 2014-05-20 and 1.7-1 dated 2014-10-21

 extracat-1.7-0/extracat/R/listen.R          |only
 extracat-1.7-0/extracat/R/resort2.R         |only
 extracat-1.7-0/extracat/man/cpcp.Rd         |only
 extracat-1.7-0/extracat/man/listen.Rd       |only
 extracat-1.7-0/extracat/man/resort.Rd       |only
 extracat-1.7-0/extracat/man/spread.Rd       |only
 extracat-1.7-1/extracat/DESCRIPTION         |   15 -
 extracat-1.7-1/extracat/MD5                 |   46 ++--
 extracat-1.7-1/extracat/NAMESPACE           |    9 
 extracat-1.7-1/extracat/R/boxplot2g.R       |   16 +
 extracat-1.7-1/extracat/R/caclust.R         |    8 
 extracat-1.7-1/extracat/R/cpcp2.R           |   38 +---
 extracat-1.7-1/extracat/R/facetshade.R      |  259 ++++++++++++++++++++++++----
 extracat-1.7-1/extracat/R/optile_skeleton.r |   30 +--
 extracat-1.7-1/extracat/R/rmb.R             |    8 
 extracat-1.7-1/extracat/R/rmbmat2.R         |    2 
 extracat-1.7-1/extracat/R/scpcp.R           |  109 +++++------
 extracat-1.7-1/extracat/R/sortca.R          |    9 
 extracat-1.7-1/extracat/R/steptile.R        |   16 -
 extracat-1.7-1/extracat/R/visid.R           |   13 -
 extracat-1.7-1/extracat/man/ahist.Rd        |    3 
 extracat-1.7-1/extracat/man/extracat.Rd     |    2 
 extracat-1.7-1/extracat/man/facetshade.Rd   |   58 +++++-
 extracat-1.7-1/extracat/man/fluctile.Rd     |    2 
 extracat-1.7-1/extracat/man/rmb.Rd          |    2 
 extracat-1.7-1/extracat/man/scpcp.Rd        |   18 +
 extracat-1.7-1/extracat/man/steptile.Rd     |   12 -
 27 files changed, 447 insertions(+), 228 deletions(-)

More information about extracat at CRAN
Permanent link

New package openssl with initial version 0.1
Package: openssl
Type: Package
Title: Bindings to OpenSSL
Version: 0.1
Date: 2014-10-20
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: This package interfaces to the OpenSSL libraries libssl and libcrypto. Currently it only implements bindings to the OpenSSL random number generator in order to generate crypto secure random bytes in R.
License: MIT + file LICENSE
URL: https://github.com/jeroenooms/openssl
BugReports: https://github.com/jeroenooms/openssl/issues
SystemRequirements: OpenSSL (libssl-dev or openssl-devel)
Packaged: 2014-10-20 19:30:34 UTC; jeroen
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-21 08:27:55

More information about openssl at CRAN
Permanent link

Package jsonlite updated to version 0.9.13 with previous version 0.9.12 dated 2014-09-27

Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of RJSONIO, but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with web APIs. The parser implementation is based on the mapping described in the vignette of the package (Ooms, 2014). In addition to drop-in replacements for toJSON and fromJSON, jsonlite contains functions to stream, validate, and prettify JSON data, and many unit tests to verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms

Diff between jsonlite versions 0.9.12 dated 2014-09-27 and 0.9.13 dated 2014-10-21

 jsonlite-0.9.12/jsonlite/R/asJSON.integer.R             |only
 jsonlite-0.9.13/jsonlite/DESCRIPTION                    |    8 +--
 jsonlite-0.9.13/jsonlite/MD5                            |   40 ++++++++--------
 jsonlite-0.9.13/jsonlite/NAMESPACE                      |    1 
 jsonlite-0.9.13/jsonlite/NEWS                           |    7 ++
 jsonlite-0.9.13/jsonlite/R/asJSON.array.R               |    4 -
 jsonlite-0.9.13/jsonlite/R/asJSON.numeric.R             |   30 ++++--------
 jsonlite-0.9.13/jsonlite/R/download.R                   |    8 ++-
 jsonlite-0.9.13/jsonlite/R/fromJSON.R                   |   14 ++---
 jsonlite-0.9.13/jsonlite/R/loadpkg.R                    |    2 
 jsonlite-0.9.13/jsonlite/R/num_to_char.R                |only
 jsonlite-0.9.13/jsonlite/R/raw_to_json.R                |only
 jsonlite-0.9.13/jsonlite/R/stream.R                     |   14 +++--
 jsonlite-0.9.13/jsonlite/inst/doc/json-mapping.pdf      |binary
 jsonlite-0.9.13/jsonlite/inst/doc/json-opencpu.pdf      |binary
 jsonlite-0.9.13/jsonlite/inst/tests/test-libjson-utf8.R |   14 ++---
 jsonlite-0.9.13/jsonlite/man/fromJSON.Rd                |    5 --
 jsonlite-0.9.13/jsonlite/man/stream_in.Rd               |    2 
 jsonlite-0.9.13/jsonlite/src/Makevars                   |    8 +--
 jsonlite-0.9.13/jsonlite/src/modp_numtoa.c              |only
 jsonlite-0.9.13/jsonlite/src/modp_numtoa.h              |only
 jsonlite-0.9.13/jsonlite/src/num_to_char.c              |only
 jsonlite-0.9.13/jsonlite/src/yajl/readme.txt            |    1 
 jsonlite-0.9.13/jsonlite/src/yajl/yajl_tree.c           |    6 ++
 24 files changed, 86 insertions(+), 78 deletions(-)

More information about jsonlite at CRAN
Permanent link

Mon, 20 Oct 2014

Package rplexos updated to version 0.10.0.1 with previous version 0.10 dated 2014-10-16

Title: Read and Analyze PLEXOS Solutions from R
Description: This package contains functions to efficiently convert PLEXOS solutions into SQLite databases and to extract information from those databases to perform analysis. It supports collation of solutions that may have divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.10 dated 2014-10-16 and 0.10.0.1 dated 2014-10-20

 DESCRIPTION           |    6 +++---
 MD5                   |   29 ++++++++++++++++++++++++++---
 R/process_solution.R  |    4 ++--
 inst/web              |only
 vignettes/rplexos.Rmd |    8 ++++----
 5 files changed, 35 insertions(+), 12 deletions(-)

More information about rplexos at CRAN
Permanent link

New package tclust with initial version 1.2-3
Package: tclust
Version: 1.2-3
Date: 2014-10-20
Title: Robust Trimmed Clustering
Author: Agustin Mayo Iscar, Luis Angel Garcia Escudero, Heinrich Fritz
Maintainer: Valentin Todorov
Description: Robust Trimmed Clustering
Depends: R (>= 2.12.0), mvtnorm, sn, mclust, cluster
License: GPL-3
Repository: CRAN
NeedsCompilation: yes
Packaged: 2014-10-20 13:49:50 UTC; TodorovV
Date/Publication: 2014-10-21 02:02:38

More information about tclust at CRAN
Permanent link

Package rex updated to version 0.1.1 with previous version 0.1.0 dated 2014-10-14

Title: Simpler Regular Expressions
Description: A simpler, human-readable interface for the construction of regular expressions.
Author: Kevin Ushey [aut], Jim Hester [cre, aut]
Maintainer: Jim Hester

Diff between rex versions 0.1.0 dated 2014-10-14 and 0.1.1 dated 2014-10-20

 DESCRIPTION                           |   17 ++++--
 MD5                                   |   26 ++++-----
 R/character_class.R                   |   17 +++---
 R/escape.R                            |    6 +-
 R/match.R                             |   50 ++++++++++++++---
 R/rex-mode.R                          |    9 +--
 build/vignette.rds                    |binary
 man/character_class.Rd                |   17 ++++--
 man/re_matches.Rd                     |    7 ++
 man/rex_mode.Rd                       |    7 +-
 tests/testthat/test-capture.R         |    4 -
 tests/testthat/test-character_class.R |   18 +++---
 tests/testthat/test-match.R           |   95 ++++++++++++++++++++++++++++++++++
 vignettes/log_parsing.Rmd             |   15 ++---
 14 files changed, 217 insertions(+), 71 deletions(-)

More information about rex at CRAN
Permanent link

Package redcapAPI updated to version 1.0.1 with previous version 1.0 dated 2014-09-15

Title: R interface to REDCap
Description: Access data stored in REDCap databases using the Application Programming Interface (API). REDCap (Research Electronic Data CAPture) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to access data and project meta data (such as the data dictionary) from the web programmatically. The redcapAPI package facilitates the process of accessing data with options to prepare an analysis-ready data set consistent with the definitions in a database's data dictionary.
Author: Benjamin Nutter. Initiated by Jeffrey Horner and Will Gray with contributions from Jeremy Stephens, and Will Beasley
Maintainer: Benjamin Nutter

Diff between redcapAPI versions 1.0 dated 2014-09-15 and 1.0.1 dated 2014-10-20

 DESCRIPTION              |    8 ++++----
 MD5                      |   29 ++++++++++++++++-------------
 NEWS                     |only
 R/apiCall.R              |only
 R/compareRedcapVersion.R |    2 +-
 R/exportMetaData.R       |   12 +++++-------
 R/exportRecords.R        |    8 ++++----
 R/exportReports.R        |    2 +-
 R/fieldToVar.R           |   17 +++++++++++++++--
 R/importRecords.R        |   14 +++++++++++++-
 R/recodeCheck.R          |    4 ++--
 R/redcapProjectInfo.R    |   42 +++++++++++++++++++++++++++++++++++-------
 README.md                |    2 ++
 inst/CITATION            |    1 +
 man/apiCall.Rd           |only
 man/fieldToVar.Rd        |    3 ++-
 man/importRecords.Rd     |    3 ++-
 17 files changed, 103 insertions(+), 44 deletions(-)

More information about redcapAPI at CRAN
Permanent link

Package npsp updated to version 0.3-6 with previous version 0.2-4 dated 2013-11-04

Title: Nonparametric spatial (geo)statistics
Description: Multidimensional nonparametric spatio-temporal geostatistics. S3 classes and methods for multidimensional: gridded data, linear binning, local polynomial kernel regression, density and variogram estimation. Nonparametric methods for trend and/or variogram inferences.
Author: Ruben Fernandez-Casal
Maintainer: Ruben Fernandez-Casal

Diff between npsp versions 0.2-4 dated 2013-11-04 and 0.3-6 dated 2014-10-20

 npsp-0.2-4/npsp/R/h.cv.R              |only
 npsp-0.3-6/npsp/DESCRIPTION           |   10 +-
 npsp-0.3-6/npsp/MD5                   |  106 +++++++++++++----------
 npsp-0.3-6/npsp/NAMESPACE             |   36 +++++++
 npsp-0.3-6/npsp/R/bin.data.R          |   62 +++++++++++--
 npsp-0.3-6/npsp/R/cov.R               |only
 npsp-0.3-6/npsp/R/cpu.time.R          |only
 npsp-0.3-6/npsp/R/data.grid.R         |    3 
 npsp-0.3-6/npsp/R/grid.par.R          |    2 
 npsp-0.3-6/npsp/R/h.cv.r              |only
 npsp-0.3-6/npsp/R/interp.R            |   31 ++++++
 npsp-0.3-6/npsp/R/locpol.bin.R        |   64 +++++++-------
 npsp-0.3-6/npsp/R/np.den.R            |   23 ++---
 npsp-0.3-6/npsp/R/np.svar.R           |  155 ++++++++++++++++++++++++++++++----
 npsp-0.3-6/npsp/R/npsp-geoR.R         |   14 ++-
 npsp-0.3-6/npsp/R/npsp-gstat.R        |   15 +--
 npsp-0.3-6/npsp/R/npsp-internals.R    |   33 +++++--
 npsp-0.3-6/npsp/R/npsp-package.R      |   34 ++++++-
 npsp-0.3-6/npsp/R/npsp-plot.R         |only
 npsp-0.3-6/npsp/R/rgraphics.R         |only
 npsp-0.3-6/npsp/R/simage.R            |only
 npsp-0.3-6/npsp/R/spersp.R            |only
 npsp-0.3-6/npsp/R/splot.R             |only
 npsp-0.3-6/npsp/R/spoints.R           |only
 npsp-0.3-6/npsp/R/svar.bin.R          |   28 +++---
 npsp-0.3-6/npsp/R/svarmod.R           |   57 +++---------
 npsp-0.3-6/npsp/R/svarmod.sb.R        |   71 ++++++++-------
 npsp-0.3-6/npsp/R/zzz.R               |   13 ++
 npsp-0.3-6/npsp/demo/00Index          |   10 +-
 npsp-0.3-6/npsp/demo/aquifer.R        |  127 ++++++++++++++++++++-------
 npsp-0.3-6/npsp/demo/binning.R        |   60 +++++--------
 npsp-0.3-6/npsp/demo/datagrid.R       |   12 +-
 npsp-0.3-6/npsp/demo/locpol.R         |   53 +++++------
 npsp-0.3-6/npsp/demo/variogram.R      |   47 ++++------
 npsp-0.3-6/npsp/inst/CHANGES          |  116 ++++++++++++++++++++++++-
 npsp-0.3-6/npsp/inst/TODO             |   45 ++-------
 npsp-0.3-6/npsp/man/aquifer.Rd        |    2 
 npsp-0.3-6/npsp/man/bin.den.Rd        |    8 -
 npsp-0.3-6/npsp/man/binning.Rd        |   30 +++++-
 npsp-0.3-6/npsp/man/covar.Rd          |   29 ++++--
 npsp-0.3-6/npsp/man/cpu.time.Rd       |only
 npsp-0.3-6/npsp/man/disc.sb.Rd        |   14 +--
 npsp-0.3-6/npsp/man/earthquakes.Rd    |    2 
 npsp-0.3-6/npsp/man/fitsvar.sb.iso.Rd |   37 ++++----
 npsp-0.3-6/npsp/man/grid.par.Rd       |    2 
 npsp-0.3-6/npsp/man/h.cv.Rd           |   71 ++++++++-------
 npsp-0.3-6/npsp/man/interp.Rd         |    5 -
 npsp-0.3-6/npsp/man/locpol.Rd         |   48 +++++-----
 npsp-0.3-6/npsp/man/np.den.Rd         |   11 --
 npsp-0.3-6/npsp/man/np.svar.Rd        |   77 +++++++++++++---
 npsp-0.3-6/npsp/man/npsp-internals.Rd |   14 ++-
 npsp-0.3-6/npsp/man/npsp-package.Rd   |   30 +++++-
 npsp-0.3-6/npsp/man/rgraphics.Rd      |only
 npsp-0.3-6/npsp/man/simage.Rd         |only
 npsp-0.3-6/npsp/man/spersp.Rd         |only
 npsp-0.3-6/npsp/man/splot.Rd          |only
 npsp-0.3-6/npsp/man/spoints.Rd        |only
 npsp-0.3-6/npsp/man/sv.Rd             |    2 
 npsp-0.3-6/npsp/man/svar.bin.Rd       |    6 -
 npsp-0.3-6/npsp/man/svar.plot.Rd      |only
 npsp-0.3-6/npsp/man/varcov.Rd         |only
 npsp-0.3-6/npsp/src/grid_module.f90   |   29 +++---
 npsp-0.3-6/npsp/src/lp_module.f90     |   62 ++++++++-----
 63 files changed, 1135 insertions(+), 571 deletions(-)

More information about npsp at CRAN
Permanent link

Package imputeYn updated to version 1.2 with previous version 1.1 dated 2013-02-24

Title: Imputing the Last Largest Censored Observation(s) under Weighted Least Squares
Description: If Kaplan-Meier weights are involved in modeling, especially solving AFT model using weighted least squares method, the package gives alternative choices to the Efron's tail correction approach that brings estimates with less bias and more efficiency
Author: Hasinur Rahaman Khan and Ewart Shaw
Maintainer: Hasinur Rahaman Khan

Diff between imputeYn versions 1.1 dated 2013-02-24 and 1.2 dated 2014-10-20

 DESCRIPTION             |   21 ++++++++-------------
 MD5                     |   20 ++++++++++----------
 NAMESPACE               |    1 +
 R/imputeYn.R            |    2 +-
 man/aft.qp.Rd           |    6 +++---
 man/data.Rd             |    2 +-
 man/imputeYn-package.Rd |   12 ++++++------
 man/imputeYn.Rd         |    9 ++++-----
 man/imputeYn.extra.Rd   |    8 ++++----
 man/lss.mod.Rd          |    6 +++---
 man/print.imputeYn.Rd   |    2 +-
 11 files changed, 42 insertions(+), 47 deletions(-)

More information about imputeYn at CRAN
Permanent link

Package Rook updated to version 1.1-1 with previous version 1.0-9 dated 2013-01-11

Title: Rook - a web server interface for R
Description: This package contains the Rook specification and convenience software for building and running Rook applications. To get started, be sure and read the 'Rook' help file first.
Author: Jeffrey Horner
Maintainer: Jeffrey Horner

Diff between Rook versions 1.0-9 dated 2013-01-11 and 1.1-1 dated 2014-10-20

 DESCRIPTION                    |   17 +++++++------
 MD5                            |   21 ++++++++--------
 NAMESPACE                      |    4 +++
 R/Brewery.R                    |   24 ++++++++++++------
 R/File.R                       |   50 ++++++++++++++++++++++++++++++++-------
 R/Rhttpd.R                     |   32 +++++++++++++++----------
 R/utils.R                      |   32 ++++++++++++++++++++++---
 README.md                      |    4 +--
 inst/exampleApps/arrayparams.R |only
 inst/servers/rApache.R         |   52 +++++++++++++++++++++++++++++++++--------
 man/Request-class.Rd           |    2 -
 man/Response-class.Rd          |    3 +-
 12 files changed, 177 insertions(+), 64 deletions(-)

More information about Rook at CRAN
Permanent link

New package ore with initial version 1.0.0
Package: ore
Version: 1.0.0
Date: 2014-10-20
Title: An R Interface to the Oniguruma Regular Expression Library
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden
Depends: R (>= 2.12.1)
Suggests: crayon, rex, testthat
Description: Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features.
Encoding: UTF-8
License: BSD_3_clause + file LICENCE
URL: https://github.com/jonclayden/ore
Packaged: 2014-10-20 15:15:03 UTC; jon
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-20 19:18:10

More information about ore at CRAN
Permanent link

New package JMdesign with initial version 1.0
Package: JMdesign
Type: Package
Title: Joint Modeling of Longitudinal and Survival Data - Power Calculation
Version: 1.0
Date: 2012-06-01
Author: Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim
Maintainer: Shannon T. Holloway
Description: Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix Sigma_theta is unknown.
License: GPL-2
Depends: methods
Packaged: 2014-10-20 15:06:06 UTC; sthollow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-20 19:18:02

More information about JMdesign at CRAN
Permanent link

Package icapca updated to version 1.1 with previous version 1.0 dated 2014-01-02

Title: Mixed ICA/PCA
Description: Implements mixed ICA/PCA model for blind source separation, potentially with inclusion of Gaussian sources
Author: Roger Woods
Maintainer: Roger Woods

Diff between icapca versions 1.0 dated 2014-01-02 and 1.1 dated 2014-10-20

 DESCRIPTION             |    8 
 MD5                     |   19 -
 R/icapca.R              |   42 ++-
 man/ica_pca.Rd          |   59 +++-
 src/AIR.h               |   26 +
 src/config.h            |    2 
 src/ica_MLCf15.c        |    5 
 src/ica_pca_R.c         |   16 -
 src/ica_sources_aic15.c |  665 ++++++++++++++++++++++++++++++++++++------------
 src/random_rotation.c   |   22 +
 src/random_rotation2.c  |only
 11 files changed, 660 insertions(+), 204 deletions(-)

More information about icapca at CRAN
Permanent link

Package ShrinkCovMat updated to version 1.0.2 with previous version 1.0.1 dated 2014-08-12

Title: Shrinkage Covariance Matrix Estimators
Description: The package ShrinkCovMat provides nonparametric Steinian shrinkage estimators of the covariance matrix that are suitable in high dimensional settings, that is when the number of variables is larger than the sample size.
Author: Anestis Touloumis
Maintainer: Anestis Touloumis

Diff between ShrinkCovMat versions 1.0.1 dated 2014-08-12 and 1.0.2 dated 2014-10-20

 ShrinkCovMat-1.0.1/ShrinkCovMat/NEWS                         |only
 ShrinkCovMat-1.0.2/ShrinkCovMat/DESCRIPTION                  |   10 ++--
 ShrinkCovMat-1.0.2/ShrinkCovMat/MD5                          |   24 +++++------
 ShrinkCovMat-1.0.2/ShrinkCovMat/NAMESPACE                    |    2 
 ShrinkCovMat-1.0.2/ShrinkCovMat/R/shrinkcovmat.equal.R       |    2 
 ShrinkCovMat-1.0.2/ShrinkCovMat/R/shrinkcovmat.identity.R    |    3 -
 ShrinkCovMat-1.0.2/ShrinkCovMat/R/shrinkcovmat.unequal.R     |    3 -
 ShrinkCovMat-1.0.2/ShrinkCovMat/R/targetselection.R          |only
 ShrinkCovMat-1.0.2/ShrinkCovMat/inst/CITATION                |   15 +++---
 ShrinkCovMat-1.0.2/ShrinkCovMat/inst/NEWS                    |only
 ShrinkCovMat-1.0.2/ShrinkCovMat/man/ShrinkCovMat-package.Rd  |    6 +-
 ShrinkCovMat-1.0.2/ShrinkCovMat/man/shrinkcovmat.equal.Rd    |    2 
 ShrinkCovMat-1.0.2/ShrinkCovMat/man/shrinkcovmat.identity.Rd |    2 
 ShrinkCovMat-1.0.2/ShrinkCovMat/man/shrinkcovmat.unequal.Rd  |    4 -
 ShrinkCovMat-1.0.2/ShrinkCovMat/man/targetselection.Rd       |only
 15 files changed, 39 insertions(+), 34 deletions(-)

More information about ShrinkCovMat at CRAN
Permanent link

Package npmlreg updated to version 0.46-1 with previous version 0.45-5 dated 2014-07-10

Title: Nonparametric maximum likelihood estimation for random effect models
Description: Nonparametric maximum likelihood estimation or Gaussian quadrature for overdispersed generalized linear models and variance component models
Author: Jochen Einbeck, Ross Darnell and John Hinde
Maintainer: Jochen Einbeck

Diff between npmlreg versions 0.45-5 dated 2014-07-10 and 0.46-1 dated 2014-10-20

 DESCRIPTION              |   12 
 MD5                      |   34 -
 R/alldist.R              | 1094 ++++++++++++++++++++++++-----------------------
 R/allvc.R                |   44 +
 R/print.glmmNPML.R       |    1 
 R/summary.glmmNPML.R     |    1 
 build/vignette.rds       |binary
 data/hosp.rda            |binary
 data/irlsuicide.rda      |binary
 data/missouri.rda        |binary
 inst/doc/npmlreg-v.Rtex  |    6 
 inst/doc/npmlreg-v.pdf   |binary
 man/alldist.Rd           |   35 +
 man/npmlreg.package.Rd   |    4 
 man/predict.glmmNPML.Rd  |    6 
 man/summary.glmmNPML.Rd  |    6 
 man/tolfind.Rd           |   11 
 vignettes/npmlreg-v.Rtex |    6 
 18 files changed, 682 insertions(+), 578 deletions(-)

More information about npmlreg at CRAN
Permanent link

New package restlos with initial version 0.1-3
Package: restlos
Type: Package
Title: Robust Estimation of Location and Scatter
Version: 0.1-3
Date: 2014-10-13
Author: Steffen Liebscher and Thomas Kirschstein
Maintainer: Steffen Liebscher
Description: The restlos package provides algorithms for robust estimation of location and scatter based on minimum spanning trees (pMST), self-organizing maps (Flood Algorithm), and Delaunay triangulations (RDELA). The functions are also suitable for outlier detection.
Depends: som, rgl, geometry, igraph
License: GPL (>= 2)
LazyLoad: yes
NeedsCompilation: no
Repository: CRAN
Packaged: 2014-10-20 07:58:57 UTC; Steffen
X-CRAN-Comment: Archived on 2014-10-03 as depends on nnclust which has been archived.
Date/Publication: 2014-10-20 10:30:59

More information about restlos at CRAN
Permanent link

Package multiwayvcov updated to version 1.2.1 with previous version 1.2.0 dated 2014-09-06

Title: Multi-way Standard Error Clustering
Description: Exports two functions implementing multi-way clustering using the method suggested by Cameron, Gelbach, & Miller (2011) and cluster (or block) bootstrapping for estimating variance-covariance matrices. Normal one and two-way clustering matches the results of other common statistical packages. Missing values are handled transparently and rudimentary parallelization support is provided.
Author: Nathaniel Graham and Mahmood Arai and Björn Hagströmer
Maintainer: Nathaniel Graham

Diff between multiwayvcov versions 1.2.0 dated 2014-09-06 and 1.2.1 dated 2014-10-20

 DESCRIPTION         |   23 ++++-----
 MD5                 |   14 ++---
 NAMESPACE           |    4 +
 R/cluster_boot.r    |  127 +++++++++++++++++++++++++++++++++++++++++++---------
 R/cluster_vcov.r    |    9 ++-
 man/cluster.boot.Rd |   56 +++++++++++++++++++---
 man/cluster.vcov.Rd |   14 ++---
 man/petersen.Rd     |    2 
 8 files changed, 189 insertions(+), 60 deletions(-)

More information about multiwayvcov at CRAN
Permanent link

Package logconPH updated to version 1.1 with previous version 1.0 dated 2014-10-18

Title: CoxPH Model with Log Concave Baseline Distribution
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman

Diff between logconPH versions 1.0 dated 2014-10-18 and 1.1 dated 2014-10-20

 DESCRIPTION                   |    6 
 MD5                           |   16 -
 R/LogConcave.R                |    4 
 src/Cpp2Source/Array.hh       |  598 +++++++++++++++++++++---------------------
 src/Cpp2Source/QuadProg++.cc  |   42 +-
 src/Cpp2Source/baseClass.cpp  |   52 +--
 src/Cpp2Source/baseClass.h    |    7 
 src/Cpp2Source/logconcave.cpp |  132 ++++-----
 src/logconPH.cpp              |   83 ++---
 9 files changed, 475 insertions(+), 465 deletions(-)

More information about logconPH at CRAN
Permanent link

New package commentr with initial version 0.1
Package: commentr
Type: Package
Title: Print Nicely Formatted Comments for use in Script Files
Version: 0.1
License: GPL-2
Date: 2014-10-13
Author: Erik Bulow
Maintainer: Erik Bulow
Description: Functions to produce nicely formatted comments to use in R-scripts (or Latex/HTML/markdown etc). A comment with formatting is printed to the console and can then be copied to a script.
Imports: stringr
Suggests: testthat
BugReports: https://github.com/cancercentrum/commentr/issues
Packaged: 2014-10-20 07:46:08 UTC; erikbulow
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-20 10:30:16

More information about commentr at CRAN
Permanent link

Sun, 19 Oct 2014

Package MDSGUI updated to version 0.1.6 with previous version 0.1.1 dated 2013-05-16

Title: A GUI for interactive MDS in R
Description: A graphical user interface (GUI) for performing Multidimensional Scaling applications and interactively analysing the results all within the GUI environment. The MDS-GUI provides means of performing Classical Scaling, Least Squares Scaling, Metric SMACOF, Non-Metric SMACOF, Kruskal's Analysis and Sammon Mapping with animated optimisation.
Author: Andrew Timm and Sugnet Gardner-Lubbe
Maintainer: Andrew Timm

Diff between MDSGUI versions 0.1.1 dated 2013-05-16 and 0.1.6 dated 2014-10-19

 MDSGUI-0.1.1/MDSGUI/doc         |only
 MDSGUI-0.1.6/MDSGUI/DESCRIPTION |   19 +-
 MDSGUI-0.1.6/MDSGUI/MD5         |    8 -
 MDSGUI-0.1.6/MDSGUI/NAMESPACE   |    2 
 MDSGUI-0.1.6/MDSGUI/R/MDSgui.R  |  255 ++++++++++++++++++++++++++++++++++------
 5 files changed, 232 insertions(+), 52 deletions(-)

More information about MDSGUI at CRAN
Permanent link

Package geonames updated to version 0.997 with previous version 0.996 dated 2014-05-07

Title: Interface to www.geonames.org web service
Description: Code for querying the web service at www.geonames.org
Author: Barry Rowlingson
Maintainer: Barry Rowlingson

Diff between geonames versions 0.996 dated 2014-05-07 and 0.997 dated 2014-10-19

 DESCRIPTION                      |    8 ++---
 MD5                              |   62 +++++++++++++++++++--------------------
 NAMESPACE                        |    2 -
 R/geonames.R                     |    8 ++---
 README.md                        |    8 ++++-
 man/GNcities.Rd                  |    2 -
 man/GNcountryCode.Rd             |    2 -
 man/GNcountryInfo.Rd             |    2 -
 man/GNcountrySubdivision.Rd      |    2 -
 man/GNearthquakes.Rd             |    2 -
 man/GNfindNearByWeather.Rd       |    2 -
 man/GNfindNearby.Rd              |    2 -
 man/GNfindNearbyPlaceName.Rd     |    2 -
 man/GNfindNearbyPostalCodes.Rd   |    2 -
 man/GNfindNearbyStreets.Rd       |    2 -
 man/GNfindNearbyWikipedia.Rd     |    2 -
 man/GNfindNearestAddress.Rd      |    2 -
 man/GNfindNearestIntersection.Rd |    2 -
 man/GNgtopo30.Rd                 |    2 -
 man/GNneighbourhood.Rd           |    2 -
 man/GNpostalCodeCountryInfo.Rd   |    2 -
 man/GNpostalCodeLookup.Rd        |    2 -
 man/GNpostalCodeSearch.Rd        |    2 -
 man/GNsearch.Rd                  |    2 -
 man/GNsrtm3.Rd                   |    2 -
 man/GNtimezone.Rd                |    2 -
 man/GNweather.Rd                 |    2 -
 man/GNweatherIcao.Rd             |    2 -
 man/GNwikipediaBoundingBox.Rd    |    2 -
 man/GNwikipediaSearch.Rd         |    2 -
 man/geonames.Rd                  |    2 -
 man/hierarchy.Rd                 |    2 -
 32 files changed, 74 insertions(+), 68 deletions(-)

More information about geonames at CRAN
Permanent link

Package TAM updated to version 1.1 with previous version 1.0-3.18-1 dated 2014-09-08

Title: Test Analysis Modules
Description: The package includes marginal and joint maximum likelihood estimation of uni- and multidimensional item response models (Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets, Structured Latent Class Analysis), fit statistics, standard error estimation, as well as plausible value imputation and weighted likelihood estimation of ability.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch

Diff between TAM versions 1.0-3.18-1 dated 2014-09-08 and 1.1 dated 2014-10-19

 TAM-1.0-3.18-1/TAM/src/tam_caux__3-04.04.c |only
 TAM-1.1/TAM/DESCRIPTION                    |   10 
 TAM-1.1/TAM/MD5                            |   43 +--
 TAM-1.1/TAM/NAMESPACE                      |    9 
 TAM-1.1/TAM/R/TAM-internal_intermediate.R  |   46 +++
 TAM-1.1/TAM/R/TAM-internal_mstep.R         |    3 
 TAM-1.1/TAM/R/TAM-internal_postproc.R      |    7 
 TAM-1.1/TAM/R/designMatrices.mfr2.R        |   23 +
 TAM-1.1/TAM/R/designMatrices_aux2.R        |   58 +++-
 TAM-1.1/TAM/R/plot.ctt.R                   |only
 TAM-1.1/TAM/R/tam.fit.R                    |   24 +
 TAM-1.1/TAM/R/tam.mml.2pl.R                |   13 -
 TAM-1.1/TAM/R/tam.mml.3pl.R                |   53 +++-
 TAM-1.1/TAM/R/tam.mml.3pl.postproc.R       |    5 
 TAM-1.1/TAM/R/tam.mml.R                    |   40 +--
 TAM-1.1/TAM/R/tam.mml.mfr.R                |    2 
 TAM-1.1/TAM/data/data.ctest1.rda           |only
 TAM-1.1/TAM/inst/NEWS                      |   40 ++-
 TAM-1.1/TAM/man/TAM-package.Rd             |    2 
 TAM-1.1/TAM/man/data.ctest.Rd              |only
 TAM-1.1/TAM/man/tam.ctt.Rd                 |   20 +
 TAM-1.1/TAM/man/tam.fit.Rd                 |   15 +
 TAM-1.1/TAM/man/tam.mml.3pl.Rd             |   10 
 TAM-1.1/TAM/man/tam.mml.Rd                 |  366 ++++++++++++++++++++++-------
 TAM-1.1/TAM/src/tam_caux.c                 |only
 25 files changed, 596 insertions(+), 193 deletions(-)

More information about TAM at CRAN
Permanent link

Package meteoForecast updated to version 0.43 with previous version 0.31 dated 2014-07-07

Title: Numerical Weather Predictions
Description: Access to several Numerical Weather Prediction services both in raster format and as a time series for a location. Currenty it works with GFS, MeteoGalicia, OpenMeteo, NAM, and RAP.
Author: Oscar Perpinan Lamigueiro [cre, aut], Marcelo Pinho Almeida [ctb]
Maintainer: Oscar Perpinan Lamigueiro

Diff between meteoForecast versions 0.31 dated 2014-07-07 and 0.43 dated 2014-10-19

 meteoForecast-0.31/meteoForecast/LICENSE                |only
 meteoForecast-0.31/meteoForecast/R/pointInMG.R          |only
 meteoForecast-0.31/meteoForecast/README.md              |only
 meteoForecast-0.31/meteoForecast/man/varsMG.Rd          |only
 meteoForecast-0.43/meteoForecast/ChangeLog              |only
 meteoForecast-0.43/meteoForecast/DESCRIPTION            |   20 -
 meteoForecast-0.43/meteoForecast/MD5                    |   51 ++--
 meteoForecast-0.43/meteoForecast/NAMESPACE              |    6 
 meteoForecast-0.43/meteoForecast/R/checkDays.R          |    2 
 meteoForecast-0.43/meteoForecast/R/composeURL.R         |  179 +++++++++++----
 meteoForecast-0.43/meteoForecast/R/envir.R              |only
 meteoForecast-0.43/meteoForecast/R/getPoint.R           |   67 +----
 meteoForecast-0.43/meteoForecast/R/getPointDays.R       |   13 -
 meteoForecast-0.43/meteoForecast/R/getPointRuns.R       |   24 +-
 meteoForecast-0.43/meteoForecast/R/getRaster.R          |  182 +++-------------
 meteoForecast-0.43/meteoForecast/R/getRasterDay.R       |   48 +---
 meteoForecast-0.43/meteoForecast/R/getRasterDays.R      |   20 +
 meteoForecast-0.43/meteoForecast/R/grepVar.R            |only
 meteoForecast-0.43/meteoForecast/R/misc.R               |only
 meteoForecast-0.43/meteoForecast/R/pointMeteoGalicia.R  |only
 meteoForecast-0.43/meteoForecast/R/pointNCDC.R          |only
 meteoForecast-0.43/meteoForecast/R/pointOpenMeteo.R     |only
 meteoForecast-0.43/meteoForecast/R/rasterGFS.R          |only
 meteoForecast-0.43/meteoForecast/R/rasterMeteoGalicia.R |only
 meteoForecast-0.43/meteoForecast/R/rasterNCDC.R         |only
 meteoForecast-0.43/meteoForecast/R/rasterOpenMeteo.R    |only
 meteoForecast-0.43/meteoForecast/R/zzz.R                |only
 meteoForecast-0.43/meteoForecast/data/varsGFS.RData     |only
 meteoForecast-0.43/meteoForecast/data/varsMG.RData      |only
 meteoForecast-0.43/meteoForecast/data/varsNAM.RData     |only
 meteoForecast-0.43/meteoForecast/data/varsOM.RData      |binary
 meteoForecast-0.43/meteoForecast/data/varsRAP.RData     |only
 meteoForecast-0.43/meteoForecast/inst                   |only
 meteoForecast-0.43/meteoForecast/man/getPoint.Rd        |   44 ++-
 meteoForecast-0.43/meteoForecast/man/getRaster.Rd       |  135 ++++++++---
 meteoForecast-0.43/meteoForecast/man/meteo-package.Rd   |   17 -
 meteoForecast-0.43/meteoForecast/man/options.Rd         |only
 meteoForecast-0.43/meteoForecast/man/vars.Rd            |only
 38 files changed, 435 insertions(+), 373 deletions(-)

More information about meteoForecast at CRAN
Permanent link

Package AdapEnetClass updated to version 1.1 with previous version 1.0 dated 2013-11-10

Title: A Class of Adaptive Elastic-net Methods for Censored Data
Description: Provides new approaches to variable selection for censored data including its high-dimensionality, based on AFT models optimized using regularized weighted least squares. Approaches namely, a weighted elastic net, an adaptive elastic net, and two of their extensions by adding censoring observations as constraints into their model optimization frameworks are provided with both simulated and real (MCL) data examples.
Author: Hasinur Rahaman Khan and Ewart Shaw
Maintainer: Hasinur Rahaman Khan

Diff between AdapEnetClass versions 1.0 dated 2013-11-10 and 1.1 dated 2014-10-19

 AdapEnetClass-1.0/AdapEnetClass/R/AdapEnetClass.R            |only
 AdapEnetClass-1.1/AdapEnetClass/DESCRIPTION                  |   14 ++--
 AdapEnetClass-1.1/AdapEnetClass/MD5                          |   36 +++++++----
 AdapEnetClass-1.1/AdapEnetClass/NAMESPACE                    |    2 
 AdapEnetClass-1.1/AdapEnetClass/R/AEnet.aft.R                |only
 AdapEnetClass-1.1/AdapEnetClass/R/AEnetCC.aft.R              |only
 AdapEnetClass-1.1/AdapEnetClass/R/Enet.wls.R                 |only
 AdapEnetClass-1.1/AdapEnetClass/R/WEnet.aft.R                |only
 AdapEnetClass-1.1/AdapEnetClass/R/WEnetCC.aft.R              |only
 AdapEnetClass-1.1/AdapEnetClass/R/cv.AWEnet.R                |only
 AdapEnetClass-1.1/AdapEnetClass/R/cv.AWEnetCC.R              |only
 AdapEnetClass-1.1/AdapEnetClass/R/mrbj.R                     |only
 AdapEnetClass-1.1/AdapEnetClass/R/plotObsEst.R               |only
 AdapEnetClass-1.1/AdapEnetClass/data                         |only
 AdapEnetClass-1.1/AdapEnetClass/man/AEnet.aft.Rd             |    9 ++
 AdapEnetClass-1.1/AdapEnetClass/man/AEnetCC.aft.Rd           |    9 ++
 AdapEnetClass-1.1/AdapEnetClass/man/AdapEnetClass-package.Rd |   31 ++++-----
 AdapEnetClass-1.1/AdapEnetClass/man/Enet.wls.Rd              |    9 ++
 AdapEnetClass-1.1/AdapEnetClass/man/MCLcleaned.Rd            |only
 AdapEnetClass-1.1/AdapEnetClass/man/WEnet.aft.Rd             |    9 ++
 AdapEnetClass-1.1/AdapEnetClass/man/WEnetCC.aft.Rd           |    9 ++
 AdapEnetClass-1.1/AdapEnetClass/man/cv.AWEnet.Rd             |   29 +++++---
 AdapEnetClass-1.1/AdapEnetClass/man/cv.AWEnetCC.Rd           |   11 ++-
 AdapEnetClass-1.1/AdapEnetClass/man/mrbj.Rd                  |   13 ++-
 AdapEnetClass-1.1/AdapEnetClass/man/plotObsEst.Rd            |    3 
 25 files changed, 118 insertions(+), 66 deletions(-)

More information about AdapEnetClass at CRAN
Permanent link

Package stylo updated to version 0.5.8-2 with previous version 0.5.8-1 dated 2014-10-01

Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder

Diff between stylo versions 0.5.8-1 dated 2014-10-01 and 0.5.8-2 dated 2014-10-19

 DESCRIPTION  |   14 ++++++--------
 MD5          |    8 ++++----
 NEWS         |    5 ++++-
 R/classify.R |    2 ++
 R/stylo.R    |   24 ++++++++++++++++++++++--
 5 files changed, 38 insertions(+), 15 deletions(-)

More information about stylo at CRAN
Permanent link

Package DEoptimR updated to version 1.0-2 with previous version 1.0-1 dated 2014-02-04

Title: Differential Evolution Optimization in pure R
Description: An implementation of the jDE variant of the Differential Evolution stochastic algorithm for global optimization of nonlinear programming problems.
Author: Eduardo L. T. Conceicao and Martin Maechler [ctb]
Maintainer: Eduardo L. T. Conceicao

Diff between DEoptimR versions 1.0-1 dated 2014-02-04 and 1.0-2 dated 2014-10-19

 DESCRIPTION     |   18 ++++++++----------
 MD5             |    4 ++--
 man/JDEoptim.Rd |   19 ++++++++++++-------
 3 files changed, 22 insertions(+), 19 deletions(-)

More information about DEoptimR at CRAN
Permanent link

Sat, 18 Oct 2014

Package tis updated to version 1.27 with previous version 1.23 dated 2013-01-08

Title: Time Indexes and Time Indexed Series
Description: Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.
Author: Jeff Hallman
Maintainer: Jeff Hallman

Diff between tis versions 1.23 dated 2013-01-08 and 1.27 dated 2014-10-18

 tis-1.23/tis/COPYRIGHTS                   |only
 tis-1.27/tis/DESCRIPTION                  |    6 
 tis-1.27/tis/MD5                          |   53 ++++---
 tis-1.27/tis/NAMESPACE                    |   12 -
 tis-1.27/tis/NEWS                         |   29 ++++
 tis-1.27/tis/R/barplot.tis.R              |    8 -
 tis-1.27/tis/R/barplot2.R                 |  216 +++++++++++++++---------------
 tis-1.27/tis/R/capitalize.R               |only
 tis-1.27/tis/R/holidays.R                 |    5 
 tis-1.27/tis/R/inferTi.R                  |    8 -
 tis-1.27/tis/R/nber.R                     |   93 +-----------
 tis-1.27/tis/R/nberShade.ggplot.R         |    8 -
 tis-1.27/tis/R/ti.R                       |    7 
 tis-1.27/tis/R/tier.R                     |    6 
 tis-1.27/tis/R/tisFromCsv.R               |   15 +-
 tis-1.27/tis/R/tisPlot.R                  |   55 ++++---
 tis-1.27/tis/R/ymdShade.R                 |only
 tis-1.27/tis/R/zooStuff.R                 |    4 
 tis-1.27/tis/inst                         |only
 tis-1.27/tis/man/barplot.tis.Rd           |   14 -
 tis-1.27/tis/man/barplot2.Rd              |only
 tis-1.27/tis/man/capitalize.Rd            |only
 tis-1.27/tis/man/holidays.Rd              |    3 
 tis-1.27/tis/man/nberShade.Rd             |   53 +------
 tis-1.27/tis/man/nberShade.ggplot.Rd      |    2 
 tis-1.27/tis/man/setDefaultFrequencies.Rd |    2 
 tis-1.27/tis/man/tis-package.Rd           |    2 
 tis-1.27/tis/man/tisFromCsv.Rd            |   16 +-
 tis-1.27/tis/man/tisLegend.Rd             |    3 
 tis-1.27/tis/man/tisPlot.Rd               |   37 +++--
 tis-1.27/tis/man/ymdShade.Rd              |only
 31 files changed, 309 insertions(+), 348 deletions(-)

More information about tis at CRAN
Permanent link

Package picasso updated to version 0.3.0 with previous version 0.2.0 dated 2014-10-06

Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Implement a new family of efficient algorithms, called PathwIse CalibrAted Sparse Shooting AlgOrithm, for a variety of sparse learning problems, including Sparse Linear Regression, Sparse Logistic Regression, Sparse Column Inverse Operator and Sparse Multivariate Regression. Different types of active set identification schemes are implemented, such as cyclic search, greedy search, stochastic search and proximal gradient search. Besides, the package provides the choices between convex (L1 norm) and non-convex (MCP and SCAD) regularizations. Moreover, group regularization, such as group Lasso, group MCP and group SCAD, are also implemented for Sparse Linear Regression, Sparse Logistic Regression and Sparse Multivariate Regression.
Author: Xingguo Li, Tuo Zhao and Han Liu
Maintainer: Xingguo Li

Diff between picasso versions 0.2.0 dated 2014-10-06 and 0.3.0 dated 2014-10-18

 DESCRIPTION            |    8 ++++----
 MD5                    |    6 +++---
 R/picasso.scio.R       |    2 +-
 man/picasso-package.Rd |    4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)

More information about picasso at CRAN
Permanent link

New package multispatialCCM with initial version 1.0
Package: multispatialCCM
Title: Multispatial Convergent Cross Mapping
Version: 1.0
Date: 2014-10-18
Author: Adam Clark
Maintainer: Adam Clark
Depends: R (>= 3.0.2)
Description: The multispatial convergent cross mapping algorithm can be used as a test for causal associations between pairs of processes represented by time series. This is a combination of convergent cross mapping (CCM), described in Sugihara et al., 2012, Science, 338, 496-500, and dew-drop regression, described in Hsieh et al., 2008, American Naturalist, 171, 71–80. The algorithm allows CCM to be implemented on data that are not from a single long time series. Instead, data can come from many short time series, which are stitched together using bootstrapping.
License: GPL (>= 2)
Encoding: UTF-8
Packaged: 2014-10-18 23:48:53 UTC; atclark
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-19 01:55:59

More information about multispatialCCM at CRAN
Permanent link

New package logconPH with initial version 1.0
Package: logconPH
Type: Package
Title: CoxPH Model with Log Concave Baseline Distribution
Version: 1.0
Date: 2014-08-19
Author: Clifford Anderson-Bergman
Maintainer: Clifford Anderson-Bergman
Description: Computes a cox PH model with a log concave baseline distribution. If no covariates are provided, estimates the log concave NPMLE. Built specifically for interval censored data, where data is a n by 2 matrix with [i, 1] as the left side of the interval for subject i and [i,2] as right side. Uncensored data can be entered by setting [i,1] = [i,2]. Alternatively, this can also handle uncensored data. If all the data is uncensored, you may enter data as a length(n) vector.
License: GPL-2
Packaged: 2014-10-18 23:32:43 UTC; Cliff
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-19 01:49:27

More information about logconPH at CRAN
Permanent link

Package flare updated to version 1.5.0 with previous version 1.4.0 dated 2014-07-09

Title: Family of Lasso Regression
Description: The package "flare" provides the implementation of a family of Lasso variants including Dantzig Selector, LAD Lasso, SQRT Lasso, Lq Lasso for estimating high dimensional sparse linear model. We adopt the alternating direction method of multipliers and convert the original optimization problem into a sequential L1 penalized least square minimization problem, which can be efficiently solved by linearization algorithm. A multi-stage screening approach is adopted for further acceleration. Besides the sparse linear model estimation, we also provide the extension of these Lasso variants to sparse Gaussian graphical model estimation including TIGER and CLIME using either L1 or adaptive penalty. Missing values can be tolerated for Dantzig selector and CLIME. The computation is memory-optimized using the sparse matrix output.
Author: Xingguo Li, Tuo Zhao, Lie Wang, Xiaoming Yuan and Han Liu
Maintainer: Xingguo Li

Diff between flare versions 1.4.0 dated 2014-07-09 and 1.5.0 dated 2014-10-18

 DESCRIPTION                |   11 +++++------
 MD5                        |   42 +++++++++++++++++++++---------------------
 NAMESPACE                  |    2 +-
 R/slim.R                   |    2 +-
 R/sugm.clime.ladm.scr.R    |    3 ---
 R/sugm.tiger.ladm.scr.R    |    1 -
 build/vignette.rds         |binary
 man/flare-package.Rd       |    4 ++--
 man/slim.Rd                |    4 ++--
 man/sugm.Rd                |    6 +++---
 man/sugm.generator.Rd      |    2 +-
 man/sugm.plot.Rd           |    2 +-
 man/sugm.roc.Rd            |    2 +-
 man/sugm.select.Rd         |    6 +++---
 src/SFGen.c                |   18 +++++++++++-------
 src/euc_proj.c             |    2 +-
 src/mymath.c               |   10 +++++-----
 src/slim_lasso_ladm_scr.c  |    7 ++++---
 src/slim_lq_ladm_scr_btr.c |    2 +-
 src/slim_sqrt_ladm_scr.c   |    4 ++--
 src/sugm_clime_ladm_scr.c  |    4 ++--
 src/sugm_tiger_ladm_scr.c  |   10 +++++-----
 22 files changed, 72 insertions(+), 72 deletions(-)

More information about flare at CRAN
Permanent link

Package checkmate updated to version 1.5.0 with previous version 1.4 dated 2014-09-03

Title: Fast and versatile argument checks
Description: Tests and assertions to perform frequent argument checks. A substantial part of the package was written in C to minimize any worries about execution time overhead.
Author: Michel Lang , Bernd Bischl
Maintainer: Michel Lang

Diff between checkmate versions 1.4 dated 2014-09-03 and 1.5.0 dated 2014-10-18

 checkmate-1.4/checkmate/src/assertions.c                        |only
 checkmate-1.4/checkmate/src/assertions.h                        |only
 checkmate-1.5.0/checkmate/DESCRIPTION                           |    6 
 checkmate-1.5.0/checkmate/MD5                                   |  113 +++---
 checkmate-1.5.0/checkmate/NAMESPACE                             |   11 
 checkmate-1.5.0/checkmate/NEWS                                  |    8 
 checkmate-1.5.0/checkmate/R/anyInfinite.r                       |only
 checkmate-1.5.0/checkmate/R/checkNamed.r                        |    2 
 checkmate-1.5.0/checkmate/R/checkNames.r                        |only
 checkmate-1.5.0/checkmate/R/checkPercentage.r                   |only
 checkmate-1.5.0/checkmate/man/anyInfinite.Rd                    |only
 checkmate-1.5.0/checkmate/man/anyMissing.Rd                     |    2 
 checkmate-1.5.0/checkmate/man/asInteger.Rd                      |    8 
 checkmate-1.5.0/checkmate/man/assert.Rd                         |    2 
 checkmate-1.5.0/checkmate/man/checkAccess.Rd                    |   10 
 checkmate-1.5.0/checkmate/man/checkArray.Rd                     |   10 
 checkmate-1.5.0/checkmate/man/checkAtomic.Rd                    |   10 
 checkmate-1.5.0/checkmate/man/checkAtomicVector.Rd              |   10 
 checkmate-1.5.0/checkmate/man/checkCharacter.Rd                 |   18 
 checkmate-1.5.0/checkmate/man/checkChoice.Rd                    |    8 
 checkmate-1.5.0/checkmate/man/checkClass.Rd                     |   10 
 checkmate-1.5.0/checkmate/man/checkComplex.Rd                   |   10 
 checkmate-1.5.0/checkmate/man/checkCount.Rd                     |   13 
 checkmate-1.5.0/checkmate/man/checkDataFrame.Rd                 |   26 -
 checkmate-1.5.0/checkmate/man/checkDirectory.Rd                 |   10 
 checkmate-1.5.0/checkmate/man/checkEnvironment.Rd               |   10 
 checkmate-1.5.0/checkmate/man/checkFactor.Rd                    |   10 
 checkmate-1.5.0/checkmate/man/checkFile.Rd                      |   10 
 checkmate-1.5.0/checkmate/man/checkFlag.Rd                      |   11 
 checkmate-1.5.0/checkmate/man/checkFunction.Rd                  |   10 
 checkmate-1.5.0/checkmate/man/checkInt.Rd                       |   13 
 checkmate-1.5.0/checkmate/man/checkInteger.Rd                   |   10 
 checkmate-1.5.0/checkmate/man/checkIntegerish.Rd                |   10 
 checkmate-1.5.0/checkmate/man/checkList.Rd                      |   16 
 checkmate-1.5.0/checkmate/man/checkLogical.Rd                   |   10 
 checkmate-1.5.0/checkmate/man/checkMatrix.Rd                    |   10 
 checkmate-1.5.0/checkmate/man/checkNamed.Rd                     |   12 
 checkmate-1.5.0/checkmate/man/checkNames.Rd                     |only
 checkmate-1.5.0/checkmate/man/checkNull.Rd                      |    2 
 checkmate-1.5.0/checkmate/man/checkNumber.Rd                    |   13 
 checkmate-1.5.0/checkmate/man/checkNumeric.Rd                   |   10 
 checkmate-1.5.0/checkmate/man/checkPathForOutput.Rd             |   10 
 checkmate-1.5.0/checkmate/man/checkPercentage.Rd                |only
 checkmate-1.5.0/checkmate/man/checkScalar.Rd                    |   13 
 checkmate-1.5.0/checkmate/man/checkScalarNA.Rd                  |    6 
 checkmate-1.5.0/checkmate/man/checkSetEqual.Rd                  |   10 
 checkmate-1.5.0/checkmate/man/checkString.Rd                    |   13 
 checkmate-1.5.0/checkmate/man/checkSubset.Rd                    |   10 
 checkmate-1.5.0/checkmate/man/checkVector.Rd                    |   10 
 checkmate-1.5.0/checkmate/man/checkmate.Rd                      |    2 
 checkmate-1.5.0/checkmate/man/qassert.Rd                        |    2 
 checkmate-1.5.0/checkmate/man/qassertr.Rd                       |    2 
 checkmate-1.5.0/checkmate/src/any_infinite.c                    |only
 checkmate-1.5.0/checkmate/src/any_infinite.h                    |only
 checkmate-1.5.0/checkmate/src/any_missing.c                     |   12 
 checkmate-1.5.0/checkmate/src/as_type.c                         |only
 checkmate-1.5.0/checkmate/src/as_type.h                         |only
 checkmate-1.5.0/checkmate/src/bounds.c                          |    8 
 checkmate-1.5.0/checkmate/src/checks.c                          |  185 ++++------
 checkmate-1.5.0/checkmate/src/checks.h                          |    1 
 checkmate-1.5.0/checkmate/tests/testthat/test_anyInfinite.r     |only
 checkmate-1.5.0/checkmate/tests/testthat/test_checkMatrix.r     |    2 
 checkmate-1.5.0/checkmate/tests/testthat/test_checkNames.r      |only
 checkmate-1.5.0/checkmate/tests/testthat/test_checkNumeric.r    |    1 
 checkmate-1.5.0/checkmate/tests/testthat/test_checkPercentage.r |only
 65 files changed, 390 insertions(+), 341 deletions(-)

More information about checkmate at CRAN
Permanent link

Package openxlsx updated to version 2.2.1 with previous version 2.0.15 dated 2014-07-27

Title: Read, Write and Edit XLSX Files.
Description: Simplifies the creation of XLSX files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre], Luca Braglia [ctb]
Maintainer: Alexander Walker

Diff between openxlsx versions 2.0.15 dated 2014-07-27 and 2.2.1 dated 2014-10-18

 openxlsx-2.0.15/openxlsx/inst/doc/Formatting.Rnw   |only
 openxlsx-2.0.15/openxlsx/inst/doc/Formatting.pdf   |only
 openxlsx-2.0.15/openxlsx/man/orderCellRef.Rd       |only
 openxlsx-2.0.15/openxlsx/vignettes/Formatting.Rnw  |only
 openxlsx-2.2.1/openxlsx/DESCRIPTION                |   12 
 openxlsx-2.2.1/openxlsx/MD5                        |   76 
 openxlsx-2.2.1/openxlsx/NAMESPACE                  |    4 
 openxlsx-2.2.1/openxlsx/NEWS                       |   50 
 openxlsx-2.2.1/openxlsx/R/RcppExports.R            |   28 
 openxlsx-2.2.1/openxlsx/R/WorkbookClass.R          |  831 +++-
 openxlsx-2.2.1/openxlsx/R/baseXML.R                |  398 --
 openxlsx-2.2.1/openxlsx/R/borderFunctions.R        |    6 
 openxlsx-2.2.1/openxlsx/R/helperFunctions.R        |  100 
 openxlsx-2.2.1/openxlsx/R/loadWorkbook.R           |  133 
 openxlsx-2.2.1/openxlsx/R/openxlsx.R               |    5 
 openxlsx-2.2.1/openxlsx/R/readWorkbook.R           |   71 
 openxlsx-2.2.1/openxlsx/R/wrappers.R               | 3889 +++++++++++----------
 openxlsx-2.2.1/openxlsx/R/writeData.R              |   27 
 openxlsx-2.2.1/openxlsx/R/writeDataTable.R         |   91 
 openxlsx-2.2.1/openxlsx/R/writexlsx.R              |  217 -
 openxlsx-2.2.1/openxlsx/build/vignette.rds         |binary
 openxlsx-2.2.1/openxlsx/inst/doc/Introduction.Rnw  |   71 
 openxlsx-2.2.1/openxlsx/inst/doc/Introduction.pdf  |binary
 openxlsx-2.2.1/openxlsx/inst/doc/formatting.Rnw    |only
 openxlsx-2.2.1/openxlsx/inst/doc/formatting.pdf    |only
 openxlsx-2.2.1/openxlsx/man/addFilter.Rd           |only
 openxlsx-2.2.1/openxlsx/man/addWorksheet.Rd        |   68 
 openxlsx-2.2.1/openxlsx/man/conditionalFormat.Rd   |   17 
 openxlsx-2.2.1/openxlsx/man/convertToDateTime.Rd   |    6 
 openxlsx-2.2.1/openxlsx/man/createStyle.Rd         |    9 
 openxlsx-2.2.1/openxlsx/man/openxlsx.Rd            |    4 
 openxlsx-2.2.1/openxlsx/man/pageSetup.Rd           |    7 
 openxlsx-2.2.1/openxlsx/man/read.xlsx.Rd           |    6 
 openxlsx-2.2.1/openxlsx/man/readWorkbook.Rd        |    4 
 openxlsx-2.2.1/openxlsx/man/removeFilter.Rd        |only
 openxlsx-2.2.1/openxlsx/man/setColWidths.Rd        |   20 
 openxlsx-2.2.1/openxlsx/man/setHeaderFooter.Rd     |only
 openxlsx-2.2.1/openxlsx/man/write.xlsx.Rd          |   35 
 openxlsx-2.2.1/openxlsx/man/writeData.Rd           |    9 
 openxlsx-2.2.1/openxlsx/man/writeDataTable.Rd      |   18 
 openxlsx-2.2.1/openxlsx/src/RcppExports.cpp        |   93 
 openxlsx-2.2.1/openxlsx/src/cppFunctions.cpp       |  474 +-
 openxlsx-2.2.1/openxlsx/vignettes/Introduction.Rnw |   71 
 openxlsx-2.2.1/openxlsx/vignettes/formatting.Rnw   |only
 44 files changed, 4313 insertions(+), 2537 deletions(-)

More information about openxlsx at CRAN
Permanent link

Package raster updated to version 2.3-12 with previous version 2.3-10 dated 2014-10-16

Title: raster: Geographic data analysis and modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut], Jacob van Etten [ctb], Matteo Mattiuzzi [ctb], Michael Sumner [ctb], Jonathan A. Greenberg [ctb], Oscar Perpinan Lamigueiro [ctb], Andrew Bevan [ctb], Etienne B. Racine [ctb], Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans

Diff between raster versions 2.3-10 dated 2014-10-16 and 2.3-12 dated 2014-10-18

 ChangeLog               |    2 +-
 DESCRIPTION             |   12 ++++++------
 MD5                     |   18 +++++++++---------
 R/erase.R               |    2 +-
 R/intersect_sp.R        |    2 +-
 R/rowMinMax.R           |   15 +++++++++++----
 inst/doc/Raster.pdf     |binary
 inst/doc/functions.pdf  |binary
 inst/doc/rasterfile.pdf |binary
 man/predict.Rd          |    2 +-
 10 files changed, 30 insertions(+), 23 deletions(-)

More information about raster at CRAN
Permanent link

Package stochprofML updated to version 1.2 with previous version 1.1 dated 2014-05-22

Title: Stochastic Profiling using Maximum Likelihood Estimation
Description: This is an R package accompanying the paper "Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles" by Sameer S Bajikar, Christiane Fuchs, Andreas Roller, Fabian J Theis and Kevin A Janes (PNAS 2014, 111(5), E626-635). In this paper, we measure expression profiles from small heterogeneous populations of cells, where each cell is assumed to be from a mixture of lognormal distributions. We perform maximum likelihood estimation in order to infer the mixture ratio and the parameters of these lognormal distributions from the cumulated expression measurements.
Author: Christiane Fuchs
Maintainer: Christiane Fuchs

Diff between stochprofML versions 1.1 dated 2014-05-22 and 1.2 dated 2014-10-18

 DESCRIPTION                    |    8 ++++----
 MD5                            |   25 +++++++++++++++----------
 NAMESPACE                      |    3 ++-
 R/analyze.sod2.R               |    4 +++-
 R/stochasticProfilingData.R    |only
 R/stochasticProfilingML.R      |only
 R/stochprof.logit.R            |    2 +-
 R/stochprofML-internal.R       |only
 data/sod2.rda                  |binary
 data/toycluster.EXPLN.rda      |binary
 data/toycluster.LNLN.rda       |binary
 data/toycluster.rLNLN.rda      |binary
 man/generate.toydata.Rd        |    6 +++++-
 man/stochasticProfilingData.Rd |only
 man/stochasticProfilingML.Rd   |only
 man/stochprofML-package.Rd     |   19 ++++++++++++++-----
 16 files changed, 44 insertions(+), 23 deletions(-)

More information about stochprofML at CRAN
Permanent link

Package rareNMtests updated to version 1.1 with previous version 1.0 dated 2014-06-06

Title: Ecological and biogeographical null model tests for comparing rarefaction curves
Description: Randomization tests for the statistical comparison of \emph{i} = two or more individual-based, sample-based or coverage-based rarefaction curves. The ecological null hypothesis is that the \emph{i} samples were all drawn randomly from a single assemblage, with (necessarily) a single underlying species abundance distribution. The biogeographic null hypothesis is that the \emph{i} samples were all drawn from different assemblages that, nonetheless, share similar species richness and species abundance distributions
Author: Luis Cayuela and Nicholas J. Gotelli
Maintainer: Luis Cayuela

Diff between rareNMtests versions 1.0 dated 2014-06-06 and 1.1 dated 2014-10-18

 DESCRIPTION             |    8 ++++----
 MD5                     |    8 ++++----
 R/BiogTest.individual.R |    9 +++++----
 R/BiogTest.sample.R     |   21 ++++++++++++++-------
 R/EcoTest.sample.R      |    1 +
 5 files changed, 28 insertions(+), 19 deletions(-)

More information about rareNMtests at CRAN
Permanent link

New package landpred with initial version 1.0
Package: landpred
Type: Package
Title: Landmark Prediction of a Survival Outcome
Version: 1.0
Author: Layla Parast
Maintainer: Layla Parast
Description: This package includes functions for landmark prediction of a survival outcome incorporating covariate and short-term event information. For more information about landmark prediction please see: Parast, Layla, Su-Chun Cheng, and Tianxi Cai. Incorporating short-term outcome information to predict long-term survival with discrete markers. Biometrical Journal 53.2 (2011): 294-307.
License: GPL
Imports: survival
Packaged: 2014-10-17 22:28:12 UTC; parast
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-18 06:36:04

More information about landpred at CRAN
Permanent link

Fri, 17 Oct 2014

New package RMKdiscrete with initial version 0.1
Package: RMKdiscrete
Version: 0.1
Date: 2014-10-17
Title: Sundry Discrete Probability Distributions
Author: Robert M. Kirkpatrick
Maintainer: Robert M. Kirkpatrick
Description: Sundry discrete probability distributions and helper functions.
Depends: stats, R (>= 2.15.0)
NeedsCompilation: yes
Repository: CRAN
License: GPL (>= 2)
Packaged: 2014-10-17 16:15:33 UTC; Rob
Date/Publication: 2014-10-17 20:23:16

More information about RMKdiscrete at CRAN
Permanent link

Package laGP updated to version 1.1-2 with previous version 1.1-1 dated 2014-09-03

Title: Local Approximate Gaussian Process Regression
Description: Performs approximate GP regression for large computer experiments and spatial datasets. The approximation is based on finding small local designs for prediction (independently) at particular inputs. OpenMP and SNOW parallelization are supported for prediction over a vast out-of-sample testing set; GPU acceleration is also supported for an important subroutine. OpenMP and GPU features may require special compilation. An interface to lower-level (full) GP inference and prediction is also provided, as are associated wrapper routines for blackbox optimization under constraints via an augmented Lagrangian scheme, and large scale computer model calibration
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy

Diff between laGP versions 1.1-1 dated 2014-09-03 and 1.1-2 dated 2014-10-17

 ChangeLog           |   14 +++
 DESCRIPTION         |   10 +-
 INSTALL             |   10 +-
 MD5                 |   44 ++++++++----
 NAMESPACE           |    4 -
 R/auglag.R          |    2 
 R/calib.R           |only
 R/gp.R              |   12 +--
 R/gp_sep.R          |only
 build               |only
 demo                |only
 inst                |only
 man/aGP.Rd          |   39 +++++++++-
 man/deleteGP.Rd     |   15 +++-
 man/discrep.est.Rd  |only
 man/fcalib.Rd       |only
 man/llikGP.Rd       |    9 +-
 man/mleGP.Rd        |  115 +++++++++++++++++++++++++------
 man/newGP.Rd        |   31 +++++---
 man/optim.auglag.Rd |    4 -
 src/covar_sep.c     |only
 src/covar_sep.h     |only
 src/gp.c            |  190 ++++++++++------------------------------------------
 src/gp_sep.c        |only
 src/gp_sep.h        |only
 src/util.c          |only
 src/util.h          |only
 vignettes           |only
 28 files changed, 272 insertions(+), 227 deletions(-)

More information about laGP at CRAN
Permanent link

Package kselection updated to version 0.1.1 with previous version 0.1.0 dated 2014-09-15

Title: Selection of k in k-means clustering
Description: Selection of k in k-means clustering based on Pham et al. paper ``Selection of k in k-means clustering''
Author: Daniel Rodriguez Perez
Maintainer: Daniel Rodriguez Perez

Diff between kselection versions 0.1.0 dated 2014-09-15 and 0.1.1 dated 2014-10-17

 DESCRIPTION               |    8 ++++----
 MD5                       |   12 +++++++-----
 NEWS                      |only
 R/kselection.R            |    2 +-
 R/pham.R                  |   17 ++++++++++++-----
 inst/tests/testPhamFix.R  |only
 man/kselection-package.Rd |    2 +-
 man/kselection.Rd         |    6 ++++--
 8 files changed, 29 insertions(+), 18 deletions(-)

More information about kselection at CRAN
Permanent link

New package highTtest with initial version 1.0
Package: highTtest
Type: Package
Title: Simultaneous Critical Values for t-Tests in Very High Dimensions
Version: 1.0
Date: 2014-10-14
Authors@R: c(person("Hongyuan", "Cao", role = c("aut"), email = "caohong@missouri.edu"), person("Michael", "Kosorok", role = c("aut"), email = "kosorok@unc.edu"), person("Shannon","Holloway", role=c("aut","cre"), email="sthollow@ncsu.edu"))
Description: Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an asymptotically valid data-driven procedure to find critical values for rejection regions controlling the k-familywise error rate, false discovery rate, and the tail probability of false discovery proportion.
License: GPL-2
Depends: methods, colorfulVennPlot
Packaged: 2014-10-17 16:31:13 UTC; sthollow
Author: Hongyuan Cao [aut], Michael Kosorok [aut], Shannon Holloway [aut, cre]
Maintainer: Shannon Holloway
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 19:54:38

More information about highTtest at CRAN
Permanent link

Package AICcmodavg updated to version 2.0-1 with previous version 2.00 dated 2014-07-15

Title: Model Selection and Multimodel Inference Based on (Q)AIC(c)
Description: This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). The package also features functions to conduct classic model averaging (multimodel inference) for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with Cox proportional hazards models and conditional logistic regression ('coxph' and 'coxme' classes), linear models ('lm' class), generalized linear models ('glm', 'vglm', 'hurdle', and 'zeroinfl' classes), linear models fit by generalized least squares ('gls' class), linear mixed models ('lme' class), generalized linear mixed models ('mer' and 'merMod' classes), multinomial and ordinal logistic regressions ('multinom'}, 'polr', 'clm', and 'clmm' classes), robust regression models ('rlm' class), beta regression models ('betareg' class), parametric survival models ('survreg' class), nonlinear models ('nls' and 'gnls' classes), and nonlinear mixed models ('nlme' and 'nlmer' classes). The package also supports various models of 'unmarkedFit' and 'maxLikeFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs' and 'rjags' classes.
Author: Marc J. Mazerolle .
Maintainer: Marc J. Mazerolle

Diff between AICcmodavg versions 2.00 dated 2014-07-15 and 2.0-1 dated 2014-10-17

 AICcmodavg-2.0-1/AICcmodavg/DESCRIPTION               |   21 
 AICcmodavg-2.0-1/AICcmodavg/MD5                       |   96 +-
 AICcmodavg-2.0-1/AICcmodavg/NAMESPACE                 |  536 ++++++++++++
 AICcmodavg-2.0-1/AICcmodavg/R/AICc.R                  |   62 +
 AICcmodavg-2.0-1/AICcmodavg/R/Custom.functions.r      |only
 AICcmodavg-2.0-1/AICcmodavg/R/Nmix.gof.test.R         |only
 AICcmodavg-2.0-1/AICcmodavg/R/aictab.R                |  232 +++++
 AICcmodavg-2.0-1/AICcmodavg/R/boot.wt.r               |  223 +++++
 AICcmodavg-2.0-1/AICcmodavg/R/dictab.r                |    4 
 AICcmodavg-2.0-1/AICcmodavg/R/extractCN.r             |only
 AICcmodavg-2.0-1/AICcmodavg/R/extractLL.R             |    8 
 AICcmodavg-2.0-1/AICcmodavg/R/extractSE.R             |    5 
 AICcmodavg-2.0-1/AICcmodavg/R/importance.R            |  225 +++++
 AICcmodavg-2.0-1/AICcmodavg/R/mb.gof.test.R           |only
 AICcmodavg-2.0-1/AICcmodavg/R/modavg.R                |  768 +++++++++++++++++-
 AICcmodavg-2.0-1/AICcmodavg/R/modavg.utility.R        |only
 AICcmodavg-2.0-1/AICcmodavg/R/modavgEffect.r          |  136 +++
 AICcmodavg-2.0-1/AICcmodavg/R/modavgPred.R            |  128 ++-
 AICcmodavg-2.0-1/AICcmodavg/R/modavgShrink.R          |  338 +++++++
 AICcmodavg-2.0-1/AICcmodavg/R/multComp.R              |only
 AICcmodavg-2.0-1/AICcmodavg/R/predictSE.R             |only
 AICcmodavg-2.0-1/AICcmodavg/inst/NEWS                 |   20 
 AICcmodavg-2.0-1/AICcmodavg/man/AICc.Rd               |   40 
 AICcmodavg-2.0-1/AICcmodavg/man/AICcCustom.Rd         |only
 AICcmodavg-2.0-1/AICcmodavg/man/AICcmodavg-package.Rd |   38 
 AICcmodavg-2.0-1/AICcmodavg/man/DIC.Rd                |    8 
 AICcmodavg-2.0-1/AICcmodavg/man/Nmix.gof.test.Rd      |   45 -
 AICcmodavg-2.0-1/AICcmodavg/man/aictab.Rd             |   91 --
 AICcmodavg-2.0-1/AICcmodavg/man/aictabCustom.Rd       |only
 AICcmodavg-2.0-1/AICcmodavg/man/boot.wt.Rd            |   35 
 AICcmodavg-2.0-1/AICcmodavg/man/bullfrog.Rd           |    2 
 AICcmodavg-2.0-1/AICcmodavg/man/calcium.Rd            |    2 
 AICcmodavg-2.0-1/AICcmodavg/man/confset.Rd            |   36 
 AICcmodavg-2.0-1/AICcmodavg/man/dictab.Rd             |    7 
 AICcmodavg-2.0-1/AICcmodavg/man/evidence.Rd           |    6 
 AICcmodavg-2.0-1/AICcmodavg/man/extractCN.Rd          |only
 AICcmodavg-2.0-1/AICcmodavg/man/extractLL.Rd          |   18 
 AICcmodavg-2.0-1/AICcmodavg/man/extractSE.Rd          |    9 
 AICcmodavg-2.0-1/AICcmodavg/man/fam.link.mer.Rd       |    9 
 AICcmodavg-2.0-1/AICcmodavg/man/importance.Rd         |   25 
 AICcmodavg-2.0-1/AICcmodavg/man/lizards.Rd            |    4 
 AICcmodavg-2.0-1/AICcmodavg/man/mb.gof.test.Rd        |   16 
 AICcmodavg-2.0-1/AICcmodavg/man/min.trap.Rd           |    2 
 AICcmodavg-2.0-1/AICcmodavg/man/modavg.Rd             |  113 +-
 AICcmodavg-2.0-1/AICcmodavg/man/modavgCustom.Rd       |only
 AICcmodavg-2.0-1/AICcmodavg/man/modavgEffect.Rd       |   65 -
 AICcmodavg-2.0-1/AICcmodavg/man/modavgPred.Rd         |   42 
 AICcmodavg-2.0-1/AICcmodavg/man/modavgShrink.Rd       |   49 -
 AICcmodavg-2.0-1/AICcmodavg/man/multComp.Rd           |   60 -
 AICcmodavg-2.0-1/AICcmodavg/man/predictSE.Rd          |   35 
 AICcmodavg-2.0-1/AICcmodavg/man/salamander.Rd         |   15 
 AICcmodavg-2.0-1/AICcmodavg/man/tortoise.Rd           |    2 
 AICcmodavg-2.00/AICcmodavg/R/Nmix.gof.test.r          |only
 AICcmodavg-2.00/AICcmodavg/R/mb.gof.test.r            |only
 AICcmodavg-2.00/AICcmodavg/R/modavg.utility.r         |only
 AICcmodavg-2.00/AICcmodavg/R/multComp.r               |only
 AICcmodavg-2.00/AICcmodavg/R/predictSE.r              |only
 57 files changed, 3092 insertions(+), 484 deletions(-)

More information about AICcmodavg at CRAN
Permanent link

New package sisVIVE with initial version 1.0
Package: sisVIVE
Type: Package
Title: Some Invalid Some Valid Instrumental Variables Estimator
Version: 1.0
Date: 2014-07-31
Author: Hyunseung Kang
Maintainer: Hyunseung Kang
Depends: lars
Suggests: MASS
Description: Selects invalid instruments amongst a candidate of potentially bad instruments. The algorithm selects potentially invalid instruments and provides an estimate of the causal effect between exposure and outcome. The paper, Instrumental Variables Estimation with Some Invalid Instruments and its Application to Mendelian Randomization by Hyunseung Kang, Anru Zhang, T. Tony Cai, and Dylan S. Small (on arXiv) has more details on this procedure.
License: GPL-2
Packaged: 2014-10-17 14:29:30 UTC; khyuns
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:39:17

More information about sisVIVE at CRAN
Permanent link

Package R2GUESS updated to version 1.5 with previous version 1.4 dated 2014-10-16

Title: Wrapper functions for GUESS
Description: Wrapper functions for GUESS, a GPU-enabled sparse Bayesian variable selection method for linear regression based analysis of possibly multivariate/correlated outcomes.
Author: Gianluca Campanella [cre], Benoit Liquet [aut], Marc Chadeau-Hyam [aut], Leonardo Bottolo [ctb], Sylvia Richardson [ctb]
Maintainer: Gianluca Campanella

Diff between R2GUESS versions 1.4 dated 2014-10-16 and 1.5 dated 2014-10-17

 DESCRIPTION       |    8 ++++----
 MD5               |    6 +++---
 R/wrapper.R       |    2 +-
 src/Main/GUESS.cc |    2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

More information about R2GUESS at CRAN
Permanent link

New package MRH with initial version 1.0
Package: MRH
Type: Package
Title: Multi-Resolution Estimation of the Hazard Rate
Version: 1.0
Date: 2013-10-28
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times.
License: GPL-2
Depends: survival, KMsurv
Suggests: R.rsp
VignetteBuilder: R.rsp
Imports: coda, HI
Packaged: 2014-10-17 15:44:27 UTC; Yolanda
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-17 17:52:12

More information about MRH at CRAN
Permanent link

New package mdscore with initial version 0.1-2
Package: mdscore
Type: Package
Title: Improved Score Tests for Generalized Linear Models
Version: 0.1-2
Date: 2014-10-15
Depends: R (>= 3.1.1), MASS
Suggests: Sleuth3
Authors@R: c(person("Antonio Hermes M.","da Silva-Junior", email = "hermes@ccet.ufrn.br", role = c("aut", "cre")), person("Damiao N.","da Silva", email = "damiao@ccet.ufrn.br", role = "aut"), person("Silvia L. P.", "Ferrari", email = "silviaferrari.usp@gmail.com", role = "ctb"))
Author: Antonio Hermes M. da Silva-Junior [aut, cre], Damiao N. da Silva [aut], Silvia L. P. Ferrari [ctb]
Maintainer: Antonio Hermes M. da Silva-Junior
Description: A set of functions to obtain modified score test for generalized linear models.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2014-10-17 12:28:47 UTC; mlfd58
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:50:40

More information about mdscore at CRAN
Permanent link

New package likert with initial version 1.2
Package: likert
Type: Package
Title: Functions to analyze and visualize likert type items
Version: 1.2
Date: 2014-09-28
Author: Jason Bryer , Kimberly Speerschneider
Maintainer: Jason Bryer
URL: http://jason.bryer.org/likert, http://github.com/jbryer/likert
BugReports: https://github.com/jbryer/likert/issues
Description: Functions to analyze and visualize likert type items
License: GPL
LazyLoad: yes
VignetteBuilder: utils
Depends: R (>= 3.0),ggplot2,xtable
Imports: psych,reshape,gridExtra,grid,plyr
Suggests: devtools,shiny
Packaged: 2014-10-17 14:01:18 UTC; jbryer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:43:09

More information about likert at CRAN
Permanent link

New package ecoval with initial version 1.0
Package: ecoval
Type: Package
Title: Procedures for Ecological Assessment of Surface Waters
Version: 1.0
Date: 2014-10-17
Author: Nele Schuwirth and Peter Reichert with contributions by Simone Langhans
Maintainer: Nele Schuwirth
Description: Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.
License: GPL (>= 2)
Depends: utility, rivernet
LazyData: true
Packaged: 2014-10-17 14:19:43 UTC; schuwine
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 17:36:36

More information about ecoval at CRAN
Permanent link

Package BcDiag updated to version 1.0.5 with previous version 1.0.4 dated 2014-08-07

Title: Diagnostics plots for Bicluster Data
Description: This package provides Diagnostic tools based on two way anova and median polish residual plots for Bicluster output obtained from packages; "biclust" by Kaiser et al.(2008),"isa2" by Csardi et al. (2010) and "fabia" by Hochreiter et al. (2010). Moreover, It provides visualization tools for bicluster output and corresponding non bicluster rows or columns outcomes. It has also extended the idea of Kaiser et al.(2008) which is, extracting bicluster output in a text format, by adding by adding two bicluster methods from fabia and isa2 r packages.
Author: Aregay Mengsteab, Martin Otava, Tatsiana Khamiakova, Ewoud De Troyer
Maintainer: Ewoud De Troyer

Diff between BcDiag versions 1.0.4 dated 2014-08-07 and 1.0.5 dated 2014-10-17

 DESCRIPTION  |   18 +++++++++++-------
 MD5          |    8 ++++----
 NAMESPACE    |    3 +++
 R/support.R  |   27 ++++++++++++++++++++++++---
 R/writeBic.R |    2 +-
 5 files changed, 43 insertions(+), 15 deletions(-)

More information about BcDiag at CRAN
Permanent link

New package CLME with initial version 1.0-1
Package: CLME
Title: Constrained Inference for Linear Mixed Effects Models.
Version: 1.0-1
Depends: R (>= 3.0.2)
Imports: MASS, quadprog, shiny, methods, Iso
Suggests: nnet
Date: 2014-09-09
Description: Implements constrained inference for linear mixed effects models using residual bootstrap methodology.
Author: Casey M. Jelsema
Maintainer: Casey M. Jelsema
BugReports: https://github.com/jelsema/CLME/issues
BuildVignettes: true
LazyLoad: yes
License: GPL-2 | GPL-3
Packaged: 2014-10-17 16:02:45 UTC; jelsemacm
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 18:22:17

More information about CLME at CRAN
Permanent link

Package WebDevelopR (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2013-04-09 1.0

Permanent link
New package pBrackets with initial version 1.0
Package: pBrackets
Version: 1.0
Date: 2014-10-17
Title: Plot Brackets
Author: Andreas Schulz
Maintainer: Andreas Schulz
Depends: R (>= 3.0.0)
Imports: grid
Description: Adds different kinds of brackets to a plot, including braces, chevrons, parentheses or square brackets.
License: GPL (>= 2.0)
Packaged: 2014-10-17 09:30:23 UTC; scu9a
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 13:08:28

More information about pBrackets at CRAN
Permanent link

Package fat2Lpoly updated to version 1.1.1 with previous version 1.0.2 dated 2014-04-02

Title: Two-locus Family-based Association Test with Polytomous Outcome
Description: Performs family-based association tests with a polytomous outcome under 2-locus and 1-locus models defined by some design matrix.
Author: Alexandre BUREAU and Jordie Croteau
Maintainer: Alexandre BUREAU

Diff between fat2Lpoly versions 1.0.2 dated 2014-04-02 and 1.1.1 dated 2014-10-17

 fat2Lpoly-1.0.2/fat2Lpoly/R/calcule.poids.r           |only
 fat2Lpoly-1.1.1/fat2Lpoly/DESCRIPTION                 |   13 -
 fat2Lpoly-1.1.1/fat2Lpoly/MD5                         |   25 +-
 fat2Lpoly-1.1.1/fat2Lpoly/NAMESPACE                   |    2 
 fat2Lpoly-1.1.1/fat2Lpoly/R/calcule.poids.Chen.R      |only
 fat2Lpoly-1.1.1/fat2Lpoly/R/calcule.poids.alphafixe.r |only
 fat2Lpoly-1.1.1/fat2Lpoly/R/fat2Lpoly.R               |    6 
 fat2Lpoly-1.1.1/fat2Lpoly/R/fat2Lpoly.withinR.R       |    4 
 fat2Lpoly-1.1.1/fat2Lpoly/R/scores.covs.R             |    4 
 fat2Lpoly-1.1.1/fat2Lpoly/man/design.endo2disease.Rd  |    5 
 fat2Lpoly-1.1.1/fat2Lpoly/man/design.full.Rd          |    2 
 fat2Lpoly-1.1.1/fat2Lpoly/man/fat2Lpoly-internal.Rd   |    3 
 fat2Lpoly-1.1.1/fat2Lpoly/man/fat2Lpoly.Rd            |   15 -
 fat2Lpoly-1.1.1/fat2Lpoly/man/fat2Lpoly.withinR.Rd    |   10 
 fat2Lpoly-1.1.1/fat2Lpoly/man/read.merlin.files.Rd    |  182 +++++++++---------
 15 files changed, 141 insertions(+), 130 deletions(-)

More information about fat2Lpoly at CRAN
Permanent link

Package ExtDist updated to version 0.3.7 with previous version 0.3.3 dated 2014-07-11

Title: Extended Probability Distribution Functions
Description: The package provides a consistent, unified and extensible framework for parameter estimation of probability distributions; it extends parameter estimation procedures to allow for weighted samples; moreover, it extends the gallery of available distributions.
Author: Haizhen Wu , A. Jonathan R. Godfrey , Kondaswamy Govindaraju
Maintainer: Haizhen Wu

Diff between ExtDist versions 0.3.3 dated 2014-07-11 and 0.3.7 dated 2014-10-17

 ExtDist-0.3.3/ExtDist/R/Beta.ab.R                                  |only
 ExtDist-0.3.3/ExtDist/man/Beta.ab.Rd                               |only
 ExtDist-0.3.7/ExtDist/DESCRIPTION                                  |   10 
 ExtDist-0.3.7/ExtDist/MD5                                          |   86 
 ExtDist-0.3.7/ExtDist/NAMESPACE                                    |  121 +
 ExtDist-0.3.7/ExtDist/R/Beta.R                                     |    2 
 ExtDist-0.3.7/ExtDist/R/Beta_ab.R                                  |only
 ExtDist-0.3.7/ExtDist/R/Burr.R                                     |only
 ExtDist-0.3.7/ExtDist/R/DistSelCriteriaValues.R                    |only
 ExtDist-0.3.7/ExtDist/R/Gamma.R                                    |only
 ExtDist-0.3.7/ExtDist/R/Gumbel.R                                   |only
 ExtDist-0.3.7/ExtDist/R/JohnsonSB.R                                |only
 ExtDist-0.3.7/ExtDist/R/JohnsonSU.R                                |only
 ExtDist-0.3.7/ExtDist/R/Logistic.R                                 |only
 ExtDist-0.3.7/ExtDist/R/Normal_sym_trunc_ab.R                      |only
 ExtDist-0.3.7/ExtDist/R/Normal_trunc_ab.R                          |only
 ExtDist-0.3.7/ExtDist/R/SRTB_ab.R                                  |only
 ExtDist-0.3.7/ExtDist/R/SSRTB.R                                    |only
 ExtDist-0.3.7/ExtDist/R/Triangular.R                               |only
 ExtDist-0.3.7/ExtDist/R/Uniform.R                                  |only
 ExtDist-0.3.7/ExtDist/R/Weibull.R                                  |only
 ExtDist-0.3.7/ExtDist/R/bestDist.R                                 |only
 ExtDist-0.3.7/ExtDist/R/eDist.R                                    |   47 
 ExtDist-0.3.7/ExtDist/R/wmle.R                                     |  917 ++++------
 ExtDist-0.3.7/ExtDist/build/vignette.rds                           |binary
 ExtDist-0.3.7/ExtDist/inst/doc/Distributions-Beta.Rmd              |  164 -
 ExtDist-0.3.7/ExtDist/inst/doc/Distributions-Beta.html             |  391 +---
 ExtDist-0.3.7/ExtDist/inst/doc/Distributions-Normal.Rmd            |  167 -
 ExtDist-0.3.7/ExtDist/inst/doc/Distributions-Normal.html           |  396 +---
 ExtDist-0.3.7/ExtDist/inst/doc/Distributions.Rmd                   |   23 
 ExtDist-0.3.7/ExtDist/inst/doc/Distributions.html                  |  258 +-
 ExtDist-0.3.7/ExtDist/inst/doc/ParaEst-and-DistSel-by-ExtDist.R    |only
 ExtDist-0.3.7/ExtDist/inst/doc/ParaEst-and-DistSel-by-ExtDist.Rmd  |only
 ExtDist-0.3.7/ExtDist/inst/doc/ParaEst-and-DistSel-by-ExtDist.pdf  |only
 ExtDist-0.3.7/ExtDist/man/Beta.Rd                                  |   10 
 ExtDist-0.3.7/ExtDist/man/Beta_ab.Rd                               |only
 ExtDist-0.3.7/ExtDist/man/Burr.Rd                                  |only
 ExtDist-0.3.7/ExtDist/man/DistSelCriteriaValues.Rd                 |only
 ExtDist-0.3.7/ExtDist/man/ExtDist-package.Rd                       |   39 
 ExtDist-0.3.7/ExtDist/man/Gamma.Rd                                 |only
 ExtDist-0.3.7/ExtDist/man/Gumbel.Rd                                |only
 ExtDist-0.3.7/ExtDist/man/JohnsonSB.Rd                             |only
 ExtDist-0.3.7/ExtDist/man/JohnsonSU.Rd                             |only
 ExtDist-0.3.7/ExtDist/man/Laplace.Rd                               |   14 
 ExtDist-0.3.7/ExtDist/man/Logistic.Rd                              |only
 ExtDist-0.3.7/ExtDist/man/Normal.Rd                                |   14 
 ExtDist-0.3.7/ExtDist/man/Normal_sym_trunc_ab.Rd                   |only
 ExtDist-0.3.7/ExtDist/man/Normal_trunc_ab.Rd                       |only
 ExtDist-0.3.7/ExtDist/man/SRTB_ab.Rd                               |only
 ExtDist-0.3.7/ExtDist/man/SSRTB.Rd                                 |only
 ExtDist-0.3.7/ExtDist/man/Triangular.Rd                            |only
 ExtDist-0.3.7/ExtDist/man/Uniform.Rd                               |only
 ExtDist-0.3.7/ExtDist/man/Weibull.Rd                               |only
 ExtDist-0.3.7/ExtDist/man/bestDist.Rd                              |only
 ExtDist-0.3.7/ExtDist/man/compareDist.Rd                           |    2 
 ExtDist-0.3.7/ExtDist/man/eDist.Rd                                 |   20 
 ExtDist-0.3.7/ExtDist/man/eval.estimation.Rd                       |    2 
 ExtDist-0.3.7/ExtDist/man/wmle.Rd                                  |    2 
 ExtDist-0.3.7/ExtDist/vignettes/Distributions-Beta.Rmd             |  164 -
 ExtDist-0.3.7/ExtDist/vignettes/Distributions-Normal.Rmd           |  167 -
 ExtDist-0.3.7/ExtDist/vignettes/Distributions.Rmd                  |   23 
 ExtDist-0.3.7/ExtDist/vignettes/ParaEst-and-DistSel-by-ExtDist.Rmd |only
 ExtDist-0.3.7/ExtDist/vignettes/bibliography.bib                   |only
 ExtDist-0.3.7/ExtDist/vignettes/header.tex                         |only
 64 files changed, 1499 insertions(+), 1540 deletions(-)

More information about ExtDist at CRAN
Permanent link

Package SemiParBIVProbit updated to version 3.2-12 with previous version 3.2-11 dated 2014-07-02

Title: Semiparametric Bivariate Probit Modelling
Description: Routine for fitting bivariate probit models with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, sample selection or partial observability. Bivariate copula models are also supported.
Author: Giampiero Marra and Rosalba Radice
Maintainer: Giampiero Marra

Diff between SemiParBIVProbit versions 3.2-11 dated 2014-07-02 and 3.2-12 dated 2014-10-17

 SemiParBIVProbit-3.2-11/SemiParBIVProbit/R/bprobgHsBB.r                        |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/R/bprobgHsSSBB.r                      |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/R/bprobgHsSSPL.r                      |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/R/copgHsBB.r                          |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/R/residuals.SemiParBIVProbit.r        |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/man/bprobgHsBB.Rd                     |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/man/bprobgHsSSBB.Rd                   |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/man/bprobgHsSSPL.Rd                   |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/man/copgHsBB.Rd                       |only
 SemiParBIVProbit-3.2-11/SemiParBIVProbit/man/residuals.SemiParBIVProbit.Rd     |only
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/ChangeLog                             |    5 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/DESCRIPTION                           |   14 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/MD5                                   |  102 --
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/NAMESPACE                             |   21 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/AT.r                                |  276 +----
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/LM.bpm.r                            |  428 ++------
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/SemiParBIVProbit.fit.R              |   74 -
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/SemiParBIVProbit.fit.post.r         |  193 +---
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/SemiParBIVProbit.r                  |  347 ++++---
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/VuongClarke.bcm.r                   |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/adjCov.r                            |    4 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/adjCovSD.r                          |    5 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/bprobgHs.r                          |  206 +++-
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/bprobgHsPL.r                        |  482 +++++++++-
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/bprobgHsPO.r                        |only
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/bprobgHsSS.r                        |  127 +-
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/copgHs.r                            |   29 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/est.prev.r                          |   20 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/gt.bpm.R                            |   28 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/plot.SemiParBIVProbit.r             |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/predict.SemiParBIVProbit.r          |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/print.AT.r                          |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/print.SemiParBIVProbit.r            |   35 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/print.est.prev.r                    |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/print.summary.SemiParBIVProbit.r    |   39 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/sem.checks.r                        |   12 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/summary.SemiParBIVProbit.r          |  114 +-
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/R/working.comp.r                      |   79 +
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/AT.Rd                             |    3 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/LM.bpm.Rd                         |   38 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/S.m.Rd                            |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/S.mPL.Rd                          |    3 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/SemiParBIVProbit-package.Rd       |   35 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/SemiParBIVProbit.Rd               |  247 +++--
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/SemiParBIVProbitObject.Rd         |   18 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/VuongClarke.bcm.Rd                |   19 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/bprobgHs.Rd                       |    5 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/bprobgHsPL.Rd                     |   14 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/bprobgHsPO.Rd                     |only
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/bprobgHsSS.Rd                     |    8 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/copgHs.Rd                         |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/est.prev.Rd                       |    6 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/gt.bpm.Rd                         |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/plot.SemiParBIVProbit.Rd          |    4 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/predict.SemiParBIVProbit.Rd       |   10 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/print.summary.SemiParBIVProbit.Rd |    2 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/summary.SemiParBIVProbit.Rd       |   16 
 SemiParBIVProbit-3.2-12/SemiParBIVProbit/man/working.comp.Rd                   |    2 
 58 files changed, 1694 insertions(+), 1392 deletions(-)

More information about SemiParBIVProbit at CRAN
Permanent link

Package R.devices updated to version 2.12.0 with previous version 2.11.0 dated 2014-09-02

Title: Unified handling of graphics devices
Description: This package provides functions for creating plots and image files in a unified way regardless of output format (EPS, PDF, PNG, SVG, TIFF, WMF, etc.). Default device options as well as scales and aspect ratios are controlled in a uniform way across all device types. Switching output format requires minimal changes in code. This package is ideal for large-scale batch processing, because it will never leave open graphics devices or incomplete image files behind, even on errors or user interrupts.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson

Diff between R.devices versions 2.11.0 dated 2014-09-02 and 2.12.0 dated 2014-10-17

 DESCRIPTION                          |   14 -
 MD5                                  |   56 ++++---
 NAMESPACE                            |   10 +
 NEWS                                 |   72 +++++++++
 R/DevEvalProduct.R                   |   79 +++++++---
 R/devEval.R                          |   25 ++-
 R/devNew.R                           |    7 
 R/devOptions.R                       |  158 ++++++++++++++++-----
 R/deviceUtils.R                      |  254 +++++++++++++++++++++++++++++++++--
 R/favicon.R                          |only
 R/toNNN.R                            |    2 
 R/withPar.R                          |   21 ++
 R/zzz.R                              |    3 
 build/vignette.rds                   |binary
 inst/doc/R.devices-overview.R        |    4 
 inst/doc/R.devices-overview.pdf      |binary
 inst/doc/R.devices-overview.tex.rsp  |   14 +
 man/DevEvalFileProduct.Rd            |    1 
 man/R.devices-package.Rd             |    2 
 man/devEval.Rd                       |    9 -
 man/devOptions.Rd                    |    9 -
 man/favicon.Rd                       |only
 man/getDataURI.DevEvalFileProduct.Rd |    9 -
 man/toNNN.Rd                         |   33 ++--
 man/withPar.Rd                       |    7 
 tests/DevEvalFileProduct.R           |    3 
 tests/dataURI.R                      |    4 
 tests/devAll.R                       |only
 tests/devOptions.R                   |only
 tests/withPar.R                      |   10 +
 vignettes/R.devices-overview.tex.rsp |   14 +
 31 files changed, 660 insertions(+), 160 deletions(-)

More information about R.devices at CRAN
Permanent link

New package segmag with initial version 1.2.2
Package: segmag
Type: Package
Version: 1.2.2
Date: 2014-10-06
Title: Determine Event Boundaries in Event Segmentation Experiments
Maintainer: Frank Papenmeier
Author: Frank Papenmeier [aut, cre], Konstantin Sering [ctb]
Authors@R: c(person("Frank","Papenmeier", role=c("aut","cre"), email="frank.papenmeier@uni-tuebingen.de"), person("Konstantin","Sering", role="ctb"))
Description: This package contains functions that help to determine event boundaries in event segmentation experiments by bootstrapping a critical segmentation magnitude under the null hypothesis that all key presses were randomly distributed across the experiment. Segmentation magnitude is defined as the sum of Gaussians centered at the times of the segmentation key presses performed by the participants. Within a participant, the maximum of the overlaid Gaussians is used to prevent an excessive influence of a single participant on the overall outcome (e.g. if a participant is pressing the key multiple times in succession). Further functions are included, such as plotting the results.
License: GPL (>= 3)
Suggests: testthat
Imports: Rcpp (>= 0.11.0)
LinkingTo: Rcpp
Packaged: 2014-10-06 15:55:49 UTC; fpapenmeier
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-10-17 10:30:45

More information about segmag at CRAN
Permanent link

Package CINOEDV updated to version 1.1 with previous version 1.0 dated 2014-07-05

Title: Co-Information based N-Order Epistasis Detector and Visualizer
Description: A package for detecting and visualizing high-order epistatic interactions
Author: Junliang Shang
Maintainer: Junliang Shang

Diff between CINOEDV versions 1.0 dated 2014-07-05 and 1.1 dated 2014-10-17

 DESCRIPTION         |    8 ++++----
 MD5                 |    4 ++--
 R/TestSNPNameFile.R |    4 ++--
 3 files changed, 8 insertions(+), 8 deletions(-)

More information about CINOEDV at CRAN
Permanent link

Thu, 16 Oct 2014

Package rplexos updated to version 0.10 with previous version 0.9.1 dated 2014-09-11

Title: Read and Analyze PLEXOS Solutions from R
Description: This package contains functions to efficiently convert PLEXOS solutions into SQLite databases and to extract information from those databases to perform analysis. It supports collation of solutions that may have divided into different time partitions, as well as the comparison across different scenarios.
Author: Eduardo Ibanez [aut, cre], National Renewable Energy Laboratory [cph]
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.9.1 dated 2014-09-11 and 0.10 dated 2014-10-16

 rplexos-0.10/rplexos/DESCRIPTION                   |   32 -
 rplexos-0.10/rplexos/LICENSE                       |    2 
 rplexos-0.10/rplexos/MD5                           |   30 -
 rplexos-0.10/rplexos/NAMESPACE                     |   13 
 rplexos-0.10/rplexos/R/RcppExports.R               |    4 
 rplexos-0.10/rplexos/R/auxiliary.R                 |   50 +
 rplexos-0.10/rplexos/R/globalVariables.R           |   12 
 rplexos-0.10/rplexos/R/help.R                      |    2 
 rplexos-0.10/rplexos/R/log_parser.R                |only
 rplexos-0.10/rplexos/R/plexos_open.R               |   40 +
 rplexos-0.10/rplexos/R/process_folder.R            |    2 
 rplexos-0.10/rplexos/R/process_solution.R          |  566 ++++++++++++---------
 rplexos-0.10/rplexos/R/query.R                     |  285 ++++++----
 rplexos-0.10/rplexos/man/is_sample_stats.Rd        |only
 rplexos-0.10/rplexos/man/query_log.Rd              |only
 rplexos-0.10/rplexos/man/query_master.Rd           |   10 
 rplexos-0.10/rplexos/src/RcppExports.cpp           |   16 
 rplexos-0.9.1/rplexos/src/expand_interval_data.cpp |only
 18 files changed, 654 insertions(+), 410 deletions(-)

More information about rplexos at CRAN
Permanent link

Package Rrdrand updated to version 0.1-10 with previous version 0.1-9 dated 2014-06-27

Title: Generate Physical Random Numbers on Intel CPUs with the RdRand instruction
Description: Make use of the physical random number accessed by the RdRand instruction in recent Intel CPUs (Ivy Bridge and later).
Author: Eiji NAKAMA , Junji NAKANO
Maintainer: Eiji NAKAMA

Diff between Rrdrand versions 0.1-9 dated 2014-06-27 and 0.1-10 dated 2014-10-16

 Changelog   |    1 +
 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 R/zzz.R     |    8 +++-----
 4 files changed, 11 insertions(+), 12 deletions(-)

More information about Rrdrand at CRAN
Permanent link

New package rivernet with initial version 1.0
Package: rivernet
Type: Package
Title: Read, Analyze and Plot River Networks
Version: 1.0
Date: 2014-10-16
Author: Peter Reichert
Maintainer: Peter Reichert
Description: Functions for reading, analysing and plotting river networks. For this package, river networks consist of sections and nodes with associated attributes, e.g. to characterise their morphological, chemical and biological state. The package provides functions to read this data from text files, to analyse the network structure and network paths and regions consisting of sections and nodes that fulfill prescribed criteria, and to plot the river network and associated properties.
License: GPL (>= 2)
LazyData: true
Packaged: 2014-10-16 07:39:29 UTC; reichert
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 23:51:16

More information about rivernet at CRAN
Permanent link

Package raster updated to version 2.3-10 with previous version 2.3-0 dated 2014-09-06

Title: raster: Geographic data analysis and modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut], Jacob van Etten [ctb], Matteo Mattiuzzi [ctb], Michael Sumner [ctb], Jonathan A. Greenberg [ctb], Oscar Perpinan Lamigueiro [ctb], Andrew Bevan [ctb], Etienne B. Racine [ctb], Ashton Shortridge [ctb]
Maintainer: Robert J. Hijmans

Diff between raster versions 2.3-0 dated 2014-09-06 and 2.3-10 dated 2014-10-16

 raster-2.3-0/raster/man/join.Rd                  |only
 raster-2.3-10/raster/ChangeLog                   |   12 
 raster-2.3-10/raster/DESCRIPTION                 |   14 -
 raster-2.3-10/raster/MD5                         |  285 +++++++++++------------
 raster-2.3-10/raster/R/AAAClasses.R              |    2 
 raster-2.3-10/raster/R/GDALtransient.R           |    1 
 raster-2.3-10/raster/R/addLayer.R                |    2 
 raster-2.3-10/raster/R/aggregate_sp.R            |   23 +
 raster-2.3-10/raster/R/alignExtent.R             |    1 
 raster-2.3-10/raster/R/as.array.R                |    2 
 raster-2.3-10/raster/R/as.logical.R              |    2 
 raster-2.3-10/raster/R/as.raster.R               |    2 
 raster-2.3-10/raster/R/bands.R                   |    2 
 raster-2.3-10/raster/R/bbox.R                    |    1 
 raster-2.3-10/raster/R/bind.R                    |   31 ++
 raster-2.3-10/raster/R/boundaries.R              |    2 
 raster-2.3-10/raster/R/boxplot.R                 |    2 
 raster-2.3-10/raster/R/buffer.R                  |    7 
 raster-2.3-10/raster/R/cellFromLine.R            |    2 
 raster-2.3-10/raster/R/cellFromPolygon.R         |    2 
 raster-2.3-10/raster/R/cellRowCol.R              |    2 
 raster-2.3-10/raster/R/cellsFromExtent.R         |    1 
 raster-2.3-10/raster/R/clearValues.R             |    2 
 raster-2.3-10/raster/R/compare_Logical.R         |    2 
 raster-2.3-10/raster/R/contour.R                 |    2 
 raster-2.3-10/raster/R/cover.R                   |    2 
 raster-2.3-10/raster/R/coverBrick.R              |    2 
 raster-2.3-10/raster/R/coverPolygons.R           |    2 
 raster-2.3-10/raster/R/cropSpatial.R             |    2 
 raster-2.3-10/raster/R/cut.R                     |    2 
 raster-2.3-10/raster/R/dataProperties.R          |    2 
 raster-2.3-10/raster/R/dataType.R                |    2 
 raster-2.3-10/raster/R/direction.R               |    2 
 raster-2.3-10/raster/R/distance.R                |    2 
 raster-2.3-10/raster/R/distanceFromPoints.R      |    2 
 raster-2.3-10/raster/R/distanceRows.R            |    2 
 raster-2.3-10/raster/R/drawPoly.R                |    1 
 raster-2.3-10/raster/R/drivers.R                 |    2 
 raster-2.3-10/raster/R/dropLayer.R               |    2 
 raster-2.3-10/raster/R/erase.R                   |   13 -
 raster-2.3-10/raster/R/extend.R                  |   53 ++--
 raster-2.3-10/raster/R/extent.R                  |   37 ++
 raster-2.3-10/raster/R/extentUnion.R             |    1 
 raster-2.3-10/raster/R/flip.R                    |    2 
 raster-2.3-10/raster/R/focal.R                   |    6 
 raster-2.3-10/raster/R/freq.R                    |    8 
 raster-2.3-10/raster/R/fullFileName.R            |    2 
 raster-2.3-10/raster/R/gdalFormats.R             |    2 
 raster-2.3-10/raster/R/getData.R                 |    2 
 raster-2.3-10/raster/R/getValuesRows.R           |    2 
 raster-2.3-10/raster/R/hdr.R                     |    2 
 raster-2.3-10/raster/R/hdrBIL.R                  |    2 
 raster-2.3-10/raster/R/hdrBov.R                  |    2 
 raster-2.3-10/raster/R/hdrEnvi.R                 |    2 
 raster-2.3-10/raster/R/hdrErdasRaw.R             |    2 
 raster-2.3-10/raster/R/hdrIDRISI.R               |    2 
 raster-2.3-10/raster/R/hdrPRJ.R                  |    2 
 raster-2.3-10/raster/R/hdrSAGA.R                 |    2 
 raster-2.3-10/raster/R/hdrVRT.R                  |    2 
 raster-2.3-10/raster/R/hdrWorldFile.R            |    2 
 raster-2.3-10/raster/R/head.R                    |    2 
 raster-2.3-10/raster/R/index.R                   |   13 -
 raster-2.3-10/raster/R/indexReplace.R            |    2 
 raster-2.3-10/raster/R/inifile.R                 |    1 
 raster-2.3-10/raster/R/init.R                    |   41 ++-
 raster-2.3-10/raster/R/intDataType.R             |    2 
 raster-2.3-10/raster/R/intersect_sp.R            |    6 
 raster-2.3-10/raster/R/is.na.R                   |    2 
 raster-2.3-10/raster/R/isLonLat.R                |    2 
 raster-2.3-10/raster/R/localFun.R                |only
 raster-2.3-10/raster/R/makeProjString.R          |    2 
 raster-2.3-10/raster/R/makeRasterList.R          |    2 
 raster-2.3-10/raster/R/ncell.R                   |    2 
 raster-2.3-10/raster/R/netCDFtoStack.R           |    2 
 raster-2.3-10/raster/R/netCDFutil.R              |   35 ++
 raster-2.3-10/raster/R/newPLot.R                 |    2 
 raster-2.3-10/raster/R/nlayers.R                 |    2 
 raster-2.3-10/raster/R/notused.R                 |    2 
 raster-2.3-10/raster/R/origin.R                  |    2 
 raster-2.3-10/raster/R/overlay.R                 |    2 
 raster-2.3-10/raster/R/persp.R                   |    2 
 raster-2.3-10/raster/R/plotRaster.R              |    2 
 raster-2.3-10/raster/R/plotRaster2.R             |    2 
 raster-2.3-10/raster/R/predict.R                 |    2 
 raster-2.3-10/raster/R/print.R                   |   15 -
 raster-2.3-10/raster/R/progressBar.R             |    2 
 raster-2.3-10/raster/R/properties.R              |    2 
 raster-2.3-10/raster/R/rasterFromASCII.R         |    2 
 raster-2.3-10/raster/R/rasterFromBIL.R           |    2 
 raster-2.3-10/raster/R/rasterFromCells.R         |    2 
 raster-2.3-10/raster/R/rasterFromSAGA.R          |    2 
 raster-2.3-10/raster/R/rasterFromSurferFile.R    |    2 
 raster-2.3-10/raster/R/rasterOptions.R           |    2 
 raster-2.3-10/raster/R/rasterToPolygons.R        |    2 
 raster-2.3-10/raster/R/rasterize.R               |    2 
 raster-2.3-10/raster/R/rasterizeLines.R          |    2 
 raster-2.3-10/raster/R/rasterizePolygons.R       |  124 +++-------
 raster-2.3-10/raster/R/rasterizePolygons3.R      |    2 
 raster-2.3-10/raster/R/replaceProperties.R       |   26 +-
 raster-2.3-10/raster/R/resolution.R              |    2 
 raster-2.3-10/raster/R/rotate.R                  |    8 
 raster-2.3-10/raster/R/roundExtent.R             |    2 
 raster-2.3-10/raster/R/rowMinMax.R               |   14 -
 raster-2.3-10/raster/R/sampleInt.R               |    2 
 raster-2.3-10/raster/R/sampleRandom.R            |    6 
 raster-2.3-10/raster/R/sampleRegular.R           |  129 +++++-----
 raster-2.3-10/raster/R/setFileExt.R              |    2 
 raster-2.3-10/raster/R/setValues.R               |    2 
 raster-2.3-10/raster/R/shp.R                     |   10 
 raster-2.3-10/raster/R/stackApply.R              |    2 
 raster-2.3-10/raster/R/stackFile.R               |    2 
 raster-2.3-10/raster/R/stackSelect.R             |    2 
 raster-2.3-10/raster/R/subs.R                    |    2 
 raster-2.3-10/raster/R/tmpFile.R                 |   11 
 raster-2.3-10/raster/R/transpose.R               |    2 
 raster-2.3-10/raster/R/union_sp.R                |   40 ---
 raster-2.3-10/raster/R/unstack.R                 |    2 
 raster-2.3-10/raster/R/validCell.R               |    2 
 raster-2.3-10/raster/R/values.R                  |    2 
 raster-2.3-10/raster/R/which.R                   |    2 
 raster-2.3-10/raster/R/which.max.R               |   41 ++-
 raster-2.3-10/raster/R/writeAllRaster.R          |    2 
 raster-2.3-10/raster/R/writeStartStop.R          |    2 
 raster-2.3-10/raster/R/writeStartStopAscii.R     |    2 
 raster-2.3-10/raster/R/writeStartStopRaster.R    |    2 
 raster-2.3-10/raster/R/xyMinMax.R                |    2 
 raster-2.3-10/raster/R/xyResolution.R            |    2 
 raster-2.3-10/raster/R/zoom.R                    |    2 
 raster-2.3-10/raster/inst/doc/Raster.pdf         |binary
 raster-2.3-10/raster/inst/doc/functions.pdf      |binary
 raster-2.3-10/raster/inst/doc/rasterfile.pdf     |binary
 raster-2.3-10/raster/inst/external/countries.csv |   10 
 raster-2.3-10/raster/man/animate.Rd              |    2 
 raster-2.3-10/raster/man/bind.Rd                 |only
 raster-2.3-10/raster/man/boundaries.Rd           |    3 
 raster-2.3-10/raster/man/buffer.Rd               |   17 -
 raster-2.3-10/raster/man/corLocal.Rd             |    2 
 raster-2.3-10/raster/man/extractIndex.Rd         |    3 
 raster-2.3-10/raster/man/init.Rd                 |   23 -
 raster-2.3-10/raster/man/localFun.Rd             |only
 raster-2.3-10/raster/man/pointdistance.Rd        |    2 
 raster-2.3-10/raster/man/raster-package.Rd       |    1 
 raster-2.3-10/raster/man/rasterize.Rd            |    6 
 raster-2.3-10/raster/man/replacement.Rd          |    1 
 raster-2.3-10/raster/man/sampleRegular.Rd        |    8 
 raster-2.3-10/raster/src/minmax.c                |only
 146 files changed, 741 insertions(+), 538 deletions(-)

More information about raster at CRAN
Permanent link

Package PtProcess updated to version 3.3-7 with previous version 3.3-6 dated 2014-08-20

Title: Time Dependent Point Process Modelling
Description: This package fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte

Diff between PtProcess versions 3.3-6 dated 2014-08-20 and 3.3-7 dated 2014-10-16

 DESCRIPTION            |   10 +++++-----
 MD5                    |   14 ++++++++------
 NAMESPACE              |    4 +++-
 R/logLik.mpp.R         |    4 ++--
 R/makeSOCKcluster.R    |only
 man/Changes.Rd         |    6 ++++++
 man/logLik.Rd          |   11 +++++++----
 man/makeSOCKcluster.Rd |only
 man/neglogLik.Rd       |    2 +-
 9 files changed, 32 insertions(+), 19 deletions(-)

More information about PtProcess at CRAN
Permanent link

Package gsg updated to version 2.0 with previous version 1.0 dated 2012-12-21

Title: Calculation of selection coefficients
Description: gsg (gam selection gradients) provides a unified approach to the regression analysis of selection from longitudinal data collected from natural populations.
Author: Michael Morrissey, Krzysztof Sakrejda
Maintainer: Michael Morrissey

Diff between gsg versions 1.0 dated 2012-12-21 and 2.0 dated 2014-10-16

 DESCRIPTION                  |   15 ++++++------
 MD5                          |   30 +++++++++++++++++--------
 NAMESPACE                    |    8 ++++--
 R/finite.dif.R               |only
 R/fitness.landscape.R        |    8 ++++--
 R/fitness.landscape2.R       |only
 R/gam.gradients.R            |   50 +++++++++++++++++++++++++++++++++++++------
 R/gppr.R                     |only
 R/gppr.gradients.R           |only
 R/predict.gppr.R             |only
 data/SoayLambs.RData         |only
 inst/doc/gsg_notes.pdf       |binary
 man/SoayLambs.Rd             |only
 man/fitness.landscape.Rd     |    2 -
 man/gam.gradients.Rd         |    2 -
 man/gppr.Rd                  |only
 man/gppr.gradients.Rd        |only
 man/gsg-package.Rd           |    4 ++-
 man/humanNeonatal.Rd         |    2 -
 man/moments.differentials.Rd |    2 -
 man/predict.gppr.Rd          |only
 21 files changed, 88 insertions(+), 35 deletions(-)

More information about gsg at CRAN
Permanent link

New package enigma with initial version 0.1.0
Package: enigma
Title: R Client for the Enigma API
Description: Enigma (https://enigma.io) holds many public datasets from governments, companies, universities, and organizations. Enigma provides an API for data, metadata, and statistics on each of the datasets. enigma is an R client to interact with the Enigma API, including getting the data and metadata for datasets in Enigma, as well as collecting statistics on datasets. In addition, you can download a gzipped csv file of a dataset if you want the whole dataset. An API key from Enigma is required to use enigma.
Version: 0.1.0
Date: 2014-10-16
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"))
License: MIT + file LICENSE
LazyData: true
Imports: httr, jsonlite, plyr
Suggests: testthat
Packaged: 2014-10-16 21:25:40 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-17 00:42:42

More information about enigma at CRAN
Permanent link

Package stochvol updated to version 0.9-0 with previous version 0.8-4 dated 2014-07-01

Title: Efficient Bayesian Inference for Stochastic Volatility (SV) Models
Description: This package provides efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods.
Author: Gregor Kastner [aut, cre]
Maintainer: Gregor Kastner

Diff between stochvol versions 0.8-4 dated 2014-07-01 and 0.9-0 dated 2014-10-16

 stochvol-0.8-4/stochvol/man/DOTsvsample.Rd                          |only
 stochvol-0.8-4/stochvol/vignettes/extrafig/predlik2.pdf             |only
 stochvol-0.9-0/stochvol/DESCRIPTION                                 |   12 
 stochvol-0.9-0/stochvol/MD5                                         |   48 
 stochvol-0.9-0/stochvol/NAMESPACE                                   |    5 
 stochvol-0.9-0/stochvol/NEWS                                        |   29 
 stochvol-0.9-0/stochvol/R/wrapper.R                                 |    8 
 stochvol-0.9-0/stochvol/R/zzz.R                                     |only
 stochvol-0.9-0/stochvol/build/vignette.rds                          |binary
 stochvol-0.9-0/stochvol/data/exrates.RData                          |binary
 stochvol-0.9-0/stochvol/inst/doc/article.R                          |  312 +++-
 stochvol-0.9-0/stochvol/inst/doc/article.Rnw                        |  625 ++++++----
 stochvol-0.9-0/stochvol/inst/doc/article.pdf                        |binary
 stochvol-0.9-0/stochvol/man/predict.svdraws.Rd                      |    2 
 stochvol-0.9-0/stochvol/man/stochvol-package.Rd                     |    4 
 stochvol-0.9-0/stochvol/man/svsample.Rd                             |    6 
 stochvol-0.9-0/stochvol/man/svsample2.Rd                            |only
 stochvol-0.9-0/stochvol/man/svsim.Rd                                |    2 
 stochvol-0.9-0/stochvol/man/updatesummary.Rd                        |    6 
 stochvol-0.9-0/stochvol/src/sampler.cpp                             |   13 
 stochvol-0.9-0/stochvol/vignettes/article.Rnw                       |  625 ++++++----
 stochvol-0.9-0/stochvol/vignettes/extrafig/predlik1.pdf             |binary
 stochvol-0.9-0/stochvol/vignettes/extrafig/predlik3.pdf             |binary
 stochvol-0.9-0/stochvol/vignettes/macros.tex                        |    6 
 stochvol-0.9-0/stochvol/vignettes/mybib.bib                         |   36 
 stochvol-0.9-0/stochvol/vignettes/vignette_sampling_draws2.RData    |binary
 stochvol-0.9-0/stochvol/vignettes/vignette_sampling_realworld.RData |binary
 27 files changed, 1156 insertions(+), 583 deletions(-)

More information about stochvol at CRAN
Permanent link

Package StMoSim updated to version 3.0 with previous version 2.2 dated 2012-11-16

Title: Plots a QQ-Norm Plot with several Gaussian simulations.
Description: Plots a QQ-Norm Plot with several Gaussian simulations.
Author: Matthias Salvisberg
Maintainer: Matthias Salvisberg

Diff between StMoSim versions 2.2 dated 2012-11-16 and 3.0 dated 2014-10-16

 DESCRIPTION            |   18 +++++++++---------
 MD5                    |   13 ++++++++-----
 NAMESPACE              |   11 +++++++----
 R/RcppExports.R        |only
 R/qqnormSim.R          |   46 +++++++++++++++++++++-------------------------
 man/StMoSim-package.Rd |   42 +++++++++++++++++++++++++++++++++++-------
 man/qqnormSim.Rd       |   23 ++++++++++++++++++-----
 src                    |only
 8 files changed, 98 insertions(+), 55 deletions(-)

More information about StMoSim at CRAN
Permanent link

New package statar with initial version 0.1
Package: statar
Title: Tools Inspired by Stata to Clean, Explore and Join Datasets
Version: 0.1
Authors@R: person("Matthieu","Gomez", email = "mattg@princeton.edu", role = c("aut", "cre"))
Description: statar includes a set of functions for vectors: mode, tag, bin and winsorize. statar includes a set of functions for data.tables: summarize (in tables or graphs), panel data operations (lag, fill in gaps, fill in missing values) and SQL-type joins.
License: GPL-2
URL: https://github.com/matthieugomez/statar
BugReports: https://github.com/matthieugomez/statar/issues
Depends: R (>= 3.1.0)
Imports: data.table, dplyr (>= 0.3), ggplot2, grid, Hmisc, lazyeval, lubridate, matrixStats, stringr, tidyr
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-10-16 15:26:12 UTC; Matthieu
Author: Matthieu Gomez [aut, cre]
Maintainer: Matthieu Gomez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 22:56:33

More information about statar at CRAN
Permanent link

Package seedy updated to version 1.0 with previous version 0.2 dated 2014-09-13

Title: Simulation of Evolutionary and Epidemiological Dynamics
Description: Suite of functions for the simulation, visualisation and analysis of bacterial evolution within- and between-host.
Author: Colin Worby
Maintainer: Colin Worby

Diff between seedy versions 0.2 dated 2014-09-13 and 1.0 dated 2014-10-16

 seedy-0.2/seedy/R/plotsnpfreq.R         |only
 seedy-1.0/seedy/DESCRIPTION             |   10 +++----
 seedy-1.0/seedy/MD5                     |   18 ++++++++-----
 seedy-1.0/seedy/R/gd.R                  |   28 +++++++++++---------
 seedy-1.0/seedy/R/librtoDNA.R           |   16 +++++------
 seedy-1.0/seedy/R/plotobservedsnps.R    |only
 seedy-1.0/seedy/R/plotsnpfreq.r         |only
 seedy-1.0/seedy/R/transroutes.r         |only
 seedy-1.0/seedy/data/transmission.rda   |only
 seedy-1.0/seedy/man/plotobservedsnps.Rd |only
 seedy-1.0/seedy/man/plotsnpfreq.Rd      |   44 +++++++++-----------------------
 seedy-1.0/seedy/man/seedy-package.Rd    |    4 +-
 seedy-1.0/seedy/man/transmission.Rd     |only
 seedy-1.0/seedy/man/transroutes.Rd      |only
 14 files changed, 56 insertions(+), 64 deletions(-)

More information about seedy at CRAN
Permanent link

Package R2GUESS updated to version 1.4 with previous version 1.3 dated 2014-03-24

Title: Wrapper functions for GUESS
Description: Wrapper functions for GUESS, a GPU-enabled sparse Bayesian variable selection method for linear regression based analysis of possibly multivariate/correlated outcomes.
Author: Gianluca Campanella [cre], Benoit Liquet [aut], Marc Chadeau-Hyam [aut], Leonardo Bottolo [ctb], Sylvia Richardson [ctb]
Maintainer: Gianluca Campanella

Diff between R2GUESS versions 1.3 dated 2014-03-24 and 1.4 dated 2014-10-16

 DESCRIPTION                                                   |   26 ++++----
 MD5                                                           |   27 ++++-----
 R/Postprocess.R2GUESS.R                                       |   19 +++++-
 R/R2GUESS.R                                                   |   30 ++++++++--
 R/R2GUESS.perm.R                                              |    8 +-
 R/Resume.R2GUESS.R                                            |   14 ++--
 R/plotMPPI.R                                                  |   10 ++-
 cleanup                                                       |    2 
 inst/Output/Example-GUESS-Y-Hopx_output_marg_prob_incl_mc.txt |only
 man/Analysis.permutation.Rd                                   |    2 
 man/FDR.permutation.Rd                                        |    2 
 man/Postprocess.R2GUESS.Rd                                    |    2 
 man/R2GUESS.Rd                                                |    2 
 man/Resume.R2GUESS.Rd                                         |    2 
 man/plotMPPI.Rd                                               |   14 +++-
 15 files changed, 101 insertions(+), 59 deletions(-)

More information about R2GUESS at CRAN
Permanent link

Package NPCirc updated to version 2.0.1 with previous version 2.0.0 dated 2013-10-23

Title: Nonparametric Circular Methods
Description: This package implements nonparametric smoothing methods for circular data.
Author: Mara Oliveira, Rosa M. Crujeiras and Alberto Rodrguez-Casal
Maintainer: Mara Oliveira

Diff between NPCirc versions 2.0.0 dated 2013-10-23 and 2.0.1 dated 2014-10-16

 DESCRIPTION                      |    9 +++++----
 MD5                              |   34 ++++++++++++++++++----------------
 NEWS                             |only
 inst                             |only
 man/NPCirc-package.Rd            |   11 +++++++----
 man/bw.CV.Rd                     |    3 +++
 man/bw.boot.Rd                   |    3 +++
 man/bw.pi.Rd                     |    3 +++
 man/bw.reg.circ.lin.Rd           |    2 ++
 man/bw.rt.Rd                     |    3 +++
 man/circsizer.density.Rd         |    7 +++++--
 man/circsizer.map.Rd             |   11 ++++-------
 man/circsizer.regression.Rd      |    7 +++++--
 man/dcircmix.Rd                  |    3 +++
 man/kern.den.circ.Rd             |    3 +++
 man/kern.reg.circ.lin.Rd         |    3 +++
 man/lines.regression.circular.Rd |    5 +++++
 man/plot.regression.circular.Rd  |    5 +++++
 man/speed.wind.Rd                |    4 ++--
 19 files changed, 79 insertions(+), 37 deletions(-)

More information about NPCirc at CRAN
Permanent link

New package RCMIP5 with initial version 1.0
Package: RCMIP5
Title: Tools for Manipulating and Summarizing CMIP5 Data
Description: Working with CMIP5 data can be tricky, forcing scientists to write custom scripts and programs. The `RCMIP5` package aims to ease this process, providing a standard, robust, and high-performance set of scripts to (i) explore what data have been downloaded, (ii) identify missing data, (iii) average (or apply other mathematical operations) across experimental ensembles, (iv) produce both temporal and spatial statistical summaries, (v) regrid data, and (vi) produce easy-to-work-with graphical and data summaries.
Imports: abind (>= 1.4-0), plyr (>= 1.8.1), reshape2 (>= 1.4), foreach (>= 1.4.2), digest
Depends: R (>= 2.11.0)
Suggests: ggplot2 (>= 0.9.3), ncdf4 (>= 1.9), ncdf (>= 1.6), doParallel (>= 1.0.8), fields(>= 7.1), testthat (>= 0.9), knitr
Version: 1.0
Authors@R: c( person("Ben", "Bond-Lamberty", role = c("aut")), person("Kathe", "Todd-Brown", role = c("aut", "cre"), email = "ktoddbrown@gmail.com") )
License: MIT + file LICENSE
VignetteBuilder: knitr
Packaged: 2014-10-15 03:07:51 UTC; ben
Author: Ben Bond-Lamberty [aut], Kathe Todd-Brown [aut, cre]
Maintainer: Kathe Todd-Brown
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-16 14:03:50

More information about RCMIP5 at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.