Fri, 18 Apr 2014

Package AnthropMMD updated to version 0.9.9 with previous version 0.9.8 dated 2014-01-29

Title: A GUI for Mean Measures of Divergence
Description: Offers a complete and interactive GUI to work out Mean Measures of Divergence, especially for anthropologists.
Author: Frederic Santos
Maintainer: Frederic Santos

Diff between AnthropMMD versions 0.9.8 dated 2014-01-29 and 0.9.9 dated 2014-04-18

 DESCRIPTION               |   10 ++---
 MD5                       |   12 +++---
 NAMESPACE                 |    2 -
 R/AnaSettings.R           |    2 -
 R/StartMMD.R              |   84 ++++++++++++++++++++++++----------------------
 man/AnthropMMD-package.Rd |    6 +--
 man/StartMMD.Rd           |    1 
 7 files changed, 62 insertions(+), 55 deletions(-)

More information about AnthropMMD at CRAN
Permanent link

Package rbundler (with last version 0.3.6) was removed from CRAN

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

2014-02-25 0.3.6

Permanent link
Package segmented updated to version 0.3-1.0 with previous version 0.3-0.0 dated 2013-11-18

Title: Segmented relationships in regression models with breakpoints/changepoints estimation
Description: Given a (generalized) linear model, segmented `updates' the model by adding one or more segmented relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo

Diff between segmented versions 0.3-0.0 dated 2013-11-18 and 0.3-1.0 dated 2014-04-18

 DESCRIPTION              |    8 +--
 MD5                      |   34 ++++++------
 NEWS                     |   16 ++++--
 R/broken.line.r          |  123 ++++++++++++++++++++++++++++++++++-------------
 R/davies.test.r          |   16 +++---
 R/plot.segmented.R       |   54 ++++++++++++++------
 R/predict.segmented.r    |   82 ++++++++++---------------------
 R/seg.glm.fit.boot.r     |    2 
 R/seg.glm.fit.r          |    2 
 R/segmented.glm.R        |  102 +++++++++++++++++++++++++-------------
 R/segmented.lm.R         |   80 +++++++++++++++++++-----------
 data/down.rda            |binary
 data/plant.rda           |binary
 data/stagnant.rda        |binary
 man/broken.line.Rd       |   36 ++++++++-----
 man/plot.segmented.Rd    |   12 ++--
 man/predict.segmented.Rd |   10 +--
 man/segmented-package.Rd |    4 -
 18 files changed, 355 insertions(+), 226 deletions(-)

More information about segmented at CRAN
Permanent link

Package clogitL1 updated to version 1.3 with previous version 1.2 dated 2014-04-09

Title: Fitting exact conditional logistic regression with lasso and elastic net penalties.
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
Author: Stephen Reid and Robert Tibshirani
Maintainer: Stephen Reid

Diff between clogitL1 versions 1.2 dated 2014-04-09 and 1.3 dated 2014-04-18

 DESCRIPTION             |    6 +++---
 MD5                     |    8 ++++----
 man/clogitL1-package.Rd |    2 +-
 src/clogisticl1_5.cpp   |    4 +++-
 src/clogisticl1_5cv.cpp |    5 +++--
 5 files changed, 14 insertions(+), 11 deletions(-)

More information about clogitL1 at CRAN
Permanent link

Package WMTregions (with last version 3.2.6) was removed from CRAN

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

2013-02-28 3.2.6
2012-05-16 3.2.5
2012-02-02 3.2.4
2011-11-02 3.1.0.2
2011-07-25 3.1.0.1
2010-11-30 2.5.4
2010-11-03 2.3.10
2010-10-21 2.3.9

Permanent link
Package StochaTR (with last version 1.0.4) was removed from CRAN

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

2011-11-03 1.0.4
2011-11-02 1.0.3

Permanent link
Package spcr updated to version 1.1 with previous version 1.0 dated 2014-04-01

Title: Sparse principal component regression
Description: This package computes the sparse principal component regression. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano

Diff between spcr versions 1.0 dated 2014-04-01 and 1.1 dated 2014-04-18

 DESCRIPTION |   10 +++++-----
 MD5         |    4 ++--
 R/spcr.R    |    2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

More information about spcr at CRAN
Permanent link

Package regRSM updated to version 0.4 with previous version 0.3 dated 2014-02-19

Title: Random Subspace Method (RSM) for linear regression.
Description: Performs Random Subspace Method (RSM) for high-dimensional linear regression to obtain variable importance measures. The final model is chosen based on validation set or Generalized Information Criterion.
Author: Pawel Teisseyre, Robert A. Klopotek
Maintainer: Pawel Teisseyre

Diff between regRSM versions 0.3 dated 2014-02-19 and 0.4 dated 2014-04-18

 DESCRIPTION            |    8 ++++----
 MD5                    |   24 ++++++++++++------------
 NAMESPACE              |    1 +
 R/parallelRSM.R        |   21 +++++++++++++++++----
 R/regRSM.r             |   24 ++++++++++++++++++++----
 man/ImpPlot.regRSM.Rd  |    2 +-
 man/plot.regRSM.Rd     |    8 ++++----
 man/predict.regRSM.Rd  |    2 +-
 man/print.regRSM.rd    |    2 +-
 man/regRSM.Rd          |   24 +++++++++++++++++++-----
 man/roc.regRSM.rd      |    2 +-
 man/summary.regRSM.rd  |    2 +-
 man/validate.regRSM.rd |    2 +-
 13 files changed, 83 insertions(+), 39 deletions(-)

More information about regRSM at CRAN
Permanent link

Package jsonlite updated to version 0.9.7 with previous version 0.9.6 dated 2014-04-05

Title: A smarter JSON encoder/decoder for R
Description: This package is a fork of the RJSONIO package by Duncan Temple Lang. It builds on the same libjson c++ parser, but implements a smarter mapping between JSON data and R classes. The vignette describes the behavior in great detail. In addition to drop-in replacements for toJSON and fromJSON, the package contains functions to serialize objects and many unit tests to make 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, Jonathan Wallace
Maintainer: Jeroen Ooms

Diff between jsonlite versions 0.9.6 dated 2014-04-05 and 0.9.7 dated 2014-04-18

 DESCRIPTION                     |    8 ++++----
 MD5                             |   23 ++++++++++++-----------
 NEWS                            |    7 +++++++
 R/fromJSON.R                    |    6 ++++--
 R/simplify.R                    |   31 ++++++++++++++++++++++++++++---
 R/simplifyDataFrame.R           |   20 ++++++++++++++------
 R/toJSON.R                      |    5 +++--
 build/vignette.rds              |binary
 inst/doc/json-mapping.pdf       |binary
 inst/tests/test-fromJSON-date.R |only
 inst/tests/test-libjson-utf8.R  |    4 ++--
 man/fromJSON.Rd                 |   10 ++++++++--
 src/rlibjson.c                  |    3 ++-
 13 files changed, 84 insertions(+), 33 deletions(-)

More information about jsonlite at CRAN
Permanent link

Package Bclim updated to version 2.3.1 with previous version 2.2 dated 2013-01-23

Title: Bayesian Palaeoclimate Reconstruction from Pollen
Description: This package takes pollen/time data from lake cores and produces a Bayesian posterior distribution of palaeoclimate from that location after fitting a non-linear non-Gaussian state-space model.
Author: Andrew Parnell, Thinh Doan and James Sweeney
Maintainer: Andrew Parnell

Diff between Bclim versions 2.2 dated 2013-01-23 and 2.3.1 dated 2014-04-18

 Bclim-2.2/Bclim/R/Bclim-internal.R     |only
 Bclim-2.2/Bclim/R/NIGB.R               |only
 Bclim-2.2/Bclim/R/NIGp3.R              |only
 Bclim-2.2/Bclim/man/NIGB.Rd            |only
 Bclim-2.2/Bclim/man/NIGp3.Rd           |only
 Bclim-2.3.1/Bclim/DESCRIPTION          |   18 -
 Bclim-2.3.1/Bclim/MD5                  |   50 +-
 Bclim-2.3.1/Bclim/NAMESPACE            |    5 
 Bclim-2.3.1/Bclim/R/BclimCompile.R     |    5 
 Bclim-2.3.1/Bclim/R/BclimInterp.R      |  326 ++++++++++---------
 Bclim-2.3.1/Bclim/R/BclimLayer.R       |    1 
 Bclim-2.3.1/Bclim/R/BclimMCMC.R        |   33 +
 Bclim-2.3.1/Bclim/R/BclimMixPar.R      |   35 --
 Bclim-2.3.1/Bclim/R/BclimMixSer.R      |   27 -
 Bclim-2.3.1/Bclim/R/plotBclim.R        |   37 +-
 Bclim-2.3.1/Bclim/R/plotBclimVol.R     |   36 +-
 Bclim-2.3.1/Bclim/R/zzz.R              |only
 Bclim-2.3.1/Bclim/man/Bclim-package.Rd |    4 
 Bclim-2.3.1/Bclim/man/BclimCompile.Rd  |    6 
 Bclim-2.3.1/Bclim/man/BclimLayer.Rd    |    6 
 Bclim-2.3.1/Bclim/man/BclimMCMC.Rd     |   31 +
 Bclim-2.3.1/Bclim/man/BclimMixPar.Rd   |    6 
 Bclim-2.3.1/Bclim/man/BclimMixSer.Rd   |    6 
 Bclim-2.3.1/Bclim/man/BclimRun.Rd      |    6 
 Bclim-2.3.1/Bclim/man/plotBclim.Rd     |    3 
 Bclim-2.3.1/Bclim/man/plotBclimVol.Rd  |   10 
 Bclim-2.3.1/Bclim/src/BclimMCMC3D.c    |  559 +++++++++++++++------------------
 Bclim-2.3.1/Bclim/src/use.c            |   35 +-
 Bclim-2.3.1/Bclim/src/use.h            |    1 
 29 files changed, 640 insertions(+), 606 deletions(-)

More information about Bclim at CRAN
Permanent link

Thu, 17 Apr 2014

Package gtools updated to version 3.4.0 with previous version 3.3.1 dated 2014-03-01

Title: Various R programming tools
Description: Various R programming tools
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes

Diff between gtools versions 3.3.1 dated 2014-03-01 and 3.4.0 dated 2014-04-17

 ChangeLog      |    5 +++++
 DESCRIPTION    |    8 ++++----
 MD5            |   14 ++++++++------
 NAMESPACE      |    1 +
 NEWS           |   10 ++++++++++
 R/ASCIIfy.R    |only
 inst/ChangeLog |    5 +++++
 inst/NEWS      |   10 ++++++++++
 man/ASCIIfy.Rd |only
 9 files changed, 43 insertions(+), 10 deletions(-)

More information about gtools at CRAN
Permanent link

New package WikipediR with initial version 0.5
Package: WikipediR
Type: Package
Title: A MediaWiki API wrapper
Version: 0.5
Date: 2014-04-13
Author: Oliver Keyes
Maintainer: Oliver Keyes
Description: WikipediR is a wrapper for the MediaWiki API, aimed particularly at the Wikimedia 'production' wikis, such as Wikipedia
License: MIT + file LICENSE
Depends: httr, jsonlite, methods
BugReports: https://github.com/Ironholds/WikipediR/issues
Classification/ACM: J.1
Packaged: 2014-04-17 17:55:16 UTC; ironholds
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-18 00:38:14

More information about WikipediR at CRAN
Permanent link

New package userfriendlyscience with initial version 0.1.1
Package: userfriendlyscience
Type: Package
Title: Userfriendlyscience: quantitative analysis made accessible
Version: 0.1.1
Date: 2014-02-25
Author: Gjalt-Jorn Peters
Maintainer: Gjalt-Jorn Peters
License: GPL (>= 2)
Description: This package contains a number of functions that serve two goals: first, make R more accessible to people migrating from SPSS by adding a number of functions that behave roughly like their SPSS equivalents; and second, make a number of slightly more advanced functions more userfriendly to relatively novice users.
URL: http://userfriendlyscience.com
Imports: lavaan, psych, GGally, pwr, plyr, grid, fBasics, e1071, ltm, MBESS, knitr, xtable, foreign
Depends: ggplot2
Packaged: 2014-04-17 16:18:32 UTC; micro_000
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-17 23:17:14

More information about userfriendlyscience at CRAN
Permanent link

New package ShrinkCovMat with initial version 1.0.0
Package: ShrinkCovMat
Type: Package
Title: Shrinkage Covariance Matrix Estimators
Version: 1.0.0
Date: 2014-04-17
Author: Anestis Touloumis
Maintainer: Anestis Touloumis
Description: This package provides nonparametric Stein-type 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.
License: GPL-2 | GPL-3
Depends: R (>= 2.10)
LazyLoad: yes
Packaged: 2014-04-17 14:20:12 UTC; toulou01
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-17 23:12:07

More information about ShrinkCovMat at CRAN
Permanent link

Package SEERaBomb updated to version 2014.4.1 with previous version 2013.4.3 dated 2013-12-12

Title: SEER Setup and Use with A-Bomb Data
Description: This package contains codes that setup SEER (Surveillance, Epidemiology and End Results) data use with R. It includes SEER and Japanese A-Bomb survivor data analysis examples. By using it, the portability of SEER R scripts should improve. This package works only with the latest SEER release of April 15, 2014.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch

Diff between SEERaBomb versions 2013.4.3 dated 2013-12-12 and 2014.4.1 dated 2014-04-17

 DESCRIPTION                                                |   12 
 MD5                                                        |   48 
 NAMESPACE                                                  |    3 
 NEWS                                                       |  129 -
 R/getFields.R                                              |   76 
 R/mkAbomb.R                                                |  124 -
 R/mkHema87.R                                               |   27 
 R/mkSEER.R                                                 |  105 -
 inst/doc/gettingData.pdf                                   |binary
 inst/doc/overview.pdf                                      |binary
 inst/doc/papers/JCO2013/MDSAMLsurvMF.R                     |  130 -
 inst/doc/papers/blood2012/blood2012fig4.R                  |   74 
 inst/doc/papers/blood2012/blood2012fig5a.R                 |   82 
 inst/doc/papers/blood2012/blood2012fig6.R                  |   66 
 inst/doc/papers/blood2012/dingliCMLFINAL3.R                |  534 ++---
 inst/doc/papers/blood2012/vIncidAPLCML.r                   |   96 -
 inst/doc/papers/radiatEnvironBiophys2013/SupplementSEER.R  | 1245 ++++++-------
 inst/doc/papers/radiatEnvironBiophys2013/supplementAbomb.R | 1038 +++++-----
 man/SEERaBomb-package.Rd                                   |   74 
 man/figures/SEERaBombFig.png                               |binary
 man/getFields.Rd                                           |   58 
 man/mkAbomb.Rd                                             |   44 
 man/mkHema87.Rd                                            |   42 
 man/mkSEER.Rd                                              |   79 
 man/pickFields.Rd                                          |   80 
 25 files changed, 2101 insertions(+), 2065 deletions(-)

More information about SEERaBomb at CRAN
Permanent link

Package poisson.glm.mix updated to version 1.2 with previous version 1.1 dated 2013-06-20

Title: Fit high dimensional mixtures of Poisson GLMs
Description: High dimensional mixtures of Poisson Generalized Linear models with three different parameterizations of Poisson means are considered. Moreover, partitioning the response variables into a set of blocks is possible. The package estimates parameters via EM algorithm. For an efficient initialization, a random splitting small-EM is introduced.
Author: Panagiotis Papastamoulis, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Panagiotis Papastamoulis

Diff between poisson.glm.mix versions 1.1 dated 2013-06-20 and 1.2 dated 2014-04-17

 DESCRIPTION      |   18 ++++++------------
 MD5              |    4 ++--
 R/pois.glm.mix.R |   35 +++++++++++++++++++++++++++++++----
 3 files changed, 39 insertions(+), 18 deletions(-)

More information about poisson.glm.mix at CRAN
Permanent link

Package mvtnorm updated to version 0.9-9999 with previous version 0.9-9998 dated 2014-04-09

Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch, Fabian Scheipl, Bjoern Bornkamp, Torsten Hothorn
Maintainer: Torsten Hothorn

Diff between mvtnorm versions 0.9-9998 dated 2014-04-09 and 0.9-9999 dated 2014-04-17

 DESCRIPTION                  |    8 ++++----
 MD5                          |   12 ++++++------
 R/mvnorm.R                   |   40 ++++++++++++++++++++++++----------------
 inst/doc/MVT_Rnews.pdf       |binary
 man/Mvnorm.Rd                |    3 ++-
 tests/bugfix-tests.R         |    2 ++
 tests/bugfix-tests.Rout.save |    9 ++++-----
 7 files changed, 42 insertions(+), 32 deletions(-)

More information about mvtnorm at CRAN
Permanent link

New package HSAUR3 with initial version 1.0-0
Package: HSAUR3
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Date: 2014-04-17
Version: 1.0-0
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
Description: Functions, data sets, analyses and examples from the third edition of the book `A Handbook of Statistical Analyses Using R' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled `An Introduction to R', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides).
URL: The publishers web page is http://www.crcpress.com/product/isbn/9781420079333
Depends: R (>= 3.0.0), tools
Suggests: boot (>= 1.3-9), lattice (>= 0.20-23), MASS (>= 7.3-29), mgcv (>= 1.7-27), rpart (>= 4.1-4), survival (>= 2.37-4), alr3 (>= 2.0.5), ape (>= 3.0-11), coin (>= 1.0-23), flexmix (>= 2.3-11), Formula (>= 1.1-1), gamair (>= 0.0.8), gamlss.data (>= 4.2.6), gee (>= 4.13-18), KernSmooth (>= 2.23-10), lme4 (>= 1.0-5), maps (>= 2.3-6), maptools (>= 0.8-27), mboost (>= 2.2-3), mclust (>= 4.2), mlbench (>= 2.1-1), mice (>= 2.18), multcomp (>= 1.3-1), mvtnorm (>= 0.9-9996), partykit (>= 0.8-0), quantreg (>= 5.05), randomForest (>= 4.6-7), rmeta (>= 2.16), sandwich (>= 2.3-0), scatterplot3d (>= 0.3-34), sp (>= 1.0-14), TH.data (>= 1.0-2), tm (>= 0.5-9.1), vcd (>= 1.3-1), wordcloud (>= 2.4)
LazyData: yes
License: GPL-2
Encoding: UTF-8
Packaged: 2014-04-17 10:31:57 UTC; hothorn
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-18 00:21:17

More information about HSAUR3 at CRAN
Permanent link

Package bayesQR updated to version 2.2 with previous version 2.1 dated 2013-02-18

Title: Bayesian quantile regression
Description: Bayesian quantile regression using the asymmetric Laplace distribution, both continuous as well as binary dependent variables are supported. The package consists of implementations of the methods of Yu & Moyeed (2001), Benoit & Van den Poel (2012) and Al-Hamzawi, Yu & Benoit (2012). To speed up the calculations, the Markov Chain Monte Carlo core of all algorithms is programmed in Fortran and called from R.
Author: Dries F. Benoit, Rahim Al-Hamzawi, Keming Yu, Dirk Van den Poel
Maintainer: Dries F. Benoit

Diff between bayesQR versions 2.1 dated 2013-02-18 and 2.2 dated 2014-04-17

 DESCRIPTION            |   18 ++++++------------
 MD5                    |   18 +++++++++---------
 R/plot.bayesQR.r       |   44 +++++++++++++++++++++++++++++++++++++++++---
 man/bayesQR.Rd         |    4 ++--
 man/plot.bayesQR.Rd    |   13 +++++++++----
 man/predict.bayesQR.Rd |    4 ++--
 src/QRb_AL_mcmc.f95    |    1 -
 src/QRb_mcmc.f95       |    3 +--
 src/QRc_AL_mcmc.f95    |    1 -
 src/QRc_mcmc.f95       |    3 +--
 10 files changed, 71 insertions(+), 38 deletions(-)

More information about bayesQR at CRAN
Permanent link

Package sjPlot updated to version 1.4.1 with previous version 1.3 dated 2014-03-27

Title: sjPlot - data visualization for statistics in social science
Description: Collection of several plotting / table output functions for visualizing data and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Luedecke

Diff between sjPlot versions 1.3 dated 2014-03-27 and 1.4.1 dated 2014-04-17

 DESCRIPTION                  |    9 
 MD5                          |  127 +-
 NAMESPACE                    |  165 +-
 NEWS                         |  546 ++++----
 R/sjImportSPSS.R             |  680 +++++-----
 R/sjPlotAnova.R              | 1397 +++++++++++-----------
 R/sjPlotClusterAnalysis.R    |   26 
 R/sjPlotCorr.R               |  960 +++++++--------
 R/sjPlotFrequencies.R        |   80 -
 R/sjPlotGroupFrequencies.R   | 2699 +++++++++++++++++++++----------------------
 R/sjPlotLikert.R             | 1540 ++++++++++++------------
 R/sjPlotLinreg.R             | 2377 ++++++++++++++++++-------------------
 R/sjPlotLinregMultiple.R     | 1156 +++++++++---------
 R/sjPlotOdds.R               | 1592 ++++++++++++-------------
 R/sjPlotOddsMultiple.R       | 1192 +++++++++---------
 R/sjPlotPropTable.R          | 1744 +++++++++++++--------------
 R/sjPlotScatter.R            |  906 +++++++-------
 R/sjPlotStackFrequencies.R   |   46 
 R/sjRecode.R                 | 2084 +++++++++++++++++----------------
 R/sjTabCorr.R                |  186 ++
 R/sjTabDataFrame.R           |  765 ++++++------
 R/sjTabFrequencies.R         |   40 
 R/sjTabItemAnalysis.R        |  759 ++++++------
 R/sjTabLinReg.R              | 1348 ++++++++++-----------
 R/sjTabOdds.R                | 1384 +++++++++++-----------
 R/sjTabPCA.R                 | 1210 +++++++++----------
 R/sjTabPropTable.R           | 1556 ++++++++++++------------
 R/sjTabSPSS.R                |  650 +++++-----
 R/sjTabStackFrq.R            | 1088 ++++++++---------
 man/sjPlot-package.Rd        |    7 
 man/sjc.cluster.Rd           |    8 
 man/sjc.qclus.Rd             |   36 
 man/sji.getValueLabels.Rd    |    3 
 man/sji.getVariableLabels.Rd |    3 
 man/sji.setValueLabels.Rd    |   27 
 man/sji.setVariableLabels.Rd |    5 
 man/sji.viewSPSS.Rd          |   43 
 man/sjp.aov1.Rd              |   14 
 man/sjp.corr.Rd              |    3 
 man/sjp.frq.Rd               |   30 
 man/sjp.glm.Rd               |   23 
 man/sjp.glm.ma.Rd            |    2 
 man/sjp.glmm.Rd              |   12 
 man/sjp.grpfrq.Rd            |  980 +++++++--------
 man/sjp.likert.Rd            |   12 
 man/sjp.lm.Rd                |  515 ++++----
 man/sjp.lm.ma.Rd             |   75 -
 man/sjp.lm1.Rd               |    2 
 man/sjp.lmm.Rd               |   12 
 man/sjp.reglin.Rd            |  197 +--
 man/sjp.scatter.Rd           |    8 
 man/sjp.stackfrq.Rd          |   38 
 man/sjp.xtab.Rd              |   57 
 man/sjt.corr.Rd              |  367 +++--
 man/sjt.df.Rd                |   21 
 man/sjt.frq.Rd               |   24 
 man/sjt.glm.Rd               |   17 
 man/sjt.itemanalysis.Rd      |  107 +
 man/sjt.lm.Rd                |   15 
 man/sjt.pca.Rd               |   16 
 man/sjt.stackfrq.Rd          |   20 
 man/sjt.xtab.Rd              |   24 
 man/sju.chi2.gof.Rd          |    3 
 man/sju.mic.Rd               |only
 man/sju.reliability.Rd       |    5 
 65 files changed, 15889 insertions(+), 15154 deletions(-)

More information about sjPlot at CRAN
Permanent link

Package seqDesign updated to version 1.0.1 with previous version 1.0.0 dated 2014-02-25

Title: Simulation and group sequential monitoring of randomized multi-arm two-stage Phase IIb/III treatment efficacy trials with time-to-event endpoints
Description: This package implements the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases), and applies generally to individual-randomized clinical trials with multiple active treatment groups and a shared placebo group, with a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment arm for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial outcomes (e.g., stopping early for efficacy futility); unconditional power for comparing treatment efficacy; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
Author: Michal Juraska and Doug Grove, with contributions from Xuesong Yu and Peter B. Gilbert
Maintainer: Michal Juraska

Diff between seqDesign versions 1.0.0 dated 2014-02-25 and 1.0.1 dated 2014-04-17

 seqDesign-1.0.0/seqDesign/inst/doc/seqDesignSampleReport.pdf     |only
 seqDesign-1.0.1/seqDesign/DESCRIPTION                            |    8 
 seqDesign-1.0.1/seqDesign/MD5                                    |   22 
 seqDesign-1.0.1/seqDesign/R/seqDesign.R                          |  822 ++--------
 seqDesign-1.0.1/seqDesign/build/vignette.rds                     |binary
 seqDesign-1.0.1/seqDesign/inst/doc/seqDesignInstructions.R       |    4 
 seqDesign-1.0.1/seqDesign/inst/doc/seqDesignInstructions.Rnw     |    6 
 seqDesign-1.0.1/seqDesign/inst/doc/seqDesignInstructions.pdf     |binary
 seqDesign-1.0.1/seqDesign/inst/extdata/seqDesignReport.Rnw       |  584 ++++++-
 seqDesign-1.0.1/seqDesign/inst/extdata/seqDesignReportSample.pdf |only
 seqDesign-1.0.1/seqDesign/man/VEpowerPP.Rd                       |   36 
 seqDesign-1.0.1/seqDesign/man/censTrial.Rd                       |    4 
 seqDesign-1.0.1/seqDesign/vignettes/seqDesignInstructions.Rnw    |    6 
 13 files changed, 798 insertions(+), 694 deletions(-)

More information about seqDesign at CRAN
Permanent link

Package rgbif updated to version 0.6.0 with previous version 0.5.0 dated 2014-02-16

Title: Interface to the Global Biodiversity Information Facility API
Description: A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre], Carl Boettiger [aut], Karthik Ram [aut], Vijay Barve [aut], Dan Mcglinn [aut]
Maintainer: Scott Chamberlain

Diff between rgbif versions 0.5.0 dated 2014-02-16 and 0.6.0 dated 2014-04-17

 DESCRIPTION                           |   12 -
 MD5                                   |  322 +++++++++++++++++++-----------
 NAMESPACE                             |    9 
 NEWS                                  |   27 ++
 R/check_wkt.r                         |only
 R/dataset_metrics.r                   |    7 
 R/dataset_search.r                    |    6 
 R/dataset_suggest.r                   |    9 
 R/datasets.r                          |    5 
 R/elevation.r                         |   21 +
 R/gist.r                              |    5 
 R/installations.r                     |    4 
 R/name_backbone.r                     |   62 +++--
 R/name_lookup.r                       |   34 +--
 R/name_suggest.r                      |   20 +
 R/name_usage.r                        |   32 ++-
 R/networks.r                          |    5 
 R/nodes.r                             |    5 
 R/occ_count.r                         |   51 ++--
 R/occ_get.r                           |   20 +
 R/occ_metadata.r                      |   14 -
 R/occ_search.r                        |  131 ++++++++----
 R/organizations.r                     |    5 
 R/parsenames.R                        |    6 
 R/rgbif-package.r                     |   12 +
 R/stylegeojson.r                      |    6 
 R/togeojson.r                         |    2 
 R/zzz.r                               |   45 ++--
 README.md                             |   32 +--
 data/typestatus.rda                   |only
 inst                                  |only
 man/blanktheme.Rd                     |    1 
 man/check_wkt.Rd                      |only
 man/commas_to_periods.Rd              |    3 
 man/count_facet.Rd                    |   13 -
 man/create_gist.Rd                    |   10 
 man/dataset_metrics.Rd                |   11 -
 man/dataset_search.Rd                 |  123 +++++------
 man/dataset_suggest.Rd                |   73 ++----
 man/datasetparser.Rd                  |    5 
 man/datasets.Rd                       |   23 +-
 man/density_spplist-deprecated.Rd     |   82 +++----
 man/densitylist-deprecated.Rd         |   49 ++--
 man/elevation.Rd                      |   27 +-
 man/gbif_capwords.Rd                  |   10 
 man/gbifdata-deprecated.Rd            |   27 +-
 man/gbifmap.Rd                        |   61 ++---
 man/gbifmap_dens-deprecated.Rd        |   61 ++---
 man/gbifmap_list-deprecated.Rd        |   61 ++---
 man/gbifparser.Rd                     |   11 -
 man/gbifparser_verbatim.Rd            |   11 -
 man/gbifxmlToDataFrame.Rd             |    8 
 man/get_credentials.Rd                |    1 
 man/gist.Rd                           |   30 +-
 man/installations.Rd                  |   51 ++--
 man/is.gbifdens-deprecated.Rd         |    3 
 man/is.gbiflist-deprecated.Rd         |    3 
 man/is.gbiflist_na-deprecated.Rd      |    3 
 man/isocodes.Rd                       |   11 -
 man/ldfast.Rd                         |    6 
 man/name_backbone.Rd                  |   69 +++---
 man/name_lookup.Rd                    |  211 +++++++++----------
 man/name_suggest.Rd                   |   29 +-
 man/name_usage.Rd                     |   88 ++++----
 man/namelkupparser.Rd                 |    6 
 man/networks.Rd                       |   35 +--
 man/nodes.Rd                          |   15 -
 man/occ_count.Rd                      |   61 ++---
 man/occ_get.Rd                        |   39 +--
 man/occ_metadata.Rd                   |   20 -
 man/occ_search.Rd                     |  362 +++++++++++++++++++---------------
 man/occurrencecount-deprecated.Rd     |  232 +++++++++------------
 man/occurrencedensity-deprecated.Rd   |    1 
 man/occurrenceget-deprecated.Rd       |   21 -
 man/occurrencelist-deprecated.Rd      |  267 ++++++++++---------------
 man/occurrencelist_all-deprecated.Rd  |   11 -
 man/occurrencelist_many-deprecated.Rd |  274 ++++++++++---------------
 man/organizations.Rd                  |   18 -
 man/parsenames.Rd                     |    8 
 man/parseresults.Rd                   |    7 
 man/print.gbifdens-deprecated.Rd      |    6 
 man/print.gbiflist-deprecated.Rd      |    6 
 man/print.gbiflist_na-deprecated.Rd   |    6 
 man/providers-deprecated.Rd           |   24 +-
 man/resources-deprecated.Rd           |   32 +--
 man/rgb_country_codes.Rd              |    8 
 man/rgbif-deprecated.Rd               |   29 +-
 man/rgbif.Rd                          |  112 +++++-----
 man/stylegeojson.Rd                   |   21 -
 man/suggestfields.Rd                  |    1 
 man/taxoncount-deprecated.Rd          |   11 -
 man/taxonget-deprecated.Rd            |    9 
 man/taxonsearch-deprecated.Rd         |   53 ++--
 man/taxrank.Rd                        |    5 
 man/togeojson.Rd                      |   46 +---
 man/typestatus.Rd                     |only
 tests/testthat/test-dataset_search.r  |    8 
 tests/testthat/test-dataset_suggest.r |    8 
 tests/testthat/test-datasets.r        |    3 
 tests/testthat/test-name_backbone.r   |   12 -
 tests/testthat/test-name_lookup.r     |    2 
 tests/testthat/test-name_suggest.r    |    4 
 tests/testthat/test-nodes.r           |    4 
 tests/testthat/test-occ_count.r       |    2 
 tests/testthat/test-occ_get.r         |   17 -
 tests/testthat/test-occ_metadata.r    |    6 
 tests/testthat/test-occ_search.r      |   73 ++++--
 tests/testthat/test-organizations.r   |    7 
 tests/testthat/test-stylegeojson.r    |    6 
 vignettes/figure                      |only
 vignettes/rgbif_vignette.Rmd          |   12 -
 vignettes/rgbif_vignette.html         |    9 
 vignettes/rgbif_vignette.md           |   12 -
 vignettes/rgbif_vignette.pdf          |binary
 vignettes/rgbif_vignette_oldapi.Rmd   |   38 +--
 vignettes/rgbif_vignette_oldapi.html  |   38 +--
 vignettes/rgbif_vignette_oldapi.md    |   38 +--
 vignettes/rgbif_vignette_oldapi.pdf   |binary
 118 files changed, 2158 insertions(+), 1971 deletions(-)

More information about rgbif at CRAN
Permanent link

Package PBD updated to version 0.9 with previous version 0.8 dated 2014-04-01

Title: Protracted birth-death model of diversification
Description: Maximum likelihood analysis of the protracted speciation model
Author: Rampal S. Etienne
Maintainer: Rampal S. Etienne

Diff between PBD versions 0.8 dated 2014-04-01 and 0.9 dated 2014-04-17

 DESCRIPTION        |    8 ++++----
 MD5                |    6 +++---
 R/pbd_loglik.R     |   10 +++++++---
 man/PBD-package.Rd |   11 ++++++++---
 4 files changed, 22 insertions(+), 13 deletions(-)

More information about PBD at CRAN
Permanent link

New package MSQC with initial version 1.0.1
Package: MSQC
Type: Package
Title: Multivariate Statistical Quality Control
Version: 1.0.1
Date: 2014-04-17
Author: Edgar Santos-Fernandez
Maintainer: Edgar Santos-Fernandez
Depends: rgl
Description: This package is a toolkit for multivariate process monitoring. It contains the main alternatives of multivariate control chart such as: Hotelling, Chi squared, MEWMA, MCUSUM and Generelized Variance control chart. Also, it includes some tools for assessing multivariate normality like: Mardia, Royston and Henze Zirkler test and the univariate D'Agostino test. Moreover, it possess ten didactic datasets.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-04-16 23:55:48 UTC; esantosf
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-17 18:28:39

More information about MSQC at CRAN
Permanent link

New package ATmet with initial version 1.2
Package: ATmet
Type: Package
Title: Advanced Tools for Metrology
Version: 1.2
Date: 2014-01-06
Author: S.Demeyer, A.Allard
Maintainer: Alexandre Allard
Depends: R (>= 2.7.0), DiceDesign, lhs, metRology, msm, sensitivity
Description: This package provides functions for smart sampling and sensitivity analysis for metrology applications, including computationally expensive problems.
License: GPL-3
Packaged: 2014-04-17 09:21:13 UTC; ALLARD
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-17 19:04:39

More information about ATmet at CRAN
Permanent link

Wed, 16 Apr 2014

Package VAR.etp updated to version 0.2 with previous version 0.1 dated 2014-04-14

Title: VAR modelling: estimation, testing, and prediction
Description: Estimation, Hypothesis Testing, Prediction for Stationary Vector Autoregressive Models
Author: Jae. H. Kim
Maintainer: Jae H. Kim

Diff between VAR.etp versions 0.1 dated 2014-04-14 and 0.2 dated 2014-04-16

 DESCRIPTION            |    8 ++++----
 MD5                    |   24 +++++++++++++-----------
 R/VAR.LRtest.R         |    6 +++---
 R/VAR.Rest.R           |    2 +-
 R/VAR1.sim.R           |only
 R/coverage.R           |only
 man/VAR.BPR.Rd         |    5 ++++-
 man/VAR.BaBPR.Rd       |    5 ++++-
 man/VAR.LRtest.Rd      |    4 ++--
 man/VAR.Rest.Rd        |    4 ++--
 man/VAR.Waldtest.Rd    |    2 +-
 man/VAR.est.Rd         |    4 ++--
 man/VAR.etp-package.Rd |    4 ++--
 man/dat.Rd             |    2 +-
 14 files changed, 39 insertions(+), 31 deletions(-)

More information about VAR.etp at CRAN
Permanent link

Package Rcpp11 updated to version 3.1.0.1 with previous version 3.1.0 dated 2014-04-11

Title: R and C++11
Description: Rcpp11 includes a header only C++11 library that facilitates integration between R and modern C++.
Author: Romain Francois [aut, cre], Kevin Ushey [aut], John Chambers [ctb]
Maintainer: Romain Francois

Diff between Rcpp11 versions 3.1.0 dated 2014-04-11 and 3.1.0.1 dated 2014-04-16

 DESCRIPTION                                      |   11 +-
 MD5                                              |   87 +++++++++++------------
 inst/include/Rcpp.h                              |   28 +++----
 inst/include/Rcpp/Array.h                        |   23 ++----
 inst/include/Rcpp/Context.h                      |   86 +++++++++++++++++++++-
 inst/include/Rcpp/DataFrame.h                    |   15 ++-
 inst/include/Rcpp/Language.h                     |    6 -
 inst/include/Rcpp/NA_Proxy.h                     |    2 
 inst/include/Rcpp/Pairlist.h                     |    8 +-
 inst/include/Rcpp/R.h                            |   56 --------------
 inst/include/Rcpp/Reference.h                    |    4 -
 inst/include/Rcpp/Timer.h                        |    8 +-
 inst/include/Rcpp/exceptions.h                   |   34 ++++++--
 inst/include/Rcpp/macros/interface.h             |    2 
 inst/include/Rcpp/macros/macros.h                |    3 
 inst/include/Rcpp/platform.h                     |only
 inst/include/Rcpp/stats/dpq/dpq.h                |   24 +++---
 inst/include/Rcpp/sugar/functions/complex.h      |    2 
 inst/include/Rcpp/sugar/functions/duplicated.h   |    2 
 inst/include/Rcpp/sugar/functions/is_nan.h       |    2 
 inst/include/Rcpp/sugar/functions/match.h        |    2 
 inst/include/Rcpp/sugar/functions/sapply.h       |    2 
 inst/include/Rcpp/sugar/functions/unique.h       |    4 -
 inst/include/Rcpp/sugar/matrix/outer.h           |    2 
 inst/include/Rcpp/sugar/tools/iterator.h         |   18 ++--
 inst/include/Rcpp/traits/is_materialized.h       |    2 
 inst/include/Rcpp/traits/is_matrix_expression.h  |   13 +--
 inst/include/Rcpp/traits/is_vector_expression.h  |    4 -
 inst/include/Rcpp/traits/named_object.h          |    4 -
 inst/include/Rcpp/transient_vector.h             |    4 -
 inst/include/Rcpp/vector/Matrix.h                |   19 ++---
 inst/include/Rcpp/vector/MatrixBase.h            |    2 
 inst/include/Rcpp/vector/MatrixColumn.h          |    8 +-
 inst/include/Rcpp/vector/MatrixRow.h             |    8 +-
 inst/include/Rcpp/vector/StrideIterator.h        |   12 +--
 inst/include/Rcpp/vector/VectorBase.h            |    4 -
 inst/include/Rcpp/vector/impl/CharacterVector.h  |   45 +++++++----
 inst/include/Rcpp/vector/impl/ExpressionVector.h |   51 +++++++------
 inst/include/Rcpp/vector/impl/List.h             |   32 +++++---
 inst/include/Rcpp/vector/impl/SimpleVector.h     |   40 ++++++----
 inst/include/Rcpp/vector/is_materialized.h       |    4 -
 inst/include/Rcpp/vector/name_proxy.h            |    2 
 inst/include/Rcpp/wrap/EnumWrapper.h             |   14 +--
 inst/include/Rcpp/wrap/range_wrap.h              |    8 +-
 inst/include/Rcpp/wrap/wrap_type.h               |    4 -
 45 files changed, 395 insertions(+), 316 deletions(-)

More information about Rcpp11 at CRAN
Permanent link

Package PopGenome updated to version 2.0.6 with previous version 2.0.5 dated 2014-03-12

Title: A swiss army knife for population genetic & genomic analysis
Description: PopGenome is an R-package for Population Genetic & Genomic Analysis
Author: Bastian Pfeifer, Ulrich Wittelsbuerger
Maintainer: Bastian Pfeifer

Diff between PopGenome versions 2.0.5 dated 2014-03-12 and 2.0.6 dated 2014-04-16

 PopGenome-2.0.5/PopGenome/src/zlib.h                                             |only
 PopGenome-2.0.6/PopGenome/DESCRIPTION                                            |    6 +-
 PopGenome-2.0.6/PopGenome/MD5                                                    |   27 ++++------
 PopGenome-2.0.6/PopGenome/NEWS                                                   |   12 ++++
 PopGenome-2.0.6/PopGenome/R/GENOME.R                                             |    7 +-
 PopGenome-2.0.6/PopGenome/R/parse_gff.R                                          |    8 ++
 PopGenome-2.0.6/PopGenome/R/readData.R                                           |    5 +
 PopGenome-2.0.6/PopGenome/inst/doc/An_introduction_to_the_PopGenome_package.Rnw  |    3 -
 PopGenome-2.0.6/PopGenome/inst/doc/An_introduction_to_the_PopGenome_package.pdf  |binary
 PopGenome-2.0.6/PopGenome/inst/doc/Integration_of_new_Methods.pdf                |binary
 PopGenome-2.0.6/PopGenome/man/Whop_readVCF.Rd                                    |    2 
 PopGenome-2.0.6/PopGenome/man/readData.Rd                                        |   11 ++--
 PopGenome-2.0.6/PopGenome/man/readSNP.Rd                                         |    2 
 PopGenome-2.0.6/PopGenome/man/readVCF.Rd                                         |    2 
 PopGenome-2.0.6/PopGenome/vignettes/An_introduction_to_the_PopGenome_package.Rnw |    3 -
 15 files changed, 62 insertions(+), 26 deletions(-)

More information about PopGenome at CRAN
Permanent link

Package ModelMap updated to version 3.0.15 with previous version 3.0.14 dated 2014-03-01

Title: Creates Random Forest and Stochastic Gradient Boosting Models, and applies them to GIS .img files to build detailed prediction maps.
Description: This package will create sophisticated models of training data and validate the models with an independent test set, cross validation, or in the case of Random Forest Models, with Out Of Bag (OOB) predictions on the training data. It will create graphs and tables of the model validation results. It will apply these models to GIS .img files of predictors to create detailed prediction surfaces. It will handle large predictor files for map making, by reading in the .img files in chunks, and output to the .txt file the prediction for each data chunk, before reading the next chunk of data.
Author: Elizabeth Freeman, Tracey Frescino
Maintainer: Elizabeth Freeman

Diff between ModelMap versions 3.0.14 dated 2014-03-01 and 3.0.15 dated 2014-04-16

 DESCRIPTION              |    8 +-
 MD5                      |   28 ++++-----
 R/internal.R             |  135 +++++++++++++++++++++++++++++++++++++----------
 R/model.build.R          |   66 ++++++++++++++++------
 R/model.diagnostics.R    |   70 ++++++++++++++++--------
 R/model.mapmake.R        |   28 ++++++++-
 build/vignette.rds       |binary
 inst/CHANGELOG           |   30 ++++++++++
 inst/README              |   66 ++++++++++++++++++----
 inst/doc/VModelMap.pdf   |binary
 man/ModelMap-package.Rd  |    4 -
 man/internal.Rd          |    1 
 man/model.build.Rd       |    2 
 man/model.diagnostics.Rd |    2 
 man/model.mapmake.Rd     |    4 +
 15 files changed, 333 insertions(+), 111 deletions(-)

More information about ModelMap at CRAN
Permanent link

Package fanplot updated to version 3.2 with previous version 3.1 dated 2014-03-21

Title: Visualisation of sequential probability distributions using fan charts.
Description: Visualise sequential distributions using a range of plotting styles. Sequential distribution data can be input as either simulations or values corresponding to percentiles over time (columns). Plots are added to existing graphic devices using the fan function. Users can choose from four different styles, including fan chart type plots, where a set of coloured polygon, with shadings corresponding to the percentile values are layered to represent different uncertainty levels.
Author: Guy J. Abel
Maintainer: "Guy J. Abel"

Diff between fanplot versions 3.1 dated 2014-03-21 and 3.2 dated 2014-04-16

 DESCRIPTION          |    6 -
 MD5                  |   21 ++--
 R/fan.R              |  264 ++++++++++++++++++++++++++++++---------------------
 R/fanplot-internal.R |  251 ++++++++++++++++++++++++------------------------
 data/boe.rda         |binary
 data/cpi.rda         |binary
 data/ips.rda         |binary
 data/th.mcmc.rda     |binary
 demo                 |only
 inst/netelicit       |only
 man/fan.Rd           |  122 +++++++++++------------
 11 files changed, 355 insertions(+), 309 deletions(-)

More information about fanplot at CRAN
Permanent link

Package cgam updated to version 1.1 with previous version 1.0 dated 2014-03-05

Title: Constrained Generalized Additive Model
Description: In this package, a constrained generalized additive model is fitted by the cgam routine. Given a set of predictors with or without shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The cone information criterion (CIC) is used to select the best combination of variables and shapes. This package depends on the R package coneproj, in which the hinge algorithm for one cone projection is effected.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao

Diff between cgam versions 1.0 dated 2014-03-05 and 1.1 dated 2014-04-16

 DESCRIPTION |   10 
 MD5         |    6 
 R/cgam.R    |  694 +++++++++++++++++++++++++++++++-----------------------------
 man/cgam.Rd |   21 +
 4 files changed, 387 insertions(+), 344 deletions(-)

More information about cgam at CRAN
Permanent link

Package scidb updated to version 1.1-2 with previous version 1.1-1 dated 2014-01-25

Title: An R interface to SciDB
Description: SciDB is an open-source array database (http://scidb.org). The scidb package provides an R interface to SciDB.
Author: Paradigm4, B. W. Lewis
Maintainer: B. W. Lewis

Diff between scidb versions 1.1-1 dated 2014-01-25 and 1.1-2 dated 2014-04-16

 scidb-1.1-1/scidb/man/misc-methods.Rd           |only
 scidb-1.1-2/scidb/.Rinstignore                  |    1 
 scidb-1.1-2/scidb/DESCRIPTION                   |   13 
 scidb-1.1-2/scidb/MD5                           |  127 ++--
 scidb-1.1-2/scidb/NAMESPACE                     |   33 +
 scidb-1.1-2/scidb/NEWS                          |   42 +
 scidb-1.1-2/scidb/R/aggregate.R                 |  153 +++--
 scidb-1.1-2/scidb/R/classes.R                   |   85 +-
 scidb-1.1-2/scidb/R/dbops.R                     |  453 +++++++++------
 scidb-1.1-2/scidb/R/distributions.R             |only
 scidb-1.1-2/scidb/R/glm.R                       |  358 +++++++++++-
 scidb-1.1-2/scidb/R/merge.R                     |only
 scidb-1.1-2/scidb/R/misc.R                      |only
 scidb-1.1-2/scidb/R/pkg.R                       |  115 +++
 scidb-1.1-2/scidb/R/schema-utils.R              |only
 scidb-1.1-2/scidb/R/scidb-arithmetic.R          |  457 +++++++++------
 scidb-1.1-2/scidb/R/scidb-functions.R           |  190 +++---
 scidb-1.1-2/scidb/R/scidb-indexing-functions.R  |  321 +++++++----
 scidb-1.1-2/scidb/R/scidb-methods.R             |  355 ++++++++----
 scidb-1.1-2/scidb/R/scidbdf-functions.R         |  145 ++---
 scidb-1.1-2/scidb/R/scidbdf-methods.R           |  176 ++++--
 scidb-1.1-2/scidb/R/utility.R                   |  696 ++++++++++++------------
 scidb-1.1-2/scidb/README                        |    6 
 scidb-1.1-2/scidb/README.md                     |   43 +
 scidb-1.1-2/scidb/inst/doc/scidb.Rnw            |  296 ++++++----
 scidb-1.1-2/scidb/inst/doc/scidb.pdf            |binary
 scidb-1.1-2/scidb/inst/misc-documentation       |only
 scidb-1.1-2/scidb/inst/misc/log                 |only
 scidb-1.1-2/scidb/man/Ops.scidb.Rd              |    8 
 scidb-1.1-2/scidb/man/aggregate-methods.Rd      |   27 
 scidb-1.1-2/scidb/man/all.equal.Rd              |only
 scidb-1.1-2/scidb/man/antijoin.Rd               |only
 scidb-1.1-2/scidb/man/attribute_rename.Rd       |    6 
 scidb-1.1-2/scidb/man/build.Rd                  |    2 
 scidb-1.1-2/scidb/man/c-methods.Rd              |only
 scidb-1.1-2/scidb/man/cast.Rd                   |    6 
 scidb-1.1-2/scidb/man/comparison-methods.Rd     |only
 scidb-1.1-2/scidb/man/diff.scidb.Rd             |    2 
 scidb-1.1-2/scidb/man/dimension_rename.Rd       |only
 scidb-1.1-2/scidb/man/dimensions.Rd             |only
 scidb-1.1-2/scidb/man/glm.fit.Rd                |   83 ++
 scidb-1.1-2/scidb/man/grand-methods.Rd          |only
 scidb-1.1-2/scidb/man/hist-method.Rd            |only
 scidb-1.1-2/scidb/man/hypergeometric-methods.Rd |only
 scidb-1.1-2/scidb/man/index_lookup.Rd           |    4 
 scidb-1.1-2/scidb/man/iquery.Rd                 |    2 
 scidb-1.1-2/scidb/man/lag.Rd                    |    2 
 scidb-1.1-2/scidb/man/merge-methods.Rd          |   44 -
 scidb-1.1-2/scidb/man/na.locf-method.Rd         |only
 scidb-1.1-2/scidb/man/persist.Rd                |only
 scidb-1.1-2/scidb/man/predict.glm_scidb.Rd      |only
 scidb-1.1-2/scidb/man/quantile.Rd               |only
 scidb-1.1-2/scidb/man/redimension.Rd            |   48 +
 scidb-1.1-2/scidb/man/repart.Rd                 |    5 
 scidb-1.1-2/scidb/man/reshape-method.Rd         |   19 
 scidb-1.1-2/scidb/man/schema.Rd                 |only
 scidb-1.1-2/scidb/man/scidb-class.Rd            |   21 
 scidb-1.1-2/scidb/man/scidb.Rd                  |   10 
 scidb-1.1-2/scidb/man/scidb_attributes.Rd       |only
 scidb-1.1-2/scidb/man/scidb_fisher.test.Rd      |only
 scidb-1.1-2/scidb/man/scidbconnect.Rd           |    4 
 scidb-1.1-2/scidb/man/scidbdf-class.Rd          |   15 
 scidb-1.1-2/scidb/man/scidbremove.Rd            |   56 +
 scidb-1.1-2/scidb/man/show_commit_log.Rd        |only
 scidb-1.1-2/scidb/man/slice.Rd                  |    6 
 scidb-1.1-2/scidb/man/sort-methods.Rd           |    3 
 scidb-1.1-2/scidb/man/subarray.Rd               |only
 scidb-1.1-2/scidb/man/subset-methods.Rd         |    3 
 scidb-1.1-2/scidb/man/substitute.Rd             |only
 scidb-1.1-2/scidb/man/summary.scidb.Rd          |    4 
 scidb-1.1-2/scidb/man/sweep-methods.Rd          |only
 scidb-1.1-2/scidb/src/scidb.c                   |  197 ++++++
 scidb-1.1-2/scidb/tests/scidb.R                 |  100 +++
 scidb-1.1-2/scidb/tests/scidbdf.R               |   15 
 scidb-1.1-2/scidb/vignettes/scidb.Rnw           |  296 ++++++----
 75 files changed, 3396 insertions(+), 1657 deletions(-)

More information about scidb at CRAN
Permanent link

Package psd updated to version 0.4-1 with previous version 0.4-0 dated 2013-09-20

Title: Adaptive, sine-multitaper power spectral density estimation
Description: Power spectral density estimates are produced through iterative refinement of the optimal number of sine-tapers at each frequency. The optimization procedure is based on the method of Riedel and Sidorenko (1995), which applies smoothing that varies with frequency to minimize the sum of variance and bias at each point.
Author: Robert L. Parker and Andrew J. Barbour
Maintainer: Andrew J. Barbour

Diff between psd versions 0.4-0 dated 2013-09-20 and 0.4-1 dated 2014-04-16

 DESCRIPTION                    |   15 +--
 MD5                            |   72 +++++++-------
 build/vignette.rds             |binary
 data/Tohoku.rda                |binary
 data/hfsnm.rda                 |binary
 data/magnet.rda                |binary
 inst/CITATION                  |   18 ++-
 inst/Examples/rdex_pspectrum.R |    2 
 inst/NEWS.Rd                   |   14 ++
 inst/doc/fftw.R                |   18 +--
 inst/doc/fftw.pdf              |binary
 inst/doc/normalization.R       |   40 ++++----
 inst/doc/normalization.Rnw     |   24 ++--
 inst/doc/normalization.pdf     |binary
 inst/doc/psd_overview.R        |   74 +++++++--------
 inst/doc/psd_overview.pdf      |binary
 man/Tohoku.Rd                  |   58 ++++++------
 man/as.tapers.Rd               |   78 +++++++---------
 man/hfsnm.Rd                   |   30 +++---
 man/magnet.Rd                  |   41 ++++----
 man/parabolic_weights.Rd       |   43 ++++----
 man/pilot_spec.Rd              |   58 +++++-------
 man/prewhiten.Rd               |  189 ++++++++++++++++++---------------------
 man/psd-environment.Rd         |   97 +++++++++-----------
 man/psd-normalization.Rd       |   61 +++++-------
 man/psd-package.Rd             |  154 ++++++++++++++++----------------
 man/psd-utilities.Rd           |  197 ++++++++++++++++++++---------------------
 man/psdcore.Rd                 |   95 +++++++++----------
 man/pspectrum.Rd               |   56 +++++------
 man/riedsid.Rd                 |   94 +++++++++----------
 man/spec-methods.Rd            |   24 ++--
 man/spec_confint.Rd            |   70 ++++++--------
 man/spectral_properties.Rd     |   49 ++++------
 man/splineGrad.Rd              |   32 +++---
 man/tapers-constraints.Rd      |  102 ++++++++++-----------
 man/tapers-methods.Rd          |   31 +++---
 vignettes/normalization.Rnw    |   24 ++--
 37 files changed, 917 insertions(+), 943 deletions(-)

More information about psd at CRAN
Permanent link

Package mizer updated to version 0.2 with previous version 0.1 dated 2013-10-08

Title: Multi-species sIZE spectrum modelling in R
Description: A set of classes and methods to set up and run multispecies, trait based and community size spectrum ecological models, focussed on the marine environment.
Author: Finlay Scott (JRC, IT) and Julia Blanchard (Sheffield University, UK) and Ken Andersen (DTU Aqua, Copenhagen, DK)
Maintainer: Finlay Scott

Diff between mizer versions 0.1 dated 2013-10-08 and 0.2 dated 2014-04-16

 mizer-0.1/mizer/vignettes/Growth_curve-eps-converted-to.pdf              |only
 mizer-0.1/mizer/vignettes/Growth_curve.eps                               |only
 mizer-0.1/mizer/vignettes/Spectrum-eps-converted-to.pdf                  |only
 mizer-0.1/mizer/vignettes/mizer_vignette-plotSpectra_community_model.pdf |only
 mizer-0.1/mizer/vignettes/recruitment-eps-converted-to.pdf               |only
 mizer-0.1/mizer/vignettes/recruitment.eps                                |only
 mizer-0.2/mizer/DESCRIPTION                                              |    6 
 mizer-0.2/mizer/MD5                                                      |   37 +--
 mizer-0.2/mizer/NEWS                                                     |    8 
 mizer-0.2/mizer/R/project.r                                              |    6 
 mizer-0.2/mizer/R/wrapper_functions.R                                    |   41 ++-
 mizer-0.2/mizer/data/NS_species_params.RData                             |binary
 mizer-0.2/mizer/data/NS_species_params_gears.RData                       |binary
 mizer-0.2/mizer/inst/doc/NS_species_params.csv                           |    6 
 mizer-0.2/mizer/inst/doc/mizer_vignette.R                                |   67 ++---
 mizer-0.2/mizer/inst/doc/mizer_vignette.Rnw                              |  116 +++++-----
 mizer-0.2/mizer/inst/doc/mizer_vignette.pdf                              |binary
 mizer-0.2/mizer/inst/examples                                            |only
 mizer-0.2/mizer/man/set_community_model.Rd                               |   32 +-
 mizer-0.2/mizer/man/set_trait_model.Rd                                   |   18 -
 mizer-0.2/mizer/vignettes/Growth_curve.pdf                               |only
 mizer-0.2/mizer/vignettes/NS_species_params.csv                          |    6 
 mizer-0.2/mizer/vignettes/mizer_vignette.Rnw                             |  116 +++++-----
 mizer-0.2/mizer/vignettes/recruitment.pdf                                |only
 24 files changed, 249 insertions(+), 210 deletions(-)

More information about mizer at CRAN
Permanent link

Package AFLPsim updated to version 0.3-3 with previous version 0.2-2 dated 2013-10-29

Title: Hybrid simulation and genome scan for dominant markers
Description: This package is developed in the Plant Reproductive Biology Lab (RNM-214) - University of Seville. It contains hybrid simulation functions for dominant genetic data. It also provides several genome scan methods.
Author: Francisco Balao [aut, cre], Juan Luis García-Castaño [aut]
Maintainer: Francisco Balao

Diff between AFLPsim versions 0.2-2 dated 2013-10-29 and 0.3-3 dated 2014-04-16

 DESCRIPTION               |    8 +++----
 MD5                       |   19 +++++++++--------
 R/gscan.R                 |    6 ++---
 R/hybridsim.R             |   49 +++++++++-------------------------------------
 R/plot.hybridsim.R        |    9 ++++----
 README.md                 |only
 inst/NEWS.Rd              |    7 ++++++
 man/AFLPsim-package.Rd    |    8 +++----
 man/hybridize.Rd          |    2 -
 man/hybridsim.Rd          |    4 +--
 man/plot.demosimhybrid.Rd |    2 -
 11 files changed, 47 insertions(+), 67 deletions(-)

More information about AFLPsim at CRAN
Permanent link

New package BEQI2 with initial version 1.0-0
Package: BEQI2
Type: Package
Title: Benthic Ecosystem Quality Index 2
Description: Benthic Ecosystem Quality Index 2. This package facilitates the analysis of benthos data. It estimates several quality indices like the total abundance of species, species richness, Shannon index, AZTI Marine Biotic Index (AMBI), and the BEQI-2 index. The package includes two additional optional features that enhance data preprocessing: (1) genus to species conversion, i.e.,taxa counts at the taxonomic genus level can optionally be converted to the species level and (2) pooling: small samples are combined to bigger samples with a standardized size to (a) meet the data requirements of the AMBI, (b) generate comparable species richness values and (c) give a higher benthos signal to noise ratio.
Version: 1.0-0
Date: 2014-04-16
Authors@R: c(person(given = "Willem", family = "van Loon", email = "willem.van.loon@rws.nl", role = c("aut", "cph")), person(given = "Dennis", family = "Walvoort", email = "dennis.Walvoort@wur.nl", role = c("aut", "cre")))
Depends: R (>= 3.0.2), methods, tcltk
Imports: knitr, markdown, RJSONIO, xtable, plyr, reshape2
Suggests: testthat
VignetteBuilder: knitr
License: GPL (>= 3)
Packaged: 2014-04-16 14:38:31 UTC; dennis
Author: Willem van Loon [aut, cph], Dennis Walvoort [aut, cre]
Maintainer: Dennis Walvoort
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-16 22:50:45

More information about BEQI2 at CRAN
Permanent link

Package greport updated to version 0.5-1 with previous version 0.5-0 dated 2014-03-02

Title: Graphical Reporting for Clinical Trials
Description: The greport package contains many functions useful for monitoring and reporting the results of clinical trials and other experiments in which treatments are compared. LaTeX is used to typeset the resulting reports, recommended to be in the context of knitr. The Hmisc and lattice packages are used by greport for high-level graphics.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr

Diff between greport versions 0.5-0 dated 2014-03-02 and 0.5-1 dated 2014-04-16

 DESCRIPTION             |   12 +--
 INDEX                   |    4 -
 MD5                     |   43 ++++++-----
 NAMESPACE               |   19 +++--
 NEWS                    |   18 ++++
 R/Misc.r                |   50 +++++++++----
 R/accrualReport.r       |   53 ++++++++++++--
 R/dReport.r             |   29 ++++++--
 R/eReport.r             |    4 -
 R/exReport.r            |  173 ++++++++++++++++++++++++++++--------------------
 R/greport-package.r     |only
 R/nriskReport.r         |only
 R/survReport.r          |   40 ++---------
 README.md               |   21 +++++
 inst/feh.bib            |only
 man/Merge.Rd            |   48 ++++++++-----
 man/accrualReport.Rd    |   11 ++-
 man/exReport.Rd         |   24 +++++-
 man/greport.Rd          |only
 man/nriskReport.Rd      |only
 man/setgreportOption.Rd |    6 +
 man/startPlot.Rd        |    2 
 man/survReport.Rd       |    4 -
 tests/report.Rnw        |   26 +++----
 tests/test.Rnw          |   35 +++++----
 25 files changed, 399 insertions(+), 223 deletions(-)

More information about greport at CRAN
Permanent link

Package Rdpack updated to version 0.4-14 with previous version 0.4-4 dated 2013-04-13

Title: Update and manipulate Rd documentation objects
Description: Functions for manipulation of Rd objects, including function reprompt for updating existing Rd documentation for functions, methods and classes, and function rebib for import of references from Bibtex files.
Author: Georgi N. Boshnakov
Maintainer: Georgi N. Boshnakov

Diff between Rdpack versions 0.4-4 dated 2013-04-13 and 0.4-14 dated 2014-04-16

 Rdpack-0.4-14/Rdpack/DESCRIPTION                         |   19 +-
 Rdpack-0.4-14/Rdpack/MD5                                 |   84 ++++++-----
 Rdpack-0.4-14/Rdpack/NAMESPACE                           |  110 ++++++++++++++-
 Rdpack-0.4-14/Rdpack/NEWS                                |   33 ++++
 Rdpack-0.4-14/Rdpack/R/Rdo2Rdf.R                         |    9 -
 Rdpack-0.4-14/Rdpack/R/alias.R                           |    2 
 Rdpack-0.4-14/Rdpack/R/bib.R                             |   11 -
 Rdpack-0.4-14/Rdpack/R/inspect.R                         |   10 -
 Rdpack-0.4-14/Rdpack/R/manip.R                           |   45 ++++--
 Rdpack-0.4-14/Rdpack/R/parse.R                           |    2 
 Rdpack-0.4-14/Rdpack/R/repromptAny.R                     |    5 
 Rdpack-0.4-14/Rdpack/R/sections.R                        |    6 
 Rdpack-0.4-14/Rdpack/R/threedots.R                       |only
 Rdpack-0.4-14/Rdpack/R/usage.R                           |   10 +
 Rdpack-0.4-14/Rdpack/R/utils.R                           |    9 -
 Rdpack-0.4-14/Rdpack/R/yytransient.R                     |only
 Rdpack-0.4-14/Rdpack/R/zzobsolete.R                      |   71 +++++++++
 Rdpack-0.4-14/Rdpack/build/partial.rdb                   |binary
 Rdpack-0.4-14/Rdpack/man/Rd_combo.Rd                     |   10 -
 Rdpack-0.4-14/Rdpack/man/Rdo_collect_metadata.Rd         |only
 Rdpack-0.4-14/Rdpack/man/Rdo_empty_sections.Rd           |    2 
 Rdpack-0.4-14/Rdpack/man/Rdo_get_argument_names.Rd       |only
 Rdpack-0.4-14/Rdpack/man/Rdo_get_item_labels.Rd          |only
 Rdpack-0.4-14/Rdpack/man/Rdo_locate.Rd                   |   48 ++++--
 Rdpack-0.4-14/Rdpack/man/Rdo_locate_leaves.Rd            |    9 -
 Rdpack-0.4-14/Rdpack/man/Rdo_sections.Rd                 |   47 +++++-
 Rdpack-0.4-14/Rdpack/man/Rdo_tags.Rd                     |only
 Rdpack-0.4-14/Rdpack/man/Rdo_which.Rd                    |only
 Rdpack-0.4-14/Rdpack/man/Rdpack-package.Rd               |   66 ++++-----
 Rdpack-0.4-14/Rdpack/man/Rdreplace_section.Rd            |only
 Rdpack-0.4-14/Rdpack/man/c_Rd.Rd                         |   20 +-
 Rdpack-0.4-14/Rdpack/man/compare_usage1.Rd               |    4 
 Rdpack-0.4-14/Rdpack/man/deparse_usage.Rd                |    2 
 Rdpack-0.4-14/Rdpack/man/format_funusage.Rd              |    2 
 Rdpack-0.4-14/Rdpack/man/get_sig_text.Rd                 |    2 
 Rdpack-0.4-14/Rdpack/man/get_usage_text.Rd               |    2 
 Rdpack-0.4-14/Rdpack/man/inspect_args.Rd                 |    2 
 Rdpack-0.4-14/Rdpack/man/inspect_signatures.Rd           |    3 
 Rdpack-0.4-14/Rdpack/man/inspect_slots.Rd                |    3 
 Rdpack-0.4-14/Rdpack/man/inspect_usage.Rd                |    2 
 Rdpack-0.4-14/Rdpack/man/parse_usage_text.Rd             |    2 
 Rdpack-0.4-14/Rdpack/man/predefined.Rd                   |   38 ++++-
 Rdpack-0.4-14/Rdpack/man/promptPackageSexpr.Rd           |    1 
 Rdpack-0.4-14/Rdpack/man/rebib.Rd                        |   19 +-
 Rdpack-0.4-14/Rdpack/man/reprompt.Rd                     |    1 
 Rdpack-0.4-14/Rdpack/man/update_aliases_tmp.Rd           |    2 
 Rdpack-0.4-4/Rdpack/man/Rdo_collect_aliases.Rd           |only
 Rdpack-0.4-4/Rdpack/man/Rdo_locate_predefined_section.Rd |only
 48 files changed, 526 insertions(+), 187 deletions(-)

More information about Rdpack at CRAN
Permanent link

New package RHive with initial version 2.0-0.0
Package: RHive
Type: Package
Title: R and Hive
Version: 2.0-0.0
Description: RHive is an R extension facilitating distributed computing via HIVE query. It provides an easy to use HQL like SQL and R objects and functions in HQL.
Author: NexR
Maintainer: Johan Ahn
License: Apache License (== 2.0)
Depends: R (>= 2.13.0), rJava (>= 0.9-0)
Suggests: RUnit
SystemRequirements: Hadoop core >= 0.20.3 (http://hadoop.apache.org/core/), Hive >= 0.8 (http://hive.apache.org/)
OS_type: unix
Repository: CRAN
Packaged: 2014-04-15 01:26:27 UTC; root
NeedsCompilation: no
X-CRAN-Comment: Archived 2013-08-07 as the former maintainer withdrew maintaienrship and the nominated new maintainer did never respond to requests to update the package.
Date/Publication: 2014-04-16 09:21:53

More information about RHive at CRAN
Permanent link

New package bigalgebra with initial version 0.8.4
Package: bigalgebra
Version: 0.8.4
Date: 2014-04-15
Title: BLAS routines for native R matrices and big.matrix objects.
Author: Michael J. Kane, Bryan Lewis, and John W. Emerson
Maintainer: Michael J. Kane
Imports: methods
Depends: bigmemory (>= 4.0.0)
LinkingTo: bigmemory, BH
Description: This package provides arithmetic functions for R matrix and big.matrix objects.
License: LGPL-3 | Apache License 2.0
Copyright: (C) 2014 Michael J. Kane, Bryan Lewis, and John W. Emerson
URL: http://www.bigmemory.org
LazyLoad: yes
Packaged: 2012-12-26 22:17:06 UTC; blewis
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-16 09:21:50

More information about bigalgebra at CRAN
Permanent link

Tue, 15 Apr 2014

Package SIS updated to version 0.7 with previous version 0.6 dated 2010-09-06

Title: Sure Independence Screening
Description: (Iterative) Sure Independence Screening for Generalized Linear Models and Cox's Proportional Hazards Models
Author: Jianqing Fan, Yang Feng, Diego Franco Saldana, Richard Samworth, Yichao Wu
Maintainer: Diego Franco Saldana

Diff between SIS versions 0.6 dated 2010-09-06 and 0.7 dated 2014-04-15

 SIS-0.6/SIS/R/SIS.r                    |only
 SIS-0.6/SIS/R/wtLassoScadCOX.r         |only
 SIS-0.6/SIS/R/wtLassoScadGLM.r         |only
 SIS-0.6/SIS/bak                        |only
 SIS-0.6/SIS/data                       |only
 SIS-0.6/SIS/man/COXvanISISscad.Rd      |only
 SIS-0.6/SIS/man/GLMvanISISscad.Rd      |only
 SIS-0.6/SIS/man/getfinalSCADcoef.Rd    |only
 SIS-0.6/SIS/man/getfinalSCADcoefCOX.Rd |only
 SIS-0.6/SIS/man/heart.data.Rd          |only
 SIS-0.6/SIS/man/lung.data.Rd           |only
 SIS-0.6/SIS/man/scadcox.Rd             |only
 SIS-0.6/SIS/man/scadglm.Rd             |only
 SIS-0.6/SIS/man/wtlassocox.Rd          |only
 SIS-0.6/SIS/man/wtlassoglm.Rd          |only
 SIS-0.6/SIS/src                        |only
 SIS-0.7/SIS/DESCRIPTION                |   18 +-
 SIS-0.7/SIS/MD5                        |only
 SIS-0.7/SIS/NAMESPACE                  |    9 -
 SIS-0.7/SIS/R/SIS.R                    |only
 SIS-0.7/SIS/R/margcoef.R               |only
 SIS-0.7/SIS/R/obtainindex.R            |only
 SIS-0.7/SIS/R/partialfits.r            |only
 SIS-0.7/SIS/R/predict.SIS.R            |only
 SIS-0.7/SIS/R/print.SIS.R              |only
 SIS-0.7/SIS/R/setsize.R                |only
 SIS-0.7/SIS/R/standardize.R            |only
 SIS-0.7/SIS/man/SIS.Rd                 |  297 ++++++++++++++++++++-------------
 SIS-0.7/SIS/man/predict.SIS.Rd         |only
 SIS-0.7/SIS/man/print.SIS.Rd           |only
 30 files changed, 198 insertions(+), 126 deletions(-)

More information about SIS at CRAN
Permanent link

Package ssym updated to version 1.2 with previous version 1.1 dated 2014-04-04

Title: Fitting Semiparametric Symmetric Regression Models
Description: This package allows to fit a semiparametric regression model suitable for data set analysis in which the conditional distribution of the response is symmetric and continuous.
Author: Luis Hernando Vanegas and Gilberto A. Paula
Maintainer: Luis Hernando Vanegas

Diff between ssym versions 1.1 dated 2014-04-04 and 1.2 dated 2014-04-15

 DESCRIPTION         |   10 
 MD5                 |   20 -
 R/itpM.R            |  212 ++++++++++++++-
 R/itpM2.R           |  461 +++++++++++++++++++++++++--------
 R/ssym.l.R          |  714 +++++++++++++++++++++++++++++++++++++++-------------
 R/ssym.nl.R         |  116 ++++----
 R/summary.ssym.R    |   34 +-
 data/Claims.rda     |only
 man/Claims.Rd       |only
 man/ssym-package.Rd |    8 
 man/ssym.l.Rd       |  127 ++++++---
 man/ssym.nl.Rd      |   92 ++++++
 12 files changed, 1383 insertions(+), 411 deletions(-)

More information about ssym at CRAN
Permanent link

Package simboot updated to version 0.2-5 with previous version 0.2-4 dated 2013-08-13

Title: Simultaneous inference for diversity indices.
Description: Package simboot provides estimation of simultaneous bootstrap and asymptotic confidence intervals for diversity indices, namely the Shannon and the Simpson index. Several pre--specified multiple comparison types are available to choose. Further user--defined contrast matrices are applicable. In addition, simboot estimates adjusted as well as unadjusted p--values for two of the three proposed bootstrap methods. Further simboot allows for comparing biological diversities of two or more groups while simultaneously testing a user-defined selection of Hill numbers of orders q, which are considered as appropriate and useful indices for measuring diversity.
Author: Ralph Scherer, Philip Pallmann
Maintainer: Ralph Scherer

Diff between simboot versions 0.2-4 dated 2013-08-13 and 0.2-5 dated 2014-04-15

 DESCRIPTION         |   10 -
 MD5                 |   72 ++++++-------
 NAMESPACE           |    3 
 NEWS                |   60 ++++++-----
 R/Boutrp.R          |   32 +++---
 R/CCdrp.R           |   60 +++++------
 R/SCIrp.R           |   90 ++++++++---------
 R/Simpson.R         |   12 +-
 R/WYht.R            |  260 ++++++++++++++++++++++++-------------------------
 R/asht.R            |   14 +-
 R/contrMat.R        |  274 ++++++++++++++++++++++++++--------------------------
 R/estShannonf.R     |   76 +++++++-------
 R/estSimpson.R      |   18 +--
 R/estSimpsonf.R     |   84 +++++++--------
 R/estThetaRow.R     |   40 +++----
 R/mcpHill.R         |  190 ++++++++++++++++++------------------
 R/rpht.R            |   58 +++++------
 R/tsht.R            |  268 +++++++++++++++++++++++++-------------------------
 README.md           |   38 +++----
 man/Boutrp.Rd       |   24 ++--
 man/CCdrp.Rd        |   20 +--
 man/SCIrp.Rd        |   24 ++--
 man/Simpson.Rd      |   46 ++++----
 man/WYht.Rd         |   36 +++---
 man/asht.Rd         |   42 +++----
 man/contrMat.Rd     |  106 ++++++++++----------
 man/corrmatgen.Rd   |   40 +++----
 man/estShannon.Rd   |   50 ++++-----
 man/estShannonWY.Rd |   68 ++++++------
 man/estShannonf.Rd  |   82 +++++++--------
 man/estSimpson.Rd   |   42 +++----
 man/estSimpsonf.Rd  |   60 +++++------
 man/estThetaRow.Rd  |   48 ++++-----
 man/rpht.Rd         |   34 +++---
 man/simboot.Rd      |  158 ++++++++++++++---------------
 man/tsht.Rd         |   34 +++---
 man/waldci.Rd       |   26 ++--
 37 files changed, 1305 insertions(+), 1294 deletions(-)

More information about simboot at CRAN
Permanent link

Package PropCIs updated to version 0.2-5 with previous version 0.2-4 dated 2013-08-04

Title: Various confidence interval methods for proportions
Description: Computes two-sample confidence intervals for single, paired and independent proportions
Author: Ralph Scherer
Maintainer: Ralph Scherer

Diff between PropCIs versions 0.2-4 dated 2013-08-04 and 0.2-5 dated 2014-04-15

 DESCRIPTION            |   10 +++++-----
 MD5                    |    4 ++--
 man/PropCIs-package.Rd |    6 +++---
 3 files changed, 10 insertions(+), 10 deletions(-)

More information about PropCIs at CRAN
Permanent link

Package MAPA updated to version 1.3 with previous version 1.2 dated 2014-03-24

Title: Multiple Aggregation Prediction Algorithm
Description: This package contains functions and wrappers for using the Multiple Aggregation Prediction Algorithm, proposed by Kourentzes et al. (2014).
Author: Nikolaos Kourentzes and Fotios Petropoulos
Maintainer: Nikolaos Kourentzes

Diff between MAPA versions 1.2 dated 2014-03-24 and 1.3 dated 2014-04-15

 ChangeLog         |only
 DESCRIPTION       |    6 -
 MD5               |   15 ++-
 R/MAPA.R          |  205 +++++++++++++++++++++++++++++++++++-------------------
 man/mapa.Rd       |    5 +
 man/mapacalc.Rd   |    5 +
 man/mapaest.Rd    |    3 
 man/mapafor.Rd    |    5 +
 man/mapasimple.Rd |    5 +
 9 files changed, 163 insertions(+), 86 deletions(-)

More information about MAPA at CRAN
Permanent link

Package GEVcdn updated to version 1.1.3 with previous version 1.1.2 dated 2012-11-14

Title: GEV conditional density estimation network
Description: A flexible nonlinear modelling framework for nonstationary generalized extreme value analysis in hydroclimatology
Author: Alex J. Cannon
Maintainer: Alex J. Cannon

Diff between GEVcdn versions 1.1.2 dated 2012-11-14 and 1.1.3 dated 2014-04-15

 DESCRIPTION             |    6 ++--
 MD5                     |    8 ++---
 man/gevcdn.bag.Rd       |   67 ++++++++++++++++++++++++------------------------
 man/gevcdn.bootstrap.Rd |   49 +++++++++++++++++------------------
 man/gevcdn.fit.Rd       |   14 +++++++---
 5 files changed, 77 insertions(+), 67 deletions(-)

More information about GEVcdn at CRAN
Permanent link

Package geomorph updated to version 2.0 with previous version 1.1-6 dated 2014-01-28

Title: Geometric morphometric analyses of 2d/3d landmark data
Description: Read, manipulate, and digitize landmark data, generate shape variables via Procrustes analysis for points, curves and surfaces, perform shape analyses, and provide graphical depictions of shapes and patterns of shape variation
Author: Dean Adams, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams

Diff between geomorph versions 1.1-6 dated 2014-01-28 and 2.0 dated 2014-04-15

 geomorph-1.1-6/geomorph/R/geomorph.r                    |only
 geomorph-1.1-6/geomorph/man/curves2d.Rd                 |only
 geomorph-1.1-6/geomorph/man/digit.curves.Rd             |only
 geomorph-2.0/geomorph/DESCRIPTION                       |   11 -
 geomorph-2.0/geomorph/MD5                               |  156 ++++++++++------
 geomorph-2.0/geomorph/NAMESPACE                         |    8 
 geomorph-2.0/geomorph/NEWS                              |   56 +++++
 geomorph-2.0/geomorph/R/arrayspecs.r                    |only
 geomorph-2.0/geomorph/R/bilat.symmetry.r                |only
 geomorph-2.0/geomorph/R/build.template.r                |only
 geomorph-2.0/geomorph/R/compare.evol.rates.r            |only
 geomorph-2.0/geomorph/R/compare.modular.partitions.r    |only
 geomorph-2.0/geomorph/R/define.modules.R                |only
 geomorph-2.0/geomorph/R/define.sliders.2d.r             |only
 geomorph-2.0/geomorph/R/define.sliders.3d.r             |only
 geomorph-2.0/geomorph/R/digit.fixed.r                   |only
 geomorph-2.0/geomorph/R/digitize2d.r                    |only
 geomorph-2.0/geomorph/R/digitsurface.r                  |only
 geomorph-2.0/geomorph/R/editTemplate.r                  |only
 geomorph-2.0/geomorph/R/estimate.missing.r              |only
 geomorph-2.0/geomorph/R/findMeanSpec.R                  |only
 geomorph-2.0/geomorph/R/fixed.angle.r                   |only
 geomorph-2.0/geomorph/R/geomorph.support.code.r         |only
 geomorph-2.0/geomorph/R/gpagen.r                        |only
 geomorph-2.0/geomorph/R/morphol.disparity.R             |only
 geomorph-2.0/geomorph/R/morphol.integr.r                |only
 geomorph-2.0/geomorph/R/pairwiseD.test.r                |only
 geomorph-2.0/geomorph/R/phylo.pls.R                     |only
 geomorph-2.0/geomorph/R/physignal.r                     |only
 geomorph-2.0/geomorph/R/plotAllSpecimens.r              |only
 geomorph-2.0/geomorph/R/plotAllometry.r                 |only
 geomorph-2.0/geomorph/R/plotGMPhyloMorphoSpace.r        |only
 geomorph-2.0/geomorph/R/plotRefToTarget.r               |only
 geomorph-2.0/geomorph/R/plotTangentSpace.r              |only
 geomorph-2.0/geomorph/R/plotspec.r                      |only
 geomorph-2.0/geomorph/R/procD.lm.r                      |only
 geomorph-2.0/geomorph/R/read.morphologika.r             |only
 geomorph-2.0/geomorph/R/read.ply.r                      |only
 geomorph-2.0/geomorph/R/readland.nts.r                  |only
 geomorph-2.0/geomorph/R/readland.tps.r                  |only
 geomorph-2.0/geomorph/R/readmulti.nts.r                 |only
 geomorph-2.0/geomorph/R/trajectory.analysis.r           |only
 geomorph-2.0/geomorph/R/two.b.pls.r                     |only
 geomorph-2.0/geomorph/R/two.d.array.r                   |only
 geomorph-2.0/geomorph/R/warpRefMesh.R                   |only
 geomorph-2.0/geomorph/R/writeland.tps.r                 |only
 geomorph-2.0/geomorph/data/hummingbirds.rda             |binary
 geomorph-2.0/geomorph/data/mosquito.rda                 |binary
 geomorph-2.0/geomorph/data/motionpaths.rda              |binary
 geomorph-2.0/geomorph/data/plethShapeFood.rda           |only
 geomorph-2.0/geomorph/data/plethodon.rda                |binary
 geomorph-2.0/geomorph/data/plethspecies.rda             |binary
 geomorph-2.0/geomorph/data/ratland.rda                  |binary
 geomorph-2.0/geomorph/data/scallopPLY.rda               |binary
 geomorph-2.0/geomorph/data/scallops.rda                 |binary
 geomorph-2.0/geomorph/man/arrayspecs.Rd                 |   24 --
 geomorph-2.0/geomorph/man/bilat.symmetry.Rd             |   52 ++---
 geomorph-2.0/geomorph/man/buildtemplate.Rd              |   53 +++--
 geomorph-2.0/geomorph/man/compare.evol.rates.Rd         |   47 +++-
 geomorph-2.0/geomorph/man/compare.modular.partitions.Rd |    5 
 geomorph-2.0/geomorph/man/define.modules.Rd             |only
 geomorph-2.0/geomorph/man/define.sliders.2d.Rd          |   19 -
 geomorph-2.0/geomorph/man/define.sliders.3d.Rd          |   33 +--
 geomorph-2.0/geomorph/man/digit.fixed.Rd                |   52 ++---
 geomorph-2.0/geomorph/man/digitize2d.Rd                 |   61 +++---
 geomorph-2.0/geomorph/man/digitsurface.Rd               |   53 ++---
 geomorph-2.0/geomorph/man/editTemplate.Rd               |   22 +-
 geomorph-2.0/geomorph/man/estimate.missing.Rd           |   77 ++++++-
 geomorph-2.0/geomorph/man/findMeanSpec.Rd               |only
 geomorph-2.0/geomorph/man/fixed.angle.Rd                |    1 
 geomorph-2.0/geomorph/man/gpagen.Rd                     |   25 +-
 geomorph-2.0/geomorph/man/hummingbirds.Rd               |    2 
 geomorph-2.0/geomorph/man/morphol.disparity.Rd          |only
 geomorph-2.0/geomorph/man/morphol.integr.Rd             |   65 ++++--
 geomorph-2.0/geomorph/man/mosquito.Rd                   |    2 
 geomorph-2.0/geomorph/man/motionpaths.Rd                |    2 
 geomorph-2.0/geomorph/man/mshape.Rd                     |    2 
 geomorph-2.0/geomorph/man/pairwiseD.test.Rd             |    2 
 geomorph-2.0/geomorph/man/phylo.pls.Rd                  |only
 geomorph-2.0/geomorph/man/physignal.Rd                  |   80 ++++++--
 geomorph-2.0/geomorph/man/plethShapeFood.Rd             |only
 geomorph-2.0/geomorph/man/plethodon.Rd                  |    2 
 geomorph-2.0/geomorph/man/plethspecies.Rd               |    2 
 geomorph-2.0/geomorph/man/plotAllSpecimens.Rd           |    2 
 geomorph-2.0/geomorph/man/plotAllometry.Rd              |   94 ++++++---
 geomorph-2.0/geomorph/man/plotGMPhyloMorphoSpace.Rd     |   21 +-
 geomorph-2.0/geomorph/man/plotRefToTarget.Rd            |   57 +++--
 geomorph-2.0/geomorph/man/plotTangentSpace.Rd           |   51 +++--
 geomorph-2.0/geomorph/man/plotspec.Rd                   |   51 +++--
 geomorph-2.0/geomorph/man/procD.lm.Rd                   |    7 
 geomorph-2.0/geomorph/man/ratland.Rd                    |    2 
 geomorph-2.0/geomorph/man/read.morphologika.Rd          |   69 +++----
 geomorph-2.0/geomorph/man/read.ply.Rd                   |   14 -
 geomorph-2.0/geomorph/man/read.vrml.Rd                  |   55 -----
 geomorph-2.0/geomorph/man/readland.nts.Rd               |   17 +
 geomorph-2.0/geomorph/man/readland.tps.Rd               |    9 
 geomorph-2.0/geomorph/man/readmulti.nts.Rd              |   14 +
 geomorph-2.0/geomorph/man/scallopPLY.Rd                 |    2 
 geomorph-2.0/geomorph/man/scallops.Rd                   |    2 
 geomorph-2.0/geomorph/man/trajectory.analysis.Rd        |    6 
 geomorph-2.0/geomorph/man/two.b.pls.Rd                  |only
 geomorph-2.0/geomorph/man/two.d.array.Rd                |    4 
 geomorph-2.0/geomorph/man/warpRefMesh.Rd                |only
 geomorph-2.0/geomorph/man/writeland.tps.Rd              |    2 
 104 files changed, 835 insertions(+), 558 deletions(-)

More information about geomorph at CRAN
Permanent link

Package GeneNet updated to version 1.2.9 with previous version 1.2.8 dated 2013-09-15

Title: Modeling and Inferring Gene Networks
Description: GeneNet is a package for analyzing gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between GeneNet versions 1.2.8 dated 2013-09-15 and 1.2.9 dated 2014-04-15

 DESCRIPTION |   12 ++++++------
 MD5         |    6 +++---
 NAMESPACE   |    3 +++
 NEWS        |    6 ++++++
 4 files changed, 18 insertions(+), 9 deletions(-)

More information about GeneNet at CRAN
Permanent link

Package gdsfmt updated to version 1.0.4 with previous version 1.0.3 dated 2014-03-19

Title: R Interface to CoreArray Genomic Data Structure (GDS) files
Description: This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers with less than 8 bits, since a single genetic/genomic variant, such like single-nucleotide polymorphism, usually occupies fewer bits than a byte. It is also allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng

Diff between gdsfmt versions 1.0.3 dated 2014-03-19 and 1.0.4 dated 2014-04-15

 gdsfmt-1.0.3/gdsfmt/src/gdsfmt_init.cpp                     |only
 gdsfmt-1.0.4/gdsfmt/DESCRIPTION                             |    8 
 gdsfmt-1.0.4/gdsfmt/MD5                                     |  144 
 gdsfmt-1.0.4/gdsfmt/NEWS                                    |   12 
 gdsfmt-1.0.4/gdsfmt/R/gdsfmt-main.r                         |  180 
 gdsfmt-1.0.4/gdsfmt/build/vignette.rds                      |binary
 gdsfmt-1.0.4/gdsfmt/inst/doc/CoreArrayTutorial.pdf          |binary
 gdsfmt-1.0.4/gdsfmt/inst/unitTests/runit.01.datatype.r      |    3 
 gdsfmt-1.0.4/gdsfmt/inst/unitTests/runit.02.dataconvert.r   |    3 
 gdsfmt-1.0.4/gdsfmt/inst/unitTests/runit.03.dimension.r     |    3 
 gdsfmt-1.0.4/gdsfmt/inst/unitTests/runit.04.datareadwrite.r |   67 
 gdsfmt-1.0.4/gdsfmt/inst/unitTests/runit.05.attribute.r     |    2 
 gdsfmt-1.0.4/gdsfmt/inst/unitTests/runit.06.apply.r         |  112 
 gdsfmt-1.0.4/gdsfmt/man/add.gdsn.Rd                         |   23 
 gdsfmt-1.0.4/gdsfmt/man/addfile.gdsn.Rd                     |    8 
 gdsfmt-1.0.4/gdsfmt/man/addfolder.gdsn.Rd                   |    3 
 gdsfmt-1.0.4/gdsfmt/man/append.gdsn.Rd                      |    3 
 gdsfmt-1.0.4/gdsfmt/man/apply.gdsn.Rd                       |   26 
 gdsfmt-1.0.4/gdsfmt/man/cleanup.gds.Rd                      |    3 
 gdsfmt-1.0.4/gdsfmt/man/closefn.gds.Rd                      |    4 
 gdsfmt-1.0.4/gdsfmt/man/clusterApply.gdsn.Rd                |   14 
 gdsfmt-1.0.4/gdsfmt/man/cnt.gdsn.Rd                         |    4 
 gdsfmt-1.0.4/gdsfmt/man/compression.gdsn.Rd                 |    3 
 gdsfmt-1.0.4/gdsfmt/man/createfn.gds.Rd                     |    4 
 gdsfmt-1.0.4/gdsfmt/man/delete.gdsn.Rd                      |    3 
 gdsfmt-1.0.4/gdsfmt/man/diagnosis.gds.Rd                    |only
 gdsfmt-1.0.4/gdsfmt/man/gds.class.Rd                        |    2 
 gdsfmt-1.0.4/gdsfmt/man/gdsfmt-package.Rd                   |   19 
 gdsfmt-1.0.4/gdsfmt/man/get.attr.gdsn.Rd                    |    3 
 gdsfmt-1.0.4/gdsfmt/man/index.gdsn.Rd                       |    3 
 gdsfmt-1.0.4/gdsfmt/man/ls.gdsn.Rd                          |    3 
 gdsfmt-1.0.4/gdsfmt/man/moveto.gdsn.Rd                      |only
 gdsfmt-1.0.4/gdsfmt/man/name.gdsn.Rd                        |    3 
 gdsfmt-1.0.4/gdsfmt/man/objdesp.gdsn.Rd                     |    3 
 gdsfmt-1.0.4/gdsfmt/man/openfn.gds.Rd                       |    7 
 gdsfmt-1.0.4/gdsfmt/man/put.attr.gdsn.Rd                    |    3 
 gdsfmt-1.0.4/gdsfmt/man/read.gdsn.Rd                        |   12 
 gdsfmt-1.0.4/gdsfmt/man/readex.gdsn.Rd                      |    9 
 gdsfmt-1.0.4/gdsfmt/man/readmode.gdsn.Rd                    |    3 
 gdsfmt-1.0.4/gdsfmt/man/rename.gdsn.Rd                      |    3 
 gdsfmt-1.0.4/gdsfmt/man/setdim.gdsn.Rd                      |    3 
 gdsfmt-1.0.4/gdsfmt/man/showfile.gds.Rd                     |    3 
 gdsfmt-1.0.4/gdsfmt/man/sync.gds.Rd                         |    4 
 gdsfmt-1.0.4/gdsfmt/man/write.gdsn.Rd                       |    3 
 gdsfmt-1.0.4/gdsfmt/src/CoreArray.cpp                       |   20 
 gdsfmt-1.0.4/gdsfmt/src/CoreArray.h                         |    7 
 gdsfmt-1.0.4/gdsfmt/src/CoreDEF.h                           |  254 -
 gdsfmt-1.0.4/gdsfmt/src/CoreGDS.cpp                         |  273 -
 gdsfmt-1.0.4/gdsfmt/src/CoreGDS.h                           |   42 
 gdsfmt-1.0.4/gdsfmt/src/Makevars                            |    7 
 gdsfmt-1.0.4/gdsfmt/src/Makevars.win                        |    7 
 gdsfmt-1.0.4/gdsfmt/src/R_CoreArray.cpp                     |only
 gdsfmt-1.0.4/gdsfmt/src/R_GDS.h                             | 1343 -----
 gdsfmt-1.0.4/gdsfmt/src/R_GDS2.h                            |  721 ++-
 gdsfmt-1.0.4/gdsfmt/src/R_GDS_CPP.h                         |only
 gdsfmt-1.0.4/gdsfmt/src/dBase.cpp                           |  534 +-
 gdsfmt-1.0.4/gdsfmt/src/dBase.h                             |  459 -
 gdsfmt-1.0.4/gdsfmt/src/dBit.h                              |  185 
 gdsfmt-1.0.4/gdsfmt/src/dBitGDS.cpp                         |   63 
 gdsfmt-1.0.4/gdsfmt/src/dBitGDS.h                           |  518 +-
 gdsfmt-1.0.4/gdsfmt/src/dFile.cpp                           |  104 
 gdsfmt-1.0.4/gdsfmt/src/dFile.h                             |   61 
 gdsfmt-1.0.4/gdsfmt/src/dParallel.cpp                       |   29 
 gdsfmt-1.0.4/gdsfmt/src/dParallel.h                         |  116 
 gdsfmt-1.0.4/gdsfmt/src/dParallel_Ext.c                     |only
 gdsfmt-1.0.4/gdsfmt/src/dPlatform.cpp                       |  208 
 gdsfmt-1.0.4/gdsfmt/src/dPlatform.h                         |  207 
 gdsfmt-1.0.4/gdsfmt/src/dStrGDS.h                           |   38 
 gdsfmt-1.0.4/gdsfmt/src/dStream.cpp                         |   78 
 gdsfmt-1.0.4/gdsfmt/src/dStream.h                           |   80 
 gdsfmt-1.0.4/gdsfmt/src/dString.h                           |   23 
 gdsfmt-1.0.4/gdsfmt/src/dStruct.cpp                         |  510 +-
 gdsfmt-1.0.4/gdsfmt/src/dStruct.h                           |  525 +-
 gdsfmt-1.0.4/gdsfmt/src/dTrait.h                            |only
 gdsfmt-1.0.4/gdsfmt/src/dType.h                             |  461 -
 gdsfmt-1.0.4/gdsfmt/src/gdsfmt.cpp                          | 2853 +++++-------
 gdsfmt-1.0.4/gdsfmt/src/gdsfmt_deprecated.h                 |only
 77 files changed, 4895 insertions(+), 5549 deletions(-)

More information about gdsfmt at CRAN
Permanent link

Package fdrtool updated to version 1.2.12 with previous version 1.2.11 dated 2013-09-15

Title: Estimation of (Local) False Discovery Rates and Higher Criticism
Description: This package allows to estimate both tail area-based false discovery rates (Fdr) as well as local false discovery rates (fdr) for a variety of null models (p-values, z-scores, correlation coefficients, t-scores). The proportion of null values and the parameters of the null distribution are adaptively estimated from the data. In addition, the package contains functions for non-parametric density estimation (Grenander estimator), for monotone regression (isotonic regression and antitonic regression with weights), for computing the greatest convex minorant (GCM) and the least concave majorant (LCM), for the half-normal and correlation distributions, and for computing empirical higher criticism (HC) scores and the corresponding decision threshold.
Author: Bernd Klaus and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between fdrtool versions 1.2.11 dated 2013-09-15 and 1.2.12 dated 2014-04-15

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 NEWS        |    6 ++++++
 R/monoreg.R |    6 +++---
 4 files changed, 16 insertions(+), 10 deletions(-)

More information about fdrtool at CRAN
Permanent link

Package effsize updated to version 0.5 with previous version 0.4.1 dated 2014-03-13

Title: Efficient effect size computation
Description: This package contains the functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha and Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.
Author: Marco Torchiano
Maintainer: Marco Torchiano

Diff between effsize versions 0.4.1 dated 2014-03-13 and 0.5 dated 2014-04-15

 DESCRIPTION            |   15 ++++++++-------
 MD5                    |   10 ++++++----
 R/CohenD.R             |   11 +++++------
 R/VD_A.R               |only
 man/VD.A.Rd            |only
 man/cohen.d.Rd         |   10 +++++-----
 man/effsize-package.Rd |   15 +++++++++------
 7 files changed, 33 insertions(+), 28 deletions(-)

More information about effsize at CRAN
Permanent link

Package sweSCB updated to version 0.3.4 with previous version 0.3.3 dated 2014-04-01

Title: An R interface to the web API of Statistics Sweden
Description: Interface for the REST API of Statistics Sweden. The package offers methods to fetch information about the data hierarchy stored behind the API; extract metadata; fetch actual data; and clean up the results.
Author: Love Hansson, Thomas Reinholdsson, Mans Magnusson
Maintainer: Mans Magnusson

Diff between sweSCB versions 0.3.3 dated 2014-04-01 and 0.3.4 dated 2014-04-15

 DESCRIPTION           |   12 ++++++------
 MD5                   |   28 ++++++++++++++--------------
 R/getData.R           |    3 ---
 README.md             |   28 +++++++++++-----------------
 man/baseURL.Rd        |    4 ++--
 man/buildPath.Rd      |    6 +++---
 man/checkForLevels.Rd |    6 +++---
 man/deparseLevels.Rd  |    4 ++--
 man/findData.Rd       |   12 ++++++------
 man/getContent.Rd     |    4 ++--
 man/scbGetData.Rd     |   30 +++++++++++++++---------------
 man/scbGetDims.Rd     |    8 ++++----
 man/scbGetLevels.Rd   |    6 +++---
 man/scbGetMetadata.Rd |    8 ++++----
 man/sweSCB.Rd         |    2 +-
 15 files changed, 76 insertions(+), 85 deletions(-)

More information about sweSCB at CRAN
Permanent link

Package scio updated to version 0.6.1 with previous version 0.4.1 dated 2012-05-06

Title: Sparse Column-wise Inverse Operator
Description: Sparse Column-wise Inverse Operator for estimating the inverse covariance matrix. Note that this is a preliminary version accompanying the arXiv paper (arXiv:1203.3896) in 2012. This version contains only the minimal set of functions for estimation and cross validation.
Author: Xi (Rossi) LUO and Weidong Liu
Maintainer: Xi (Rossi) LUO

Diff between scio versions 0.4.1 dated 2012-05-06 and 0.6.1 dated 2014-04-15

 ChangeLog         |    8 ++++++++
 DESCRIPTION       |   16 ++++++----------
 MD5               |   15 ++++++++++-----
 NAMESPACE         |    2 ++
 R/likelihood.R    |only
 R/scio.cv.R       |only
 R/scio.refit.R    |only
 man/scio.Rd       |    4 ++--
 man/scio.cv.Rd    |only
 man/scio.refit.Rd |only
 man/sciopath.Rd   |    5 +++--
 11 files changed, 31 insertions(+), 19 deletions(-)

More information about scio at CRAN
Permanent link

Package RGIFT updated to version 0.1-5 with previous version 0.1-4 dated 2013-10-01

Title: Create quizzes in GIFT Format
Description: This package provides some functions to create quizzes in the GIFT format. This format is used by several Virtual Learning Environments such as Moodle.
Author: María José Haro-Delicado, Virgilio Gómez-Rubio and Francisco Parreño-Torres
Maintainer: Virgilio Gómez-Rubio

Diff between RGIFT versions 0.1-4 dated 2013-10-01 and 0.1-5 dated 2014-04-15

 RGIFT-0.1-4/RGIFT/inst/doc/CochesBig.sav |only
 RGIFT-0.1-4/RGIFT/inst/doc/DExample.R    |only
 RGIFT-0.1-4/RGIFT/inst/doc/EExample.R    |only
 RGIFT-0.1-4/RGIFT/inst/doc/MCQExample.R  |only
 RGIFT-0.1-4/RGIFT/inst/doc/MQExample.R   |only
 RGIFT-0.1-4/RGIFT/inst/doc/MWQExample.R  |only
 RGIFT-0.1-4/RGIFT/inst/doc/NQExample.R   |only
 RGIFT-0.1-4/RGIFT/inst/doc/RGIFT.bib     |only
 RGIFT-0.1-4/RGIFT/inst/doc/SAQExample.R  |only
 RGIFT-0.1-4/RGIFT/inst/doc/TFQExample.R  |only
 RGIFT-0.1-4/RGIFT/inst/doc/UTF8.R        |only
 RGIFT-0.1-4/RGIFT/inst/doc/exams         |only
 RGIFT-0.1-5/RGIFT/DESCRIPTION            |    8 ++++----
 RGIFT-0.1-5/RGIFT/MD5                    |   31 ++++++++++++++++---------------
 RGIFT-0.1-5/RGIFT/inst/doc/RGIFT.pdf     |binary
 RGIFT-0.1-5/RGIFT/vignettes              |only
 16 files changed, 20 insertions(+), 19 deletions(-)

More information about RGIFT at CRAN
Permanent link

Package INLABMA updated to version 0.1-4 with previous version 0.1-3 dated 2013-10-03

Title: Bayesian Model Averaging with INLA
Description: Spatial Econometrics models using Bayesian Model Averaging on models fitted with INLA. The INLA package can be obtained from http://www.r-inla.org . We recommend the testing version, which can be downloaded by running: source("http://www.math.ntnu.no/inla/givemeINLA-testing.R")
Author: Virgilio Gomez Rubio , Roger Bivand
Maintainer: Virgilio Gomez Rubio

Diff between INLABMA versions 0.1-3 dated 2013-10-03 and 0.1-4 dated 2014-04-15

 DESCRIPTION              |   16 ++++---
 MD5                      |   20 ++++-----
 NAMESPACE                |    5 +-
 R/BMArho.R               |    2 
 R/SE-utils.R             |   37 +++++++++++-------
 man/BMA2.Rd              |    7 +--
 man/BMArho.Rd            |    2 
 man/recompute.impacts.Rd |    6 +-
 man/rescalemarg.Rd       |    2 
 man/sem.Rd               |   95 ++++++++++++++++++++++++++++++++++++++++++++++-
 man/trIrhoWinv.Rd        |    2 
 11 files changed, 151 insertions(+), 43 deletions(-)

More information about INLABMA at CRAN
Permanent link

New package HiLMM with initial version 1.0
Package: HiLMM
Type: Package
Title: Estimation of heritability in high dimensional Linear Mixed Models
Version: 1.0
Date: 2014-04-10
Author: Anna Bonnet
Maintainer: Anna Bonnet
Description: HiLMM provides estimation of heritability with confidence intervals in linear mixed models.
License: GPL-2
Packaged: 2014-04-15 13:09:37 UTC; levyleduc
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-15 18:21:12

More information about HiLMM at CRAN
Permanent link

New package StereoMorph with initial version 1.0
Package: StereoMorph
Title: Stereo Camera Calibration and Reconstruction
Description: StereoMorph provides functions for the collection of 3D points and curves using a stereo camera setup.
Version: 1.0
Depends: grid
Suggests: rgl
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen
License: GPL-2
Packaged: 2014-04-15 03:34:20 UTC; aaron
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-15 15:47:06

More information about StereoMorph at CRAN
Permanent link

Package scar updated to version 0.2-1 with previous version 0.2-0 dated 2014-04-08

Title: Shape-Constrained Additive Regression: a Maximum Likelihood Approach
Description: This package computes the maximum likelihood estimator of the generalised additive and index regression with shape constraints. Each additive component function is assumed to obey one of the nine possible shape restrictions: linear, increasing, decreasing, convex, convex increasing, convex decreasing, concave, concave increasing, or concave decreasing.
Author: Yining Chen and Richard Samworth
Maintainer: Yining Chen

Diff between scar versions 0.2-0 dated 2014-04-08 and 0.2-1 dated 2014-04-15

 DESCRIPTION            |    9 ++++-----
 MD5                    |   14 +++++++-------
 NEWS                   |    8 ++++++--
 R/scair.R              |   11 +++++++----
 man/PhDPublications.Rd |    8 ++++++--
 man/scair.Rd           |   25 ++++++++++++++++++-------
 man/scar-package.Rd    |   14 +++++++++-----
 man/scar.Rd            |   15 +++++++++------
 8 files changed, 66 insertions(+), 38 deletions(-)

More information about scar at CRAN
Permanent link

New package MPCI with initial version 1.0.6
Package: MPCI
Type: Package
Title: Multivariate Process Capability Indices (MPCI)
Version: 1.0.6
Date: 2014-04-13
Author: Edgar Santos-Fernandez, Michele Scagliarini.
Maintainer: Edgar Santos-Fernandez
Description: MPCI package performs the followings Multivariate Process Capability Indices: Shahriari et al. (1995) Multivariate Capability Vector, Taam et al. (1993) Multivariate Capability Index (MCpm), Pan and Lee (2010) proposal (NMCpm) and the followings based on Principal Component Analysis (PCA):Wang and Chen (1998), Xekalaki and Perakis (2002) and Wang (2005). Moreover, it includes two datasets.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-04-14 23:18:37 UTC; esantosf
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-15 15:31:19

More information about MPCI at CRAN
Permanent link

New package Johnson with initial version 1.4
Package: Johnson
Type: Package
Title: Johnson Transformation
Version: 1.4
Date: 2014-04-15
Author: Edgar Santos Fernandez
Maintainer: Edgar Santos Fernandez
Description: RE.Johnson performs the Johnson Transformation to increase the normality.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2014-04-14 23:37:38 UTC; esantosf
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-15 15:55:00

More information about Johnson at CRAN
Permanent link

Package EMP updated to version 1.0.1 with previous version 1.0 dated 2014-03-31

Title: EMP: Expected Maximum Profit for Credit Scoring.
Description: Functions for estimating EMP (Expected Maximum Profit Measure) in Credit Scoring, according to Verbraken et al (2014).
Author: Cristian Bravo and Thomas Verbraken
Maintainer: Cristian Bravo

Diff between EMP versions 1.0 dated 2014-03-31 and 1.0.1 dated 2014-04-15

 DESCRIPTION        |   10 +++++-----
 MD5                |    7 ++++---
 inst               |only
 man/EMP-package.Rd |   10 +++++-----
 man/EMP_CS.Rd      |    5 ++---
 5 files changed, 16 insertions(+), 16 deletions(-)

More information about EMP at CRAN
Permanent link

Mon, 14 Apr 2014

Package YuGene updated to version 1.1.1 with previous version 1.1 dated 2014-02-20

Title: YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses
Description: YuGene is a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.
Author: Kim-Anh Le Cao, Florian Rohart, Leo McHugh, Othmar Korn, Christine A. Wells
Maintainer: Florian Rohart

Diff between YuGene versions 1.1 dated 2014-02-20 and 1.1.1 dated 2014-04-14

 DESCRIPTION           |   11 ++++++-----
 MD5                   |    6 +++---
 man/YuGene-package.Rd |    6 ++++--
 man/YuGene.Rd         |    6 ++++--
 4 files changed, 17 insertions(+), 12 deletions(-)

More information about YuGene at CRAN
Permanent link

New package VAR.etp with initial version 0.1
Package: VAR.etp
Type: Package
Title: VAR modelling: estimation, testing, and prediction
Version: 0.1
Date: 2014-04-14
Author: Jae. H. Kim
Maintainer: Jae H. Kim
Description: Estimation, Hypothesis Testing, Prediction for Stationary Vector Autoregressive Models
License: GPL-2
Packaged: 2014-04-14 20:21:51 UTC; jkim
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-15 00:32:09

More information about VAR.etp at CRAN
Permanent link

Package NBPSeq updated to version 0.3.0 with previous version 0.1.8 dated 2012-11-19

Title: Negative Binomial Models for RNA-Sequencing Data
Description: Negative Binomial (NB) models for two-group comparisons and regression inferences from RNA-Sequencing Data.
Author: Yanming Di , Daniel W Schafer , with contributions from Jason S Cumbie and Jeff H Chang .
Maintainer: Yanming Di

Diff between NBPSeq versions 0.1.8 dated 2012-11-19 and 0.3.0 dated 2014-04-14

 NBPSeq-0.1.8/NBPSeq/R/estimate.disp.mapl.R       |only
 NBPSeq-0.1.8/NBPSeq/R/nbp-classes.R              |only
 NBPSeq-0.1.8/NBPSeq/R/nbp-exact-test.R           |only
 NBPSeq-0.1.8/NBPSeq/R/nbp-main.R                 |only
 NBPSeq-0.1.8/NBPSeq/R/nbp-mcle.R                 |only
 NBPSeq-0.1.8/NBPSeq/R/nbp-plots.R                |only
 NBPSeq-0.1.8/NBPSeq/R/nbpseq.package.R           |only
 NBPSeq-0.3.0/NBPSeq/DESCRIPTION                  |   21 -
 NBPSeq-0.3.0/NBPSeq/MD5                          |   69 ++-
 NBPSeq-0.3.0/NBPSeq/NAMESPACE                    |   21 -
 NBPSeq-0.3.0/NBPSeq/R/NBPSeq.package.R           |only
 NBPSeq-0.3.0/NBPSeq/R/hoa.1d.R                   |    8 
 NBPSeq-0.3.0/NBPSeq/R/hoa.hd.R                   |   16 
 NBPSeq-0.3.0/NBPSeq/R/log.likelihood.R           |   20 -
 NBPSeq-0.3.0/NBPSeq/R/nb.glm.R                   |  277 ++++----------
 NBPSeq-0.3.0/NBPSeq/R/nb.glm.dispersion.models.R |only
 NBPSeq-0.3.0/NBPSeq/R/nb.glm.main.R              |  434 +++++++++++++----------
 NBPSeq-0.3.0/NBPSeq/R/nb.glm.optim.disp.R        |only
 NBPSeq-0.3.0/NBPSeq/R/nbp.classes.R              |only
 NBPSeq-0.3.0/NBPSeq/R/nbp.exact.test.R           |only
 NBPSeq-0.3.0/NBPSeq/R/nbp.main.R                 |only
 NBPSeq-0.3.0/NBPSeq/R/nbp.optim.disp.R           |only
 NBPSeq-0.3.0/NBPSeq/R/nbp.plots.R                |only
 NBPSeq-0.3.0/NBPSeq/R/normalization.R            |only
 NBPSeq-0.3.0/NBPSeq/R/plot.nb.data.R             |only
 NBPSeq-0.3.0/NBPSeq/R/smart.plot.R               |  193 +++++++---
 NBPSeq-0.3.0/NBPSeq/inst                         |only
 NBPSeq-0.3.0/NBPSeq/man/NBPSeq-package.Rd        |only
 NBPSeq-0.3.0/NBPSeq/man/arab.Rd                  |   64 +--
 NBPSeq-0.3.0/NBPSeq/man/estimate.disp.Rd         |  165 ++++----
 NBPSeq-0.3.0/NBPSeq/man/estimate.dispersion.Rd   |  113 +++--
 NBPSeq-0.3.0/NBPSeq/man/estimate.norm.factors.Rd |   81 ++--
 NBPSeq-0.3.0/NBPSeq/man/exact.nb.test.Rd         |  205 +++++-----
 NBPSeq-0.3.0/NBPSeq/man/irls.nb.1.Rd             |only
 NBPSeq-0.3.0/NBPSeq/man/nb.glm.test.Rd           |  144 +++----
 NBPSeq-0.3.0/NBPSeq/man/nbp.test.Rd              |  396 ++++++++++----------
 NBPSeq-0.3.0/NBPSeq/man/plot.nb.data.Rd          |only
 NBPSeq-0.3.0/NBPSeq/man/plot.nb.dispersion.Rd    |only
 NBPSeq-0.3.0/NBPSeq/man/plot.nbp.Rd              |   33 -
 NBPSeq-0.3.0/NBPSeq/man/prepare.nb.data.Rd       |   33 -
 NBPSeq-0.3.0/NBPSeq/man/prepare.nbp.Rd           |  181 ++++-----
 NBPSeq-0.3.0/NBPSeq/man/print.nb.data.Rd         |only
 NBPSeq-0.3.0/NBPSeq/man/print.nb.dispersion.Rd   |only
 NBPSeq-0.3.0/NBPSeq/man/print.nb.test.Rd         |only
 NBPSeq-0.3.0/NBPSeq/man/print.nbp.Rd             |   33 -
 NBPSeq-0.3.0/NBPSeq/man/test.coefficient.Rd      |  181 ++++++---
 46 files changed, 1413 insertions(+), 1275 deletions(-)

More information about NBPSeq at CRAN
Permanent link

Package mapStats updated to version 1.17 with previous version 1.14 dated 2014-02-28

Title: Geographic display of survey data statistics
Description: A package for calculating and visualizing survey data statistics on a color-coded map.
Author: Samuel Ackerman
Maintainer: Samuel Ackerman

Diff between mapStats versions 1.14 dated 2014-02-28 and 1.17 dated 2014-04-14

 DESCRIPTION              |   18 ++----
 MD5                      |   23 ++++----
 NAMESPACE                |    2 
 R/calcQuantiles.R        |   14 ++---
 R/calcStats.R            |   14 ++---
 R/jiggleClass.R          |    2 
 R/mapStats.R             |   20 +++----
 R/plotStats.R            |    8 +-
 demo/map_examples.R      |   22 +++----
 man/jiggleClass.Rd       |   14 ++---
 man/mapStats-internal.Rd |only
 man/mapStats.Rd          |  130 +++++++++++++++++++++--------------------------
 man/usMap.Rd             |    3 -
 13 files changed, 126 insertions(+), 144 deletions(-)

More information about mapStats at CRAN
Permanent link

Package LaF updated to version 0.6 with previous version 0.5 dated 2013-04-25

Title: Fast access to large ASCII files
Description: Methods for fast access to large ASCII files. Currently the following file formats are supported: comma separated format (csv) and fixed width format. It is assumed that the files are too large to fit into memory, although the package can also be used to efficiently access files that do fit into memory. Methods are provided to access and process files blockwise. Furthermore, an opened file can be accessed as one would an ordinary data.frame. The LaF vignette gives an overview of the functionality provided.
Author: Jan van der Laan
Maintainer: Jan van der Laan

Diff between LaF versions 0.5 dated 2013-04-25 and 0.6 dated 2014-04-14

 LaF-0.5/LaF/inst/doc/LaF-benchmark.Rnw.orig |only
 LaF-0.5/LaF/inst/tests                      |only
 LaF-0.5/LaF/man/begin-methods.Rd            |only
 LaF-0.5/LaF/man/current_line-methods.Rd     |only
 LaF-0.5/LaF/man/data_model.Rd               |only
 LaF-0.5/LaF/man/goto-methods.Rd             |only
 LaF-0.5/LaF/man/laf-package.Rd              |only
 LaF-0.5/LaF/man/next_block-methods.Rd       |only
 LaF-0.5/LaF/man/process_blocks-methods.Rd   |only
 LaF-0.5/LaF/man/read_lines-methods.Rd       |only
 LaF-0.5/LaF/tests/tests.R                   |only
 LaF-0.6/LaF/DESCRIPTION                     |   31 ++--
 LaF-0.6/LaF/MD5                             |  101 +++++++-------
 LaF-0.6/LaF/NAMESPACE                       |   48 ++++++
 LaF-0.6/LaF/NEWS                            |    6 
 LaF-0.6/LaF/R/generics.R                    |  104 ++++++++++++--
 LaF-0.6/LaF/R/laf.R                         |  159 +++++++++++++++-------
 LaF-0.6/LaF/R/laf_column.R                  |   82 +++++++----
 LaF-0.6/LaF/R/meta.R                        |  197 ++++++++++++++++++++++++++++
 LaF-0.6/LaF/R/open.R                        |  108 ++++++++++++++-
 LaF-0.6/LaF/R/read_dm_blaise.R              |   47 ++++++
 LaF-0.6/LaF/R/stats.R                       |   90 ++++++++----
 LaF-0.6/LaF/R/textutils.R                   |   83 +++++++++++
 LaF-0.6/LaF/build                           |only
 LaF-0.6/LaF/inst/doc/LaF-benchmark.pdf      |binary
 LaF-0.6/LaF/inst/doc/LaF-manual.R           |only
 LaF-0.6/LaF/inst/doc/LaF-manual.pdf         |binary
 LaF-0.6/LaF/man/begin.Rd                    |only
 LaF-0.6/LaF/man/cindexing.Rd                |only
 LaF-0.6/LaF/man/close.Rd                    |only
 LaF-0.6/LaF/man/current_line.Rd             |only
 LaF-0.6/LaF/man/datamodels.Rd               |only
 LaF-0.6/LaF/man/detect_dm_csv.Rd            |  102 ++++++++------
 LaF-0.6/LaF/man/determine_nlines.Rd         |   50 +++----
 LaF-0.6/LaF/man/get_lines.Rd                |   42 ++---
 LaF-0.6/LaF/man/goto.Rd                     |only
 LaF-0.6/LaF/man/indexing.Rd                 |only
 LaF-0.6/LaF/man/laf-class.Rd                |  124 ++---------------
 LaF-0.6/LaF/man/laf_column-class.Rd         |   62 +-------
 LaF-0.6/LaF/man/laf_open.Rd                 |   48 +++---
 LaF-0.6/LaF/man/laf_open_csv.Rd             |   90 +++++++-----
 LaF-0.6/LaF/man/laf_open_fwf.Rd             |  119 +++++-----------
 LaF-0.6/LaF/man/levels.Rd                   |only
 LaF-0.6/LaF/man/names.Rd                    |only
 LaF-0.6/LaF/man/ncol.Rd                     |only
 LaF-0.6/LaF/man/next_block.Rd               |only
 LaF-0.6/LaF/man/nrow.Rd                     |only
 LaF-0.6/LaF/man/process_blocks.Rd           |only
 LaF-0.6/LaF/man/read_dm_blaise.Rd           |   63 ++++----
 LaF-0.6/LaF/man/read_lines.Rd               |only
 LaF-0.6/LaF/man/sample_lines.Rd             |   57 ++++----
 LaF-0.6/LaF/man/show.Rd                     |only
 LaF-0.6/LaF/man/stats.Rd                    |  119 ++++++++--------
 LaF-0.6/LaF/src/doublecolumn.h              |    5 
 LaF-0.6/LaF/src/factorcolumn.h              |    4 
 LaF-0.6/LaF/src/stats.cpp                   |    2 
 LaF-0.6/LaF/tests/test-all.R                |only
 LaF-0.6/LaF/tests/testthat                  |only
 LaF-0.6/LaF/vignettes                       |only
 59 files changed, 1230 insertions(+), 713 deletions(-)

More information about LaF at CRAN
Permanent link

Package etasFLP updated to version 1.0.3 with previous version 1.0.2 dated 2014-04-02

Title: Estimation of an ETAS model. Mixed FLP (Forward Likelihood Predictive) and ML estimation of non-parametric and parametric components of the ETAS model for earthquake description.
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre], Giada Adelfio [aut]
Maintainer: Marcello Chiodi

Diff between etasFLP versions 1.0.2 dated 2014-04-02 and 1.0.3 dated 2014-04-14

 ChangeLog                    |    9 +++++++++
 DESCRIPTION                  |   12 ++++++------
 MD5                          |   26 +++++++++++++-------------
 NAMESPACE                    |   10 ++++++++--
 R/etas.mod2.R                |   14 +++++++-------
 R/etasclass.R                |   17 +++++++++--------
 R/flp1.etas.nlm.R            |    2 +-
 R/plot.etasclass.R           |    5 +++--
 R/profile.etasclass.R        |   12 +++++-------
 R/summary.eqcat.R            |    8 ++++----
 data/californiacatalog.RData |binary
 data/italycatalog.RData      |binary
 man/etasFLP-package.Rd       |    4 ++--
 man/plot.etasclass.Rd        |    3 +--
 14 files changed, 68 insertions(+), 54 deletions(-)

More information about etasFLP at CRAN
Permanent link

Package ensembleBMA updated to version 5.0.8 with previous version 5.0.7 dated 2014-01-30

Title: Probabilistic Forecasting using Ensembles and Bayesian Model Averaging
Description: Bayesian Model Averaging to create probabilistic forecasts from ensemble forecasts and weather observations.
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter, Tilmann Gneiting, University of Washington.
Maintainer: Chris Fraley

Diff between ensembleBMA versions 5.0.7 dated 2014-01-30 and 5.0.8 dated 2014-04-14

 CHANGELOG                        |    3 +++
 DESCRIPTION                      |    8 ++++----
 MD5                              |    8 ++++----
 R/quantileForecast.fitBMAgamma.R |    2 +-
 man/fitBMAgamma.Rd               |   11 +++--------
 5 files changed, 15 insertions(+), 17 deletions(-)

More information about ensembleBMA at CRAN
Permanent link

Package ecoengine updated to version 1.3 with previous version 1.2.6 dated 2014-03-24

Title: Programmatic interface to the API serving UC Berkeley's Natural History Data
Description: The ecoengine (http://ecoengine.berkeley.edu/) provides access to more than 2 million georeferenced specimen records from the Berkeley Natural History Museums. http://bnhm.berkeley.edu/
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram

Diff between ecoengine versions 1.2.6 dated 2014-03-24 and 1.3 dated 2014-04-14

 DESCRIPTION               |    6 +++---
 MD5                       |   18 +++++++++---------
 NEWS                      |    5 +++++
 R/ee_observations.R       |    3 +--
 R/ee_photos.R             |    1 -
 R/ee_search.R             |    1 -
 R/ee_sensor_aggregation.R |    1 -
 R/ee_sensors.R            |    1 -
 README.md                 |    4 ++--
 man/ee_observations.Rd    |    2 +-
 10 files changed, 21 insertions(+), 21 deletions(-)

More information about ecoengine at CRAN
Permanent link

Package Blaunet updated to version 1.0.1 with previous version 1.0.0 dated 2014-01-20

Title: Calculate and Analyze Blau statuses for measuring social distance
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to organizations. Relational (network) data may be incorporated for additional analyses.
Author: Michael Genkin [aut], George Berry [aut], Liyuan Chen [aut], Matthew Brashears [aut]
Maintainer: Michael Genkin

Diff between Blaunet versions 1.0.0 dated 2014-01-20 and 1.0.1 dated 2014-04-14

 DESCRIPTION             |    8 +++----
 MD5                     |   50 ++++++++++++++++++++++++------------------------
 R/blau.R                |   31 +++++++++++++++++++++--------
 R/calc.dyadic.R         |    4 +--
 R/calc.niches.R         |    2 -
 R/calc.niches.ecology.R |    4 +--
 R/calc.nodal.R          |   10 ++++-----
 R/calc.nodal.ecology.R  |    6 ++---
 R/calc.nodal.network.R  |   11 +++++-----
 R/correctFormat.R       |    4 +--
 R/ecology.summary.R     |   12 +++++------
 R/getPresentCases.R     |    2 -
 R/isBinary.R            |    2 -
 R/isCorrectLength.R     |    2 -
 R/niche.summary.R       |    8 +++----
 R/nodal.global.R        |    2 -
 man/TwoCities.Rd        |    2 -
 man/blau.Rd             |   16 ++++++++++++---
 man/blaunet-package.Rd  |   16 +++++++--------
 man/dyadic.Rd           |   13 +++++-------
 man/export.dyadic.Rd    |    6 +++--
 man/export.nodal.Rd     |    2 -
 man/niche.summary.Rd    |    2 -
 man/nodal.global.Rd     |    2 -
 man/nodal.local.Rd      |    2 -
 man/nodal.network.Rd    |    6 +++--
 26 files changed, 126 insertions(+), 99 deletions(-)

More information about Blaunet at CRAN
Permanent link

Package soundecology updated to version 1.1.1 with previous version 1.1 dated 2013-11-25

Title: Soundscape ecology
Description: Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.
Author: Luis J. Villanueva-Rivera and Bryan C. Pijanowski
Maintainer: Luis J. Villanueva-Rivera

Diff between soundecology versions 1.1 dated 2013-11-25 and 1.1.1 dated 2014-04-14

 soundecology-1.1.1/soundecology/DESCRIPTION                 |   12 
 soundecology-1.1.1/soundecology/MD5                         |   23 -
 soundecology-1.1.1/soundecology/NAMESPACE                   |   13 
 soundecology-1.1.1/soundecology/NEWS                        |    3 
 soundecology-1.1.1/soundecology/build/vignette.rds          |binary
 soundecology-1.1.1/soundecology/inst/doc/changeADI.Rmd      |    2 
 soundecology-1.1.1/soundecology/inst/doc/changeADI.html     |    2 
 soundecology-1.1.1/soundecology/inst/doc/intro.Rmd          |   20 -
 soundecology-1.1.1/soundecology/inst/doc/intro.html         |  215 +-----------
 soundecology-1.1.1/soundecology/man/soundecology.package.Rd |    4 
 soundecology-1.1.1/soundecology/vignettes/changeADI.Rmd     |    2 
 soundecology-1.1.1/soundecology/vignettes/intro.Rmd         |   20 -
 soundecology-1.1/soundecology/inst/doc/intro.R              |only
 13 files changed, 74 insertions(+), 242 deletions(-)

More information about soundecology at CRAN
Permanent link

Package sdcTable updated to version 0.15.0 with previous version 0.14.0 dated 2014-04-01

Title: Methods for statistical disclosure control in tabular data
Description: Implementation of methods for statistical disclosure control in tabular data
Author: Bernhard Meindl
Maintainer: Bernhard Meindl

Diff between sdcTable versions 0.14.0 dated 2014-04-01 and 0.15.0 dated 2014-04-14

 DESCRIPTION               |    8 ++++----
 MD5                       |    6 +++---
 R/export_functions.r      |   16 ++++++++++++++--
 R/methods_class_dataObj.r |    3 +--
 4 files changed, 22 insertions(+), 11 deletions(-)

More information about sdcTable at CRAN
Permanent link

Package rsm updated to version 2.05 with previous version 2.04 dated 2014-02-05

Title: Response-surface analysis
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth

Diff between rsm versions 2.04 dated 2014-02-05 and 2.05 dated 2014-04-14

 DESCRIPTION        |    8 +++---
 MD5                |    8 +++---
 R/rsm.R            |   68 ++++++++++++++++++++++++++++++++---------------------
 build/vignette.rds |binary
 inst/NEWS          |    6 ++++
 5 files changed, 56 insertions(+), 34 deletions(-)

More information about rsm at CRAN
Permanent link

Package QuasiSeq updated to version 1.0-4 with previous version 1.0-3 dated 2014-02-12

Title: Analyzing RNA sequence count tables using quasi-likelihood
Description: This package is used to apply the QL, QLShrink and QLSpline methods (Lund, Nettleton, McCarthy, and Smyth, 2012) to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data.
Author: Steve Lund and Long Qu
Maintainer: Steve Lund

Diff between QuasiSeq versions 1.0-3 dated 2014-02-12 and 1.0-4 dated 2014-04-14

 DESCRIPTION    |   10 ++++------
 MD5            |   16 ++++++++--------
 NAMESPACE      |    2 +-
 R/NBDev.R      |   42 +++++++++++++++++++++++++++++++++++++++++-
 R/QL.fit.R     |   29 +++++++++++++++--------------
 R/QL.results.R |    8 +-------
 R/negbin.br.R  |    2 +-
 man/NBDev.Rd   |    6 ++++--
 man/QL.fit.Rd  |    3 ++-
 9 files changed, 77 insertions(+), 41 deletions(-)

More information about QuasiSeq at CRAN
Permanent link

Package pumilioR updated to version 1.3 with previous version 1.2 dated 2014-02-04

Title: Pumilio in R
Description: R package to query and get data out of a Pumilio sound archive system (http://ljvillanueva.github.io/pumilio/).
Author: Luis J. Villanueva-Rivera
Maintainer: Luis J. Villanueva-Rivera

Diff between pumilioR versions 1.2 dated 2014-02-04 and 1.3 dated 2014-04-14

 DESCRIPTION                |    8 ++++----
 MD5                        |   20 ++++++++++----------
 NEWS                       |    5 +++++
 R/getFile.R                |   34 ++++++++++++++++++++++++++--------
 build/vignette.rds         |binary
 inst/doc/pumiliosetup.Rmd  |    2 +-
 inst/doc/pumiliosetup.html |    2 +-
 man/getFile.Rd             |   25 ++++++++++++++++++++-----
 man/pumilioR.package.Rd    |    4 ++--
 vignettes/pumiliosetup.Rmd |    2 +-
 vignettes/pumiliosetup.md  |    2 +-
 11 files changed, 71 insertions(+), 33 deletions(-)

More information about pumilioR at CRAN
Permanent link

Package psych updated to version 1.4.4 with previous version 1.4.3 dated 2014-03-25

Title: Procedures for Psychological, Psychometric, and Personality Research
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle

Diff between psych versions 1.4.3 dated 2014-03-25 and 1.4.4 dated 2014-04-14

 DESCRIPTION                |    8 ++--
 MD5                        |   32 +++++++++----------
 R/alpha.R                  |    7 ++--
 R/cor.ci.R                 |    7 ++--
 R/corr.test.R              |   75 +++++++++++++++++++++++++++++++++++++++------
 R/fa.R                     |    2 -
 R/fa.ci.R                  |    6 +++
 R/print.psych.fa.R         |    2 -
 R/statsBy.r                |   19 +++++++++--
 inst/CITATION              |    4 +-
 inst/NEWS.Rd               |   37 +++++++++++++++++++---
 inst/doc/overview.pdf      |binary
 inst/doc/psych_for_sem.pdf |binary
 man/corr.test.Rd           |   15 ++++++---
 man/fa.Rd                  |    5 ++-
 man/factor.congruence.Rd   |    4 +-
 man/statsBy.Rd             |    6 +--
 17 files changed, 170 insertions(+), 59 deletions(-)

More information about psych at CRAN
Permanent link

Package pairwise updated to version 0.2.4 with previous version 0.2.2 dated 2014-04-07

Title: Rasch Model Parameters by Pairwise Algorithm
Description: The package pairwise offers functions for the explicit calculation -- not estimation! -- of the Rasch item parameters for dichotomous and polytomous item responses, using a pairwise comparison approach. Person parameters (WLE) are calculated according to Warm's weighted likelihood approach.
Author: Joerg-Henrik Heine
Maintainer: Joerg-Henrik Heine

Diff between pairwise versions 0.2.2 dated 2014-04-07 and 0.2.4 dated 2014-04-14

 pairwise-0.2.2/pairwise/man/pairwise.Rd            |only
 pairwise-0.2.4/pairwise/DESCRIPTION                |   32 ++++----
 pairwise-0.2.4/pairwise/MD5                        |   78 ++++++++++-----------
 pairwise-0.2.4/pairwise/NAMESPACE                  |    1 
 pairwise-0.2.4/pairwise/NEWS                       |   10 ++
 pairwise-0.2.4/pairwise/R/catprob.R                |    6 -
 pairwise-0.2.4/pairwise/R/esc.R                    |    4 -
 pairwise-0.2.4/pairwise/R/ftab.R                   |   10 +-
 pairwise-0.2.4/pairwise/R/gif.R                    |    4 -
 pairwise-0.2.4/pairwise/R/grm.R                    |   12 +--
 pairwise-0.2.4/pairwise/R/i.expscore.R             |    6 +
 pairwise-0.2.4/pairwise/R/i.ptb.R                  |   18 ++--
 pairwise-0.2.4/pairwise/R/i.pvx.R                  |    2 
 pairwise-0.2.4/pairwise/R/make.incidenz.R          |   16 ++--
 pairwise-0.2.4/pairwise/R/pair.R                   |    8 +-
 pairwise-0.2.4/pairwise/R/pairSE.R                 |   12 +--
 pairwise-0.2.4/pairwise/R/pairwise-package.r       |   22 ++++-
 pairwise-0.2.4/pairwise/R/pairwise.item.fit.R      |   18 +++-
 pairwise-0.2.4/pairwise/R/pairwise.person.fit.R    |   16 ++--
 pairwise-0.2.4/pairwise/R/pers.R                   |   78 +++++++++++----------
 pairwise-0.2.4/pairwise/R/plot.pairSE.R            |    2 
 pairwise-0.2.4/pairwise/R/plot.pers.R              |only
 pairwise-0.2.4/pairwise/R/ptbis.R                  |   19 +++--
 pairwise-0.2.4/pairwise/R/summary.pers.R           |   47 +++++-------
 pairwise-0.2.4/pairwise/man/bfiN_miss.Rd           |    2 
 pairwise-0.2.4/pairwise/man/catprob.Rd             |   14 ++-
 pairwise-0.2.4/pairwise/man/cogBOOKLET.Rd          |    2 
 pairwise-0.2.4/pairwise/man/esc.Rd                 |    4 -
 pairwise-0.2.4/pairwise/man/gif.Rd                 |    2 
 pairwise-0.2.4/pairwise/man/grm.Rd                 |   23 ++----
 pairwise-0.2.4/pairwise/man/make.incidenz.Rd       |   20 ++---
 pairwise-0.2.4/pairwise/man/pair.Rd                |   13 ++-
 pairwise-0.2.4/pairwise/man/pairSE.Rd              |   33 ++++----
 pairwise-0.2.4/pairwise/man/pairwise-package.Rd    |only
 pairwise-0.2.4/pairwise/man/pairwise.item.fit.Rd   |   16 +++-
 pairwise-0.2.4/pairwise/man/pairwise.person.fit.Rd |   18 ++--
 pairwise-0.2.4/pairwise/man/pers.Rd                |   24 +++---
 pairwise-0.2.4/pairwise/man/plot.pairSE.Rd         |    2 
 pairwise-0.2.4/pairwise/man/plot.pers.Rd           |only
 pairwise-0.2.4/pairwise/man/ptbis.Rd               |    8 +-
 pairwise-0.2.4/pairwise/man/sim200x3.Rd            |    2 
 pairwise-0.2.4/pairwise/man/summary.pers.Rd        |   15 ++--
 42 files changed, 350 insertions(+), 269 deletions(-)

More information about pairwise at CRAN
Permanent link

New package OceanView with initial version 1.0
Package: OceanView
Version: 1.0
Title: Visualisation of Oceanographic Data and Model Output.
Author: Karline Soetaert
Maintainer: Karline Soetaert
Depends: plot3D, plot3Drgl, R (>= 2.10)
Imports: shape
Description: Functions for transforming and viewing 2-D and 3-D (oceanographic) data and model output.
License: GPL (>= 3.0)
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: plot3d
Repository/R-Forge/Revision: 80
Repository/R-Forge/DateTimeStamp: 2014-04-11 08:12:26
Date/Publication: 2014-04-14 19:18:54
Packaged: 2014-04-11 10:18:52 UTC; rforge
NeedsCompilation: yes

More information about OceanView at CRAN
Permanent link

Package longitudinal updated to version 1.1.9 with previous version 1.1.8 dated 2013-09-15

Title: Analysis of Multiple Time Course Data
Description: This package contains general data structures and functions for longitudinal data with multiple variables, repeated measurements, and irregularly spaced time points. It also implements a shrinkage estimator of dynamical correlation and dynamical covariance.
Author: Rainer Opgen-Rhein and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between longitudinal versions 1.1.8 dated 2013-09-15 and 1.1.9 dated 2014-04-14

 DESCRIPTION |    8 ++++----
 MD5         |    6 +++---
 NAMESPACE   |    3 +++
 NEWS        |    4 ++++
 4 files changed, 14 insertions(+), 7 deletions(-)

More information about longitudinal at CRAN
Permanent link

Package fscaret updated to version 0.8.5.6 with previous version 0.8.5.5 dated 2014-04-01

Title: Automated caret feature selection
Description: Automated feature selection using variety of models provided by caret package
Author: Jakub Szlek , acknowledgments to Aleksander Mendyk, contributions from stackoverflow and r-help@r-project.org mailing list community. Acknowledgments: This work was funded by Poland-Singapore bilateral cooperation project no 2/3/POL-SIN/2012.
Maintainer: Jakub Szlek

Diff between fscaret versions 0.8.5.5 dated 2014-04-01 and 0.8.5.6 dated 2014-04-14

 DESCRIPTION            |    8 ++++----
 MD5                    |   14 +++++++-------
 R/fscaret.R            |    2 +-
 build/vignette.rds     |binary
 inst/NEWS.Rd           |    8 ++++++++
 inst/doc/fscaret.pdf   |binary
 man/fscaret-package.Rd |    4 ++--
 man/fscaret.Rd         |    2 +-
 8 files changed, 23 insertions(+), 15 deletions(-)

More information about fscaret at CRAN
Permanent link

Package BH updated to version 1.54.0-2 with previous version 1.54.0-1 dated 2014-04-08

Title: Boost C++ header files
Description: Boost provides free peer-reviewed portable C++ source libraries. A large part of Boost is provided as C++ template code which is resolved entirely at compile-time without linking. This package aims to provide the most useful subset of Boost libraries for template use among CRAN package. By placing these libraries in this package, we offer a more efficient distribution system for CRAN as replication of this code in the sources of other packages is avoided.
Author: Dirk Eddelbuettel, John W. Emerson and Michael J. Kane
Maintainer: Dirk Eddelbuettel

Diff between BH versions 1.54.0-1 dated 2014-04-08 and 1.54.0-2 dated 2014-04-14

 ChangeLog                           |only
 DESCRIPTION                         |    8 ++++----
 MD5                                 |    7 ++++---
 inst/NEWS.Rd                        |    7 +++++++
 inst/include/boost/lexical_cast.hpp |    2 ++
 5 files changed, 17 insertions(+), 7 deletions(-)

More information about BH at CRAN
Permanent link

Package seqminer updated to version 2.7 with previous version 2.2 dated 2014-01-27

Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL format) into R
Description: Integrate sequencing data (VCF) or meta-analysis results in R
Author: Xiaowei Zhan and Dajiang Liu , with contributions of Jean-loup Gailly and Mark Adler (they wrote zlib and provide license so we include zlib source code), Julian Seward (this author wrote bzip2 and with BSD license we include bzip2 source codes) and Heng Li (this author wrote tabix and with MIT license we include tabix source codes).
Maintainer: Xiaowei Zhan

Diff between seqminer versions 2.2 dated 2014-01-27 and 2.7 dated 2014-04-14

 ChangeLog                          |   23 
 DESCRIPTION                        |   10 
 MD5                                |   85 +-
 NAMESPACE                          |    6 
 R/seqminer.R                       |  580 +++++++++-----
 inst/tabanno                       |only
 inst/tests/testthat.R              |   11 
 man/annotateGene.Rd                |only
 man/annotatePlain.Rd               |only
 man/annotateVcf.Rd                 |only
 man/getRefBase.Rd                  |only
 man/makeAnnotationParameter.Rd     |only
 man/rvmeta.writeScoreData.Rd       |    5 
 man/tabix.read.header.Rd           |    4 
 man/validateAnnotationParameter.Rd |only
 src/AnnotationController.h         |only
 src/AnnotationInputFile.h          |only
 src/AnnotationOutput.h             |only
 src/AnnotationOutputFile.h         |only
 src/AnnotationResult.h             |only
 src/AnnotationResultCollection.h   |only
 src/AnnotationString.h             |only
 src/BCFReader.cpp                  |    2 
 src/BedReader.h                    |only
 src/Codon.h                        |only
 src/Common.h                       |only
 src/FileFormat.h                   |    2 
 src/FreqTable.h                    |only
 src/Gene.h                         |only
 src/GeneAnnotation.h               |only
 src/GeneFormat.h                   |only
 src/GenomeScore.h                  |only
 src/GenomeSequence.h               |only
 src/IO.cpp                         |    4 
 src/IO.h                           |    4 
 src/LogFile.h                      |only
 src/Maximum.h                      |    4 
 src/ModelParser.h                  |only
 src/OrderedMap.h                   |  178 ++--
 src/Priority.h                     |only
 src/Range.h                        |only
 src/RangeList.cpp                  |    4 
 src/RangeList.h                    |    9 
 src/Rannotation.cpp                |only
 src/Rannotation.h                  |only
 src/SequenceUtil.h                 |only
 src/StringTemplate.h               |only
 src/StringUtil.h                   |only
 src/TabixData.h                    |only
 src/Type.h                         |only
 src/TypeConversion.h               |   26 
 src/Utils.h                        |  452 ++++-------
 src/VCFInputFile.cpp               |    7 
 src/rvMetaLoader.cpp               |    8 
 src/seqForStat.c                   |only
 src/tabix_index.c                  | 1495 ++++++++++++++++++-------------------
 src/vcf2genoLoader.cpp             |    2 
 57 files changed, 1587 insertions(+), 1334 deletions(-)

More information about seqminer at CRAN
Permanent link

New package LumiWCluster with initial version 1.0.2
Package: LumiWCluster
Version: 1.0.2
Date: 2010-09-02
Title: Weighted model based clustering
Author: Pei Fen Kuan , Xin Zhou
Maintainer: Xin Zhou
Depends: R (>= 2.10.0)
Description: The LumiWCluster package implements the proposed weighted model based clustering for Illumina Methylation BeadArray (Kuan et al., 2010). There are two parts to this package. The first part provides function to normalize the methylation data from the Illumina GoldenGate platform. We will include the normalization for Illumina Infinium platform in future. The second part provides function to identify subgroups with distinct methylation profiles in Illumina BeadArray. It works for both Infinium and GoldenGate platform, as well as any other platforms including gene expression arrays. The core of the algorithm is based on the paper by Wang and Zhu (2008), which automatically selects important CpGs/probes. LumiWCluster incorporates the detection p-values (a quality measure of probe performance reported by Illumina BeadStudio or GenomeStudio) systematically in the clustering algorithm and avoids arbitrary cutoff for excluding unreliable probes. Further details and motivation can be found in Kuan et al. (2010).
License: GPL (>= 2)
Packaged: 2014-04-13 23:11:57 UTC; peifenkuan
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-14 18:40:03

More information about LumiWCluster at CRAN
Permanent link

Package flip updated to version 2.4.1 with previous version 2.4 dated 2013-10-09

Title: Multivariate Permutation Tests
Description: It implements many univariate and multivariate permutation (and rotation) tests. Allowed tests: the t one and two samples, ANOVA, linear models, Chi Squared test, rank tests (i.e. Wilcoxon, Mann-Whitney, Kruskal-Wallis), Sign test and McNemar. Test on Linear Models are performed also in presence of covariates (i.e. nuisance parameters). The permutation and the rotation methods to get the null distribution of the test statistics are available. It also implements methods for multiplicity control such as Westfall-Young minP procedure and Closed Testing (Marcus, 1976) and k-FWER. Moreover, it allows to test for fixed effects in mixed effects models.
Author: Livio Finos, with contributions by Dario Basso, Aldo Solari, Jelle Goeman and Marco Rinaldo. Special thanks are due to Ivan Marin-Franch and Fredrik Nilsson for the debugging and the good questions.
Maintainer: Livio Finos

Diff between flip versions 2.4 dated 2013-10-09 and 2.4.1 dated 2014-04-14

 ChangeLog                |   12 ++-
 DESCRIPTION              |   16 ++--
 MD5                      |   48 +++++++-------
 NAMESPACE                |    7 +-
 R/Padjust.R              |   30 ++++++--
 R/between.R              |  160 ++++++++++++++++++++++++++++-------------------
 R/dependence.R           |   36 ++++++----
 R/estimateSu.R           |    8 +-
 R/flip-object.R          |   87 ++++++++++++++++++-------
 R/flip.R                 |   18 ++---
 R/flipMix.R              |   34 ++++++---
 R/flipMixWithin.R        |   10 +-
 R/kfwer.R                |only
 R/npc.R                  |   17 ++--
 R/obs2coeffWithin.R      |   94 ++++++++++++++++-----------
 R/permSpace.R            |   33 ++++++---
 R/symmetry.R             |   19 ++---
 R/utilities.R            |   87 ++++++++++++++-----------
 README                   |only
 man/flip.Rd              |   21 +++---
 man/flip.object-class.Rd |   13 ++-
 man/flipMix.Rd           |   30 ++++----
 man/multiplicity.Rd      |   21 ++++--
 man/permutationSpace.Rd  |   23 +++++-
 src                      |only
 25 files changed, 512 insertions(+), 312 deletions(-)

More information about flip at CRAN
Permanent link

New package DivE with initial version 1.0
Package: DivE
Type: Package
Title: Diversity Estimator
Version: 1.0
Date: 2014-04-01
Author: Daniel Laydon, Aaron Sim, Charles Bangham, Becca Asquith
Maintainer: Daniel Laydon
Depends: deSolve, FME, rgeos, sp, R (>= 2.15.3)
Description: R-package DivE contains functions for the DivE estimator (Laydon, D. et al., Quantification of HTLV-1 clonality and TCR diversity, PLOS Comput. Biol. 2014). The DivE estimator is a heuristic approach to estimate the number of classes or the number of species (species richness) in a population.
License: GPL (>= 2)
LazyData: TRUE
Packaged: 2014-04-14 12:24:21 UTC; aaronsim
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-14 19:07:04

More information about DivE at CRAN
Permanent link

New package compositions with initial version 1.40-0
Package: compositions
Version: 1.40-0
Date: 2013-04-08
Title: Compositional Data Analysis
Author: K. Gerald van den Boogaart , Raimon Tolosana, Matevz Bren
Maintainer: K. Gerald van den Boogaart
Depends: R (>= 2.2.0), tensorA, robustbase, energy, bayesm
Suggests: rgl
Description: The package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by Aitchison and Pawlowsky-Glahn.
License: GPL (>= 2)
URL: http://www.stat.boogaart.de/compositions
Packaged: 2014-04-12 09:04:49 UTC; boogaart
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-14 18:36:22

More information about compositions at CRAN
Permanent link

Package netmeta updated to version 0.4-3 with previous version 0.4-2 dated 2014-03-31

Title: Network meta-analysis with R
Description: Network meta-analysis following methods by Rücker (2012) and Krahn et al. (2013)
Author: Gerta Rücker [aut], Guido Schwarzer [aut, cre], Ulrike Krahn [aut]
Maintainer: Guido Schwarzer

Diff between netmeta versions 0.4-2 dated 2014-03-31 and 0.4-3 dated 2014-04-14

 DESCRIPTION               |   17 ++++++++-----
 MD5                       |   12 ++++-----
 NEWS                      |   20 +++++++++++++++
 R/forest.netmeta.R        |    6 ++++
 R/netmeta.R               |   13 ++++++++--
 R/nma.ruecker.R           |   58 +++++++++++++++++++++++++---------------------
 R/print.summary.netmeta.R |    3 --
 7 files changed, 87 insertions(+), 42 deletions(-)

More information about netmeta at CRAN
Permanent link

New package rHealthDataGov with initial version 1.0.0
Package: rHealthDataGov
Type: Package
Title: Retrieve data sets from the HealthData.gov data API
Version: 1.0.0
Date: 2014-04-13
Author: Erin LeDell
Maintainer: Erin LeDell
Description: An R interface for the HealthData.gov data API. For each data resource, you can filter results (server-side) to select subsets of data.
License: GPL-2
Depends: R (>= 3.0.1), bit64, httr, jsonlite
LazyLoad: yes
LazyData: yes
Packaged: 2014-04-14 00:08:14 UTC; ledell
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-14 14:14:26

More information about rHealthDataGov at CRAN
Permanent link

Package multiPIM updated to version 1.4-1 with previous version 1.3-1 dated 2013-01-18

Title: Variable Importance Analysis with Population Intervention Models
Description: Performs variable importance analysis using a causal inference approach. This is done by fitting Population Intervention Models. The default is to use a Targeted Maximum Likelihood Estimator (TMLE). The other available estimators are Inverse Probability of Censoring Weighted (IPCW), Double-Robust IPCW (DR-IPCW), and Graphical Computation (G-COMP) estimators. Inference can be obtained from the influence curve (plug-in) or by bootstrapping.
Author: Stephan Ritter , Alan Hubbard , Nicholas Jewell
Maintainer: Stephan Ritter

Diff between multiPIM versions 1.3-1 dated 2013-01-18 and 1.4-1 dated 2014-04-14

 ChangeLog           |    7 +++++++
 DESCRIPTION         |   27 ++++++++++-----------------
 MD5                 |   13 +++++++------
 NAMESPACE           |    5 +++++
 inst                |only
 man/Candidates.Rd   |    4 ++--
 man/multiPIM.Rd     |    4 ++--
 man/multiPIMboot.Rd |    4 ++--
 8 files changed, 35 insertions(+), 29 deletions(-)

More information about multiPIM at CRAN
Permanent link

New package mdatools with initial version 0.5.1
Package: mdatools
Title: Multivariate data analysis for chemometrics
Version: 0.5.1
Date: 2014-04-13
Author: Sergey Kucheryavskiy
Maintainer: Sergey Kucheryavskiy
Description: The package implements projection based methods for preprocessing, exploring and analysis of multivariate data used in chemometrics.
Suggests:
Depends:
License: GPL-3
Packaged: 2014-04-14 06:03:36 UTC; svkucheryavski
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-14 14:13:42

More information about mdatools at CRAN
Permanent link

Package Luminescence updated to version 0.3.3 with previous version 0.3.2 dated 2014-01-07

Title: Package for Luminescence Dating data analysis
Description: Package provides a collection of various R functions for Luminescence Dating data analysis.
Author: Sebastian Kreutzer [aut, trl, cre], Christoph Schmidt [aut], Margret C. Fuchs [aut], Michael Dietze [aut], Manfred Fischer [aut, trl], Christoph Burow [aut], Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer

Diff between Luminescence versions 0.3.2 dated 2014-01-07 and 0.3.3 dated 2014-04-14

 Luminescence-0.3.2/Luminescence/man/calc_FadingCorr.rd                   |only
 Luminescence-0.3.3/Luminescence/DESCRIPTION                              |   12 
 Luminescence-0.3.3/Luminescence/MD5                                      |  210 -
 Luminescence-0.3.3/Luminescence/NEWS                                     |  187 +
 Luminescence-0.3.3/Luminescence/R/Analyse_SAR.OSLdata.R                  |   52 
 Luminescence-0.3.3/Luminescence/R/CW2pHMi.R                              |    6 
 Luminescence-0.3.3/Luminescence/R/CW2pLM.R                               |    6 
 Luminescence-0.3.3/Luminescence/R/CW2pLMi.R                              |    6 
 Luminescence-0.3.3/Luminescence/R/CW2pPMi.R                              |    4 
 Luminescence-0.3.3/Luminescence/R/RLum.Analysis-class.R                  |   43 
 Luminescence-0.3.3/Luminescence/R/RLum.Data.Curve-class.R                |    4 
 Luminescence-0.3.3/Luminescence/R/RLum.Data.Spectrum-class.R             |    8 
 Luminescence-0.3.3/Luminescence/R/RLum.Results-class.R                   |   42 
 Luminescence-0.3.3/Luminescence/R/Risoe.BINfileData2RLum.Analysis.R      |   69 
 Luminescence-0.3.3/Luminescence/R/Risoe.BINfileData2RLum.Data.Curve.R    |    8 
 Luminescence-0.3.3/Luminescence/R/RisoeBINfileData-class.R               |   14 
 Luminescence-0.3.3/Luminescence/R/Second2Gray.R                          |   10 
 Luminescence-0.3.3/Luminescence/R/analyse_IRSAR.RF.R                     |  101 
 Luminescence-0.3.3/Luminescence/R/analyse_SAR.CWOSL.R                    |   91 
 Luminescence-0.3.3/Luminescence/R/analyse_SAR.TL.R                       |   50 
 Luminescence-0.3.3/Luminescence/R/apply_CosmicRayRemoval.R               |only
 Luminescence-0.3.3/Luminescence/R/apply_EfficiencyCorrection.R           |only
 Luminescence-0.3.3/Luminescence/R/calc_AliquotSize.R                     |  329 ++
 Luminescence-0.3.3/Luminescence/R/calc_CentralDose.R                     |   21 
 Luminescence-0.3.3/Luminescence/R/calc_CommonDose.R                      |    4 
 Luminescence-0.3.3/Luminescence/R/calc_CosmicDoseRate.R                  | 1131 +++++-----
 Luminescence-0.3.3/Luminescence/R/calc_FadingCorr.R                      |   60 
 Luminescence-0.3.3/Luminescence/R/calc_FiniteMixture.R                   |  931 ++++++--
 Luminescence-0.3.3/Luminescence/R/calc_FuchsLang2001.R                   |  135 -
 Luminescence-0.3.3/Luminescence/R/calc_HomogeneityTest.R                 |   31 
 Luminescence-0.3.3/Luminescence/R/calc_MaxDose3.R                        |   96 
 Luminescence-0.3.3/Luminescence/R/calc_MinDose3.R                        |   90 
 Luminescence-0.3.3/Luminescence/R/calc_MinDose4.R                        |  108 
 Luminescence-0.3.3/Luminescence/R/calc_OSLLxTxRatio.R                    |  250 +-
 Luminescence-0.3.3/Luminescence/R/calc_Statistics.R                      |only
 Luminescence-0.3.3/Luminescence/R/calc_TLLxTxRatio.R                     |    6 
 Luminescence-0.3.3/Luminescence/R/fit_CWCurve.R                          |   37 
 Luminescence-0.3.3/Luminescence/R/fit_LMCurve.R                          |   89 
 Luminescence-0.3.3/Luminescence/R/merge_Risoe.BINfileData.R              |   63 
 Luminescence-0.3.3/Luminescence/R/plot_AbanicoPlot.R                     |only
 Luminescence-0.3.3/Luminescence/R/plot_DRTResults.R                      |only
 Luminescence-0.3.3/Luminescence/R/plot_GrowthCurve.R                     |  114 -
 Luminescence-0.3.3/Luminescence/R/plot_Histogram.R                       |  150 -
 Luminescence-0.3.3/Luminescence/R/plot_KDE.R                             |  984 +++++---
 Luminescence-0.3.3/Luminescence/R/plot_RLum.Analysis.R                   |   20 
 Luminescence-0.3.3/Luminescence/R/plot_RLum.Data.Curve.R                 |   18 
 Luminescence-0.3.3/Luminescence/R/plot_RLum.Data.Spectrum.R              |  427 +++
 Luminescence-0.3.3/Luminescence/R/plot_RLum.R                            |    8 
 Luminescence-0.3.3/Luminescence/R/plot_RadialPlot.R                      |  479 +++-
 Luminescence-0.3.3/Luminescence/R/plot_Risoe.BINfileData.R               |   12 
 Luminescence-0.3.3/Luminescence/R/readBIN2R.R                            |   14 
 Luminescence-0.3.3/Luminescence/R/readXSYG2R.R                           |  174 -
 Luminescence-0.3.3/Luminescence/R/writeR2BIN.R                           |    4 
 Luminescence-0.3.3/Luminescence/data/ExampleData.XSYG.RData              |only
 Luminescence-0.3.3/Luminescence/data/datalist                            |    1 
 Luminescence-0.3.3/Luminescence/inst/NEWS.Rd                             |  177 +
 Luminescence-0.3.3/Luminescence/inst/doc/S4-class_objects.pdf            |binary
 Luminescence-0.3.3/Luminescence/man/Analyse_SAR.OSLdata.Rd               |   15 
 Luminescence-0.3.3/Luminescence/man/BaseDataSet.CosmicDoseRate.Rd        |  244 +-
 Luminescence-0.3.3/Luminescence/man/CW2pHMi.Rd                           |    3 
 Luminescence-0.3.3/Luminescence/man/CW2pLM.Rd                            |    3 
 Luminescence-0.3.3/Luminescence/man/CW2pLMi.Rd                           |    3 
 Luminescence-0.3.3/Luminescence/man/CW2pPMi.Rd                           |    1 
 Luminescence-0.3.3/Luminescence/man/ExampleData.BINfileData.Rd           |    4 
 Luminescence-0.3.3/Luminescence/man/ExampleData.FittingLM.Rd             |    2 
 Luminescence-0.3.3/Luminescence/man/ExampleData.XSYG.Rd                  |only
 Luminescence-0.3.3/Luminescence/man/Luminescence-package.Rd              |   22 
 Luminescence-0.3.3/Luminescence/man/RLum-class.Rd                        |    2 
 Luminescence-0.3.3/Luminescence/man/RLum.Analysis-class.Rd               |   15 
 Luminescence-0.3.3/Luminescence/man/RLum.Data-class.Rd                   |    7 
 Luminescence-0.3.3/Luminescence/man/RLum.Data.Curve-class.Rd             |    2 
 Luminescence-0.3.3/Luminescence/man/RLum.Data.Spectrum-class.Rd          |    8 
 Luminescence-0.3.3/Luminescence/man/RLum.Results-class.Rd                |    2 
 Luminescence-0.3.3/Luminescence/man/Risoe.BINfileData-class.Rd           |    4 
 Luminescence-0.3.3/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd   |   13 
 Luminescence-0.3.3/Luminescence/man/Risoe.BINfileData2RLum.Data.Curve.Rd |    5 
 Luminescence-0.3.3/Luminescence/man/Second2Gray.Rd                       |    9 
 Luminescence-0.3.3/Luminescence/man/analyse_IRSAR.RF.Rd                  |    8 
 Luminescence-0.3.3/Luminescence/man/analyse_SAR.CWOSL.Rd                 |   10 
 Luminescence-0.3.3/Luminescence/man/analyse_SAR.TL.Rd                    |    7 
 Luminescence-0.3.3/Luminescence/man/apply_CosmicRayRemoval.Rd            |only
 Luminescence-0.3.3/Luminescence/man/apply_EfficiencyCorrection.Rd        |only
 Luminescence-0.3.3/Luminescence/man/calc_AliquotSize.Rd                  |   64 
 Luminescence-0.3.3/Luminescence/man/calc_CentralDose.Rd                  |    2 
 Luminescence-0.3.3/Luminescence/man/calc_CommonDose.Rd                   |    3 
 Luminescence-0.3.3/Luminescence/man/calc_CosmicDoseRate.Rd               |   18 
 Luminescence-0.3.3/Luminescence/man/calc_FadingCorr.Rd                   |only
 Luminescence-0.3.3/Luminescence/man/calc_FiniteMixture.Rd                |   85 
 Luminescence-0.3.3/Luminescence/man/calc_FuchsLang2001.rd                |   23 
 Luminescence-0.3.3/Luminescence/man/calc_HomogeneityTest.Rd              |    9 
 Luminescence-0.3.3/Luminescence/man/calc_MaxDose3.Rd                     |   25 
 Luminescence-0.3.3/Luminescence/man/calc_MinDose3.Rd                     |   19 
 Luminescence-0.3.3/Luminescence/man/calc_MinDose4.Rd                     |   12 
 Luminescence-0.3.3/Luminescence/man/calc_OSLLxTxRatio.Rd                 |   43 
 Luminescence-0.3.3/Luminescence/man/calc_Statistics.Rd                   |only
 Luminescence-0.3.3/Luminescence/man/calc_TLLxTxRatio.Rd                  |    3 
 Luminescence-0.3.3/Luminescence/man/fit_CWCurve.Rd                       |    9 
 Luminescence-0.3.3/Luminescence/man/fit_LMCurve.Rd                       |    7 
 Luminescence-0.3.3/Luminescence/man/merge_Risoe.BINfileData.Rd           |   36 
 Luminescence-0.3.3/Luminescence/man/plot_AbanicoPlot.Rd                  |only
 Luminescence-0.3.3/Luminescence/man/plot_DRTResults.Rd                   |only
 Luminescence-0.3.3/Luminescence/man/plot_GrowthCurve.Rd                  |  235 +-
 Luminescence-0.3.3/Luminescence/man/plot_Histogram.Rd                    |   35 
 Luminescence-0.3.3/Luminescence/man/plot_KDE.Rd                          |  169 -
 Luminescence-0.3.3/Luminescence/man/plot_RLum.Analysis.Rd                |    5 
 Luminescence-0.3.3/Luminescence/man/plot_RLum.Data.Curve.Rd              |    5 
 Luminescence-0.3.3/Luminescence/man/plot_RLum.Data.Spectrum.Rd           |   76 
 Luminescence-0.3.3/Luminescence/man/plot_RLum.Rd                         |    5 
 Luminescence-0.3.3/Luminescence/man/plot_RadialPlot.Rd                   |   85 
 Luminescence-0.3.3/Luminescence/man/plot_Risoe.BINfileData.Rd            |    9 
 Luminescence-0.3.3/Luminescence/man/readBIN2R.Rd                         |   13 
 Luminescence-0.3.3/Luminescence/man/readXSYG2R.Rd                        |   64 
 Luminescence-0.3.3/Luminescence/man/writeR2BIN.Rd                        |    5 
 113 files changed, 5548 insertions(+), 2791 deletions(-)

More information about Luminescence at CRAN
Permanent link

New package ibs with initial version 1.0
Package: ibs
Type: Package
Title: Integrated B-spline
Version: 1.0
Date: 2014-04-12
Author: Feng Chen
Maintainer: Feng Chen
Description: Calculate B-spline basis functions with a given set of knots and order, or a B-spline function with a given set of knots and order and set of de Boor points (coefficients), or the integral of a B-spline function.
License: GPL (>= 2)
Packaged: 2014-04-13 22:43:15 UTC; z3243864
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-14 14:12:30

More information about ibs at CRAN
Permanent link

New package binda with initial version 1.0.0
Package: binda
Version: 1.0.0
Date: 2014-04-14
Title: Multi-Class Discriminant Analysis using Binary Predictors
Author: Sebastian Gibb and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
Depends: R (>= 2.15.1), entropy (>= 1.2.0)
Suggests: MASS
Description: The "binda" package implements functions for multi-class discriminant analysis using binary predictors, for corresponding variable selection, and for dichotomizing continuous data.
License: GPL (>= 3)
URL: http://strimmerlab.org/software/binda/
Packaged: 2014-04-14 00:26:52 UTC; strimmer
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-14 14:54:59

More information about binda at CRAN
Permanent link

Package AMORE updated to version 0.2-15 with previous version 0.2-14 dated 2013-12-17

Title: A MORE flexible neural network package
Description: This package was born to release the TAO robust neural network algorithm to the R users. It has grown and I think it can be of interest for the users wanting to implement their own training algorithms as well as for those others whose needs lye only in the "user space".
Author: Manuel Castejon Limas, Joaquin B. Ordieres Mere, Ana Gonzalez Marcos, Francisco Javier Martinez de Pison Ascacibar, Alpha V. Pernia Espinoza, Fernando Alba Elias, Jose Maria Perez Ramos
Maintainer: Manuel Castejón Limas

Diff between AMORE versions 0.2-14 dated 2013-12-17 and 0.2-15 dated 2014-04-14

 ChangeLog       |   10 ++++++++++
 DESCRIPTION     |    8 ++++----
 MD5             |   10 +++++-----
 R/sim.R         |   20 ++++++++++++++++++++
 src/BATCHgd.c   |   17 +++++++++++++----
 src/BATCHgdwm.c |   20 ++++++++++++++++----
 6 files changed, 68 insertions(+), 17 deletions(-)

More information about AMORE at CRAN
Permanent link

Sun, 13 Apr 2014

New package LOGICOIL with initial version 0.99.0
Package: LOGICOIL
Type: Package
Version: 0.99.0
Date: 2014-04-12
Title: LOGICOIL: multi-state prediction of coiled-coil oligomeric state.
Author: Thomas L. Vincent , Peter J. Green and Derek N. Woolfson
Maintainer: Thomas L. Vincent
Depends: R (>= 2.12), nnet
LazyData: true
ZipData: no
License: GPL (>= 2)
Description: This package contains the functions necessary to run the LOGICOIL algorithm. LOGICOIL can be used to differentiate between antiparallel dimers, parallel dimers, trimers and higher-order coiled-coil sequence. By covering >90 percent of the known coiled-coil structures, LOGICOIL is a net improvement compared with other existing methods, which achieve a predictive coverage of around 31 percent of this population. As such, LOGICOIL is particularly useful for researchers looking to characterize novel coiled-coil sequences or studying coiled-coil containing protein assemblies. It may also be used to assist in the structural characterization of synthetic coiled-coil sequences.
Repository: CRAN
URL: http://coiledcoils.chm.bris.ac.uk/LOGICOIL
Packaged: 2014-04-13 21:36:51 UTC; ThomasVincent
NeedsCompilation: no
Date/Publication: 2014-04-14 00:04:00

More information about LOGICOIL at CRAN
Permanent link

New package freqweights with initial version 0.0.1
Package: freqweights
Type: Package
Title: Working with frequency tables
Version: 0.0.1
Date: 2014-04-03
Author: Emilio Torres-Manzanera
Maintainer: Emilio Torres-Manzanera
Description: The frequency of a particular data value is the number of times it occurs. A frequency table is a table of values with their corresponding frequencies. Frequency weights are integer numbers that indicate how many cases each case represents. This package provides some functions to work with such type of collected data.
License: GPL-3
Imports: plyr, data.table, dplyr, biglm, fastcluster
Suggests: MASS, hflights, cluster, ggplot2
Packaged: 2014-04-13 00:49:45 UTC; emilio
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-14 00:05:17

More information about freqweights at CRAN
Permanent link

New package FisHiCal with initial version 1.0
Package: FisHiCal
Type: Package
Title: Iterative FISH-based Calibration of Hi-C Data
Version: 1.0
Date: 2014-04-09
Author: Yoli Shavit, Fiona Kathryn Hamey and Pietro Lio'
Maintainer: Yoli Shavit
Description: FisHiCal integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.
License: GPL
Depends: R (>= 3.0.2), igraph, RcppArmadillo (>= 0.4.100.2.1)
Suggests: rgl
LinkingTo: Rcpp (>= 0.11.1), RcppArmadillo (>= 0.4.100.2.1)
Packaged: 2014-04-13 18:55:42 UTC; ys388
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-13 23:26:01

More information about FisHiCal at CRAN
Permanent link

Package aftgee updated to version 0.4-3 with previous version 0.4-2 dated 2014-02-05

Title: Accelerated Failure Time Model with Generalized Estimating Equations
Description: This package features both rank-based estimates and least square estimates to the Accelerated Failure Time (AFT) model. For rank-based estimation, it provides approaches that include the computationally efficient Gehan's weight and the general's weight such as the logrank weight. For the least square estimation, the estimating equation is solved with Generalized Estimating Equations (GEE). Moreover, in multivariate cases, the dependence working correlation structure can be specified in GEE's setting.
Author: Sy Han (Steven) Chiou, Sangwook Kang, Jun Yan
Maintainer: Sy Han (Steven) Chiou

Diff between aftgee versions 0.4-2 dated 2014-02-05 and 0.4-3 dated 2014-04-13

 ChangeLog             |   57 --------
 DESCRIPTION           |    9 -
 MD5                   |   20 +--
 NAMESPACE             |    2 
 R/aftgee.R            |   55 +++++---
 R/aftsrr.R            |  198 +++++++++++++++++-------------
 man/aftgee-package.Rd |   26 ++--
 man/aftgee.Rd         |   91 ++++++++------
 man/aftgee.control.Rd |   11 -
 man/aftsrr.Rd         |   95 +++++++-------
 src/aftgee.c          |  323 +++++++++++++++++++++++++++++++++++++++++++++-----
 11 files changed, 582 insertions(+), 305 deletions(-)

More information about aftgee at CRAN
Permanent link

Package SensoMineR updated to version 1.20 with previous version 1.18 dated 2013-07-09

Title: Sensory data analysis with R
Description: an R package for analysing sensory data
Author: Francois Husson, Sebastien Le, Marine Cadoret
Maintainer: Francois Husson

Diff between SensoMineR versions 1.18 dated 2013-07-09 and 1.20 dated 2014-04-13

 SensoMineR-1.18/SensoMineR/SensoMineR-Ex.R             |only
 SensoMineR-1.20/SensoMineR/DESCRIPTION                 |   11 -
 SensoMineR-1.20/SensoMineR/MD5                         |  141 ++++++++---------
 SensoMineR-1.20/SensoMineR/NAMESPACE                   |    5 
 SensoMineR-1.20/SensoMineR/R/ConsensualWords.R         |    9 -
 SensoMineR-1.20/SensoMineR/R/IdMap.r                   |   25 +--
 SensoMineR-1.20/SensoMineR/R/IdMapConsumer.r           |only
 SensoMineR-1.20/SensoMineR/R/WilliamsDesign.r          |    6 
 SensoMineR-1.20/SensoMineR/R/carto.R                   |    2 
 SensoMineR-1.20/SensoMineR/R/construct.axes.R          |    2 
 SensoMineR-1.20/SensoMineR/R/cpa.R                     |    2 
 SensoMineR-1.20/SensoMineR/R/fast.r                    |    4 
 SensoMineR-1.20/SensoMineR/R/hsortplot.R               |    2 
 SensoMineR-1.20/SensoMineR/R/nappeplot.R               |   41 ++--
 SensoMineR-1.20/SensoMineR/R/optimaldesign.R           |    2 
 SensoMineR-1.20/SensoMineR/R/panellipse.r              |    4 
 SensoMineR-1.20/SensoMineR/R/panelmatch.R              |    1 
 SensoMineR-1.20/SensoMineR/R/plotpanelist.R            |    1 
 SensoMineR-1.20/SensoMineR/R/triangle.pair.test.R      |    4 
 SensoMineR-1.20/SensoMineR/data/cream_id.rda           |only
 SensoMineR-1.20/SensoMineR/data/cream_signa.rda        |only
 SensoMineR-1.20/SensoMineR/data/hedochoc.rda           |binary
 SensoMineR-1.20/SensoMineR/data/sensopanels.rda        |binary
 SensoMineR-1.20/SensoMineR/man/ConsensualWords.rd      |    2 
 SensoMineR-1.20/SensoMineR/man/ConsistencyIdeal.Rd     |    4 
 SensoMineR-1.20/SensoMineR/man/IdMap.Rd                |   23 +-
 SensoMineR-1.20/SensoMineR/man/IdMapConsumer.Rd        |only
 SensoMineR-1.20/SensoMineR/man/WordCountAna.Rd         |    2 
 SensoMineR-1.20/SensoMineR/man/ardi.Rd                 |    2 
 SensoMineR-1.20/SensoMineR/man/averagetable.Rd         |    2 
 SensoMineR-1.20/SensoMineR/man/barrow.Rd               |    2 
 SensoMineR-1.20/SensoMineR/man/boot.Rd                 |    2 
 SensoMineR-1.20/SensoMineR/man/boxprod.Rd              |    4 
 SensoMineR-1.20/SensoMineR/man/calculate.average.Rd    |   12 -
 SensoMineR-1.20/SensoMineR/man/cards.rd                |    2 
 SensoMineR-1.20/SensoMineR/man/chocolates.Rd           |    2 
 SensoMineR-1.20/SensoMineR/man/coltable.Rd             |    2 
 SensoMineR-1.20/SensoMineR/man/compo.cocktail.Rd       |    2 
 SensoMineR-1.20/SensoMineR/man/construct.axes.Rd       |    8 
 SensoMineR-1.20/SensoMineR/man/cpa.Rd                  |    6 
 SensoMineR-1.20/SensoMineR/man/cream_id.Rd             |only
 SensoMineR-1.20/SensoMineR/man/cream_signa.Rd          |only
 SensoMineR-1.20/SensoMineR/man/decat.Rd                |    2 
 SensoMineR-1.20/SensoMineR/man/fcp.Rd                  |    2 
 SensoMineR-1.20/SensoMineR/man/graphinter.Rd           |    2 
 SensoMineR-1.20/SensoMineR/man/hedo.cocktail.Rd        |    2 
 SensoMineR-1.20/SensoMineR/man/hedochoc.Rd             |    2 
 SensoMineR-1.20/SensoMineR/man/histprod.Rd             |    2 
 SensoMineR-1.20/SensoMineR/man/indscal.Rd              |    2 
 SensoMineR-1.20/SensoMineR/man/interact.Rd             |    2 
 SensoMineR-1.20/SensoMineR/man/magicsort.Rd            |    2 
 SensoMineR-1.20/SensoMineR/man/nappeplot.Rd            |    4 
 SensoMineR-1.20/SensoMineR/man/napping.Rd              |    2 
 SensoMineR-1.20/SensoMineR/man/napping.don.Rd          |    2 
 SensoMineR-1.20/SensoMineR/man/napping.words.Rd        |    2 
 SensoMineR-1.20/SensoMineR/man/paneliperf.Rd           |    2 
 SensoMineR-1.20/SensoMineR/man/panellipse.Rd           |    8 
 SensoMineR-1.20/SensoMineR/man/panellipse.session.Rd   |    8 
 SensoMineR-1.20/SensoMineR/man/panelmatch.Rd           |    6 
 SensoMineR-1.20/SensoMineR/man/panelperf.Rd            |    2 
 SensoMineR-1.20/SensoMineR/man/plotellipse.Rd          |    2 
 SensoMineR-1.20/SensoMineR/man/plotellipseinter.Rd     |    2 
 SensoMineR-1.20/SensoMineR/man/plotellipseinterhmfa.Rd |    2 
 SensoMineR-1.20/SensoMineR/man/plotpanelist.Rd         |    2 
 SensoMineR-1.20/SensoMineR/man/pmfa.Rd                 |    4 
 SensoMineR-1.20/SensoMineR/man/scalebypanelist.Rd      |    2 
 SensoMineR-1.20/SensoMineR/man/search.desc.Rd          |    2 
 SensoMineR-1.20/SensoMineR/man/senso.cocktail.Rd       |    2 
 SensoMineR-1.20/SensoMineR/man/sensochoc.Rd            |    2 
 SensoMineR-1.20/SensoMineR/man/sensopanels.Rd          |    2 
 SensoMineR-1.20/SensoMineR/man/simulation.Rd           |    4 
 SensoMineR-1.20/SensoMineR/man/smoothies.Rd            |    2 
 SensoMineR-1.20/SensoMineR/man/triangle.design.Rd      |    2 
 SensoMineR-1.20/SensoMineR/man/triangle.pair.test.Rd   |    2 
 SensoMineR-1.20/SensoMineR/man/triangle.test.Rd        |    2 
 75 files changed, 222 insertions(+), 205 deletions(-)

More information about SensoMineR at CRAN
Permanent link

Package rms updated to version 4.2-0 with previous version 4.1-3 dated 2014-03-02

Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. rms is a collection of functions that assist with and streamline modeling. It also contains functions for binary and ordinal logistic regression models, ordinal models for continuous Y with a variety of distribution families, and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. rms works with almost any regression model, but it was especially written to work with binary or ordinal regression models, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr

Diff between rms versions 4.1-3 dated 2014-03-02 and 4.2-0 dated 2014-04-13

 rms-4.1-3/rms/R/survfit.formula.s     |only
 rms-4.1-3/rms/R/survplot.survfit.s    |only
 rms-4.1-3/rms/man/survfit.formula.Rd  |only
 rms-4.2-0/rms/DESCRIPTION             |    8 ++---
 rms-4.2-0/rms/INDEX                   |    3 +
 rms-4.2-0/rms/MD5                     |   42 +++++++++++++-------------
 rms-4.2-0/rms/NAMESPACE               |    5 +--
 rms-4.2-0/rms/NEWS                    |   10 ++++++
 rms-4.2-0/rms/R/cph.s                 |    7 ++--
 rms-4.2-0/rms/R/hazard.ratio.plot.s   |    3 -
 rms-4.2-0/rms/R/npsurv.s              |only
 rms-4.2-0/rms/R/orm.fit.s             |    8 +++--
 rms-4.2-0/rms/R/psm.s                 |    4 +-
 rms-4.2-0/rms/R/rmsMisc.s             |    4 +-
 rms-4.2-0/rms/R/survfit.cph.s         |    4 +-
 rms-4.2-0/rms/R/survplot.npsurv.s     |only
 rms-4.2-0/rms/README.md               |    5 ++-
 rms-4.2-0/rms/man/bj.Rd               |    4 +-
 rms-4.2-0/rms/man/npsurv.Rd           |only
 rms-4.2-0/rms/man/psm.Rd              |    8 ++---
 rms-4.2-0/rms/man/rms.trans.Rd        |   12 +++----
 rms-4.2-0/rms/man/survest.psm.Rd      |    4 +-
 rms-4.2-0/rms/man/survplot.Rd         |   54 ++++++++++++++++++----------------
 rms-4.2-0/rms/man/zzzrmsOverview.Rd   |    4 +-
 rms-4.2-0/rms/tests/orm3.r            |only
 rms-4.2-0/rms/tests/survfit.timedep.s |only
 26 files changed, 105 insertions(+), 84 deletions(-)

More information about rms at CRAN
Permanent link


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