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(-)

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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

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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

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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

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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 
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 R/mkHema87.R                                               |   27 
 R/mkSEER.R                                                 |  105 -
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 inst/doc/overview.pdf                                      |binary
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 inst/doc/papers/blood2012/blood2012fig6.R                  |   66 
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 inst/doc/papers/radiatEnvironBiophys2013/supplementAbomb.R | 1038 +++++-----
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 man/getFields.Rd                                           |   58 
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 man/mkSEER.Rd                                              |   79 
 man/pickFields.Rd                                          |   80 
 25 files changed, 2101 insertions(+), 2065 deletions(-)

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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(-)

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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

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 inst/doc/MVT_Rnews.pdf       |binary
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 tests/bugfix-tests.R         |    2 ++
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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

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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 ++++++------------
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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 +-
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 R/sjImportSPSS.R             |  680 +++++-----
 R/sjPlotAnova.R              | 1397 +++++++++++-----------
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 R/sjPlotFrequencies.R        |   80 -
 R/sjPlotGroupFrequencies.R   | 2699 +++++++++++++++++++++----------------------
 R/sjPlotLikert.R             | 1540 ++++++++++++------------
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 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 ++++++++++-----------
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 R/sjTabPCA.R                 | 1210 +++++++++----------
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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 ++++++-
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 seqDesign-1.0.1/seqDesign/vignettes/seqDesignInstructions.Rnw    |    6 
 13 files changed, 798 insertions(+), 694 deletions(-)

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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 -
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 R/check_wkt.r                         |only
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 tests/testthat/test-name_lookup.r     |    2 
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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(-)

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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

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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

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