Sat, 19 Apr 2014

Package investr updated to version 1.0.1 with previous version 1.0 dated 2013-08-09

Title: Inverse estimation/calibration functions
Description: This package provides functions to facilitate inverse estimation/calibration with linear and nonlinear regression models. A generic function is also provided for plotting fitted regression models with or without confidence/prediction bands that may be of use to the general user.
Author: Brandon M. Greenwell
Maintainer: Brandon M. Greenwell

Diff between investr versions 1.0 dated 2013-08-09 and 1.0.1 dated 2014-04-19

 investr-1.0.1/investr/DESCRIPTION                 |   21 
 investr-1.0.1/investr/MD5                         |   38 -
 investr-1.0.1/investr/NAMESPACE                   |    3 
 investr-1.0.1/investr/NEWS                        |   16 
 investr-1.0.1/investr/R/calibrate.R               |   54 +-
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 investr-1.0.1/investr/R/utilities.R               |  476 +---------------------
 investr-1.0.1/investr/README.md                   |   94 ++++
 investr-1.0.1/investr/inst/CITATION               |    5 
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 investr-1.0.1/investr/man/investr-package.Rd      |   20 
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 22 files changed, 512 insertions(+), 858 deletions(-)

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Package RTextureMetrics updated to version 1.1 with previous version 1.0 dated 2014-01-04

Title: Functions for calculation of texture metrics for Grey Level Co-occurrence Matrices
Description: This package contains several functions for calculation of texture metrics for Grey Level Co-occurrence matrices
Author: Hans-Joachim Klemmt
Maintainer: Hans-Joachim Klemmt

Diff between RTextureMetrics versions 1.0 dated 2014-01-04 and 1.1 dated 2014-04-19

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New package RApiSerialize with initial version 0.1.0
Package: RApiSerialize
Type: Package
Title: R API Serialization
Version: 0.1.0
Date: 2014-04-19
Author: Dirk Eddelbuettel, Junji Nakano, Ei-ji Nakama, and R Core (original code)
Maintainer: Dirk Eddelbuettel
Description: This package provides other packages with access to the internal R serialization code. Access to this code is provided at the C function level by using the registration of native function mechanism. Client packages simply include a single header file RApiSerializeAPI.h provided by this package. This packages builds on the Rhpc package by Junji Nakano and Ei-ji Nakama which also includes a (partial) copy of the file src/main/serialize.c from R itself. The R Core group is the original author of the serialization code made available by this package.
License: GPL (>= 2)
Packaged: 2014-04-19 13:45:33.622462 UTC; edd
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-04-19 18:49:29

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Package markovchain updated to version 0.0.9 with previous version 0.0.8 dated 2014-02-10

Title: A package to handle and analyse discrete Markov chains
Description: A package for easily handling discrete Markov chains
Author: Giorgio Alfredo Spedicato
Maintainer: Giorgio Alfredo Spedicato

Diff between markovchain versions 0.0.8 dated 2014-02-10 and 0.0.9 dated 2014-04-19

 ChangeLog                                            |    5 
 DESCRIPTION                                          |   10 
 MD5                                                  |   28 
 NAMESPACE                                            |    1 
 NEWS                                                 |    8 
 R/classesAndMethods.R                                |   17 
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Package multicon updated to version 1.2 with previous version 1.1 dated 2014-01-13

Title: Multivariate Constructs
Description: This packages includes functions designed to examine relationships among multivariate constructs.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman

Diff between multicon versions 1.1 dated 2014-01-13 and 1.2 dated 2014-04-19

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Package meta updated to version 3.5-0 with previous version 3.2-1 dated 2014-03-26

Title: Meta-Analysis with R
Description: Fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot.
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer

Diff between meta versions 3.2-1 dated 2014-03-26 and 3.5-0 dated 2014-04-19

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Package seqminer updated to version 3.0 with previous version 2.7 dated 2014-04-14

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 2.7 dated 2014-04-14 and 3.0 dated 2014-04-19

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Package Reol updated to version 1.55 with previous version 1.53 dated 2013-12-06

Title: R interface to the Encyclopedia of Life
Description: An R interface to the Encyclopedia of Life API. Includes functions for downloading and extracting information off the EOL pages.
Author: Barb Banbury , Brian O'Meara
Maintainer: Barb Banbury

Diff between Reol versions 1.53 dated 2013-12-06 and 1.55 dated 2014-04-19

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Package openNLP updated to version 0.2-3 with previous version 0.2-2 dated 2014-01-25

Title: Apache OpenNLP Tools Interface
Description: An interface to the Apache OpenNLP tools (version 1.5.3). The Apache OpenNLP library is a machine learning based toolkit for the processing of natural language text written in Java. It supports the most common NLP tasks, such as tokenization, sentence segmentation, part-of-speech tagging, named entity extraction, chunking, parsing, and coreference resolution. See for more information.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik

Diff between openNLP versions 0.2-2 dated 2014-01-25 and 0.2-3 dated 2014-04-19

 DESCRIPTION    |    8 ++++----
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Package pdfetch updated to version 0.1.3 with previous version 0.1.2 dated 2014-03-15

Title: Fetch economic and financial time series data from public sources
Description: A package for downloading economic and financial time series from public sources.
Author: Abiel Reinhart
Maintainer: Abiel Reinhart

Diff between pdfetch versions 0.1.2 dated 2014-03-15 and 0.1.3 dated 2014-04-19

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 NAMESPACE                 |    3 
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Package NLP updated to version 0.1-2 with previous version 0.1-1 dated 2014-01-25

Title: Natural Language Processing Infrastructure
Description: Basic classes and methods for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik

Diff between NLP versions 0.1-1 dated 2014-01-25 and 0.1-2 dated 2014-04-19

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Fri, 18 Apr 2014

Package RWebLogo updated to version 1.0.1 with previous version 1.0.0 dated 2014-03-20

Title: plotting custom sequence logos
Description: RWebLogo is a wrapper for the WebLogo python package that allows generating of customised sequence logos. Sequence logos are graphical representations of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences). Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
Author: Omar Wagih
Maintainer: Omar Wagih

Diff between RWebLogo versions 1.0.0 dated 2014-03-20 and 1.0.1 dated 2014-04-18

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New package rWBclimate with initial version 0.1.3
Package: rWBclimate
Authors@R: c(person("Edmund", "Hart", role = c("aut", "cre"), email = "edmund.m.hart@gmail.com"))
Version: 0.1.3
License: MIT + file LICENSE
URL: http://github.com/ropensci/rWBclimate
BugReports: http://github.com/ropensci/rWBclimate/issues
Type: Package
Title: A package for accessing World Bank climate data
Description: This package will download model predictions from 15 different global circulation models in 20 year intervals from the world bank. Users can also access historical data, and create maps at 2 different spatial scales.
LazyData: True
VignetteBuilder: knitr
Suggests: knitr
Imports: ggplot2, httr, plyr, rgdal, jsonlite, reshape2, sp
Packaged: 2014-04-18 21:09:16 UTC; tedhart
Author: Edmund Hart [aut, cre]
Maintainer: Edmund Hart
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-19 00:53:12

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Package rsm updated to version 2.06 with previous version 2.05 dated 2014-04-14

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 2.05 dated 2014-04-14 and 2.06 dated 2014-04-18

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Package freestats updated to version 0.0.2 with previous version 0.0.1 dated 2014-03-29

Title: Statistical algorithms used in common data mining course
Description: A collections of useful statistical functions used in Columbia course W4240/W4400.
Author: Xiaoyao Yang
Maintainer: Xiaoyao Yang

Diff between freestats versions 0.0.1 dated 2014-03-29 and 0.0.2 dated 2014-04-18

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Package care updated to version 1.1.4 with previous version 1.1.3 dated 2013-09-15

Title: High-Dimensional Regression and CAR Score Variable Selection
Description: The "care" package implements the regression approach of Zuber and Strimmer (2011) "High-dimensional regression and variable selection using CAR scores" SAGMB 10: 34. CAR scores measure the correlation between the response and the Mahalanobis-decorrelated predictors. The squared CAR score is a natural measure of variable importance and provides a canonical ordering of variables. This package provides functions for estimating CAR scores, for variable selection using CAR scores, and for estimating corresponding regression coefficients. Both shrinkage as well as empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between care versions 1.1.3 dated 2013-09-15 and 1.1.4 dated 2014-04-18

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Package st updated to version 1.2.2 with previous version 1.2.1 dated 2013-09-01

Title: Shrinkage t Statistic and CAT Score
Description: This package implements the "shrinkage t" statistic introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate of the "correlation-adjusted t-score" (CAT score) described in Zuber and Strimmer (2009). It also offers a convenient interface to a number of other regularized t-statistics commonly employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer

Diff between st versions 1.2.1 dated 2013-09-01 and 1.2.2 dated 2014-04-18

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New package QuantifQuantile with initial version 0.1
Package: QuantifQuantile
Type: Package
Title: Estimation of conditional quantiles using optimal quantization
Version: 0.1
Date: 2014-04-18
Author: Isabelle Charlier and Davy Paindaveine and Jerome Saracco
Maintainer: Isabelle Charlier
Description: Estimation of conditional quantiles using optimal quantization. Construction of an optimal grid of N quantizers, estimation of conditional quantiles and data driven selection of the size N of the grid. Graphical illustrations for the selection of N and of resulting estimated curves or surfaces when the dimension of the covariable is one or two.
License: GPL (>= 2.0)
Depends: rgl
Packaged: 2014-04-18 14:24:25 UTC; isabellecharlier
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-18 19:41:42

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Package QCA3 updated to version 0.0-6 with previous version 0.0-5 dated 2012-04-10

Title: Yet another package for Qualitative Comparative Analysis
Description: A set of functions for Qualitative Comparative Analysis (QCA). It can be used for various types of QCA (csQCA, mvQCA fsQCA and crip set TQCA and time-serious QCA). It has methods for simplifying assumption, contradictory simplifying assumption.
Author: Ronggui HUANG
Maintainer: Ronggui HUANG

Diff between QCA3 versions 0.0-5 dated 2012-04-10 and 0.0-6 dated 2014-04-18

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Package geomorph updated to version 2.0.1 with previous version 2.0 dated 2014-04-15

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 2.0 dated 2014-04-15 and 2.0.1 dated 2014-04-18

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Package yuima updated to version 1.0.9 with previous version 1.0.2 dated 2014-03-20

Title: The YUIMA Project package for SDEs
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus

Diff between yuima versions 1.0.2 dated 2014-03-20 and 1.0.9 dated 2014-04-18

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Package sda updated to version 1.3.3 with previous version 1.3.2 dated 2014-01-10

Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Description: This package provides an efficient framework for high-dimensional linear and diagonal discriminant analysis with variable selection. The classifier is trained using James-Stein-type shrinkage estimators and predictor variables are ranked using correlation-adjusted t-scores (CAT scores). Variable selection error is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer

Diff between sda versions 1.3.2 dated 2014-01-10 and 1.3.3 dated 2014-04-18

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Package Rbitcoin updated to version 0.9 with previous version 0.8.5 dated 2014-03-07

Title: R & bitcoin integration
Description: Utilities related to Bitcoin: markets API interface (bitstamp, kraken, btce, bitmarket). Both public and private API calls. Integration of data structures for all markets. Support SSL. Read Rbitcoin documentation (command: ?btc) for more information.
Author: Jan Gorecki
Maintainer: Jan Gorecki

Diff between Rbitcoin versions 0.8.5 dated 2014-03-07 and 0.9 dated 2014-04-18

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New package Density.T.HoldOut with initial version 1.02
Encoding: UTF-8
Package: Density.T.HoldOut
Type: Package
Title: Density.T.HoldOut: Non-combinatorial T-estimation Hold-Out for density estimation
Version: 1.02
Date: 2014-01-08
Author: Nelo Magalhães (Univ. Paris Sud 11 - INRIA team Select) and Yves Rozenholc (Univ. Paris Descartes - INRIA team Select)
Maintainer: Nelo Magalhães
Description: Implementation in the density framework of the non-combinatorial algorithm and its greedy version, introduced by Magalhães and Rozenholc (2014), for T-estimation Hold-Out proposed in Birgé (2006, Section 9). The package provide an implementation which uses several families of estimators (regular and irregular histograms, kernel estimators) which may be used alone or combined. As a complement, provides also a comparison with other Held-Out derived from least-squares and maximum-likelihood.
License: GPL (>= 2)
Imports: histogram
Packaged: 2014-04-17 18:33:01 UTC; rozen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-04-18 16:17:26

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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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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

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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

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More information about sjPlot at CRAN
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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

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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

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More information about rgbif at CRAN
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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 ++++----
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 4 files changed, 22 insertions(+), 13 deletions(-)

More information about PBD at CRAN
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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

More information about MSQC at CRAN
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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

More information about ATmet at CRAN
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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

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More information about VAR.etp at CRAN
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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

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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

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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

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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

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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

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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

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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

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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

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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 Garca-Castao [aut]
Maintainer: Francisco Balao

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

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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

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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

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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

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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

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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

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More information about ssym at CRAN
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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

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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

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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

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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

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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

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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

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 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

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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

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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

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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

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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

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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: Mara Jos Haro-Delicado, Virgilio Gmez-Rubio and Francisco Parreo-Torres
Maintainer: Virgilio Gmez-Rubio

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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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 17 files changed, 170 insertions(+), 59 deletions(-)

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