Mon, 15 Sep 2014

Package qpcR updated to version 1.4-0 with previous version 1.3-9 dated 2014-08-11

Title: Modelling and analysis of real-time PCR data
Description: Model fitting, optimal model selection and calculation of various features that are essential in the analysis of quantitative real-time polymerase chain reaction (qPCR).
Author: Andrej-Nikolai Spiess
Maintainer: Andrej-Nikolai Spiess

Diff between qpcR versions 1.3-9 dated 2014-08-11 and 1.4-0 dated 2014-09-15

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New package SOR with initial version 0.22
Package: SOR
Type: Package
Title: Estimation using Sequential Offsetted Regression
Version: 0.22
Date: 2014-9-15
Author: Lee S. McDaniel, Jonathan S. Schildcrout
Maintainer: Lee S. McDaniel
Depends: Matrix, stats
Description: Estimation for longitudinal data following outcome dependent sampling using the sequential offsetted regression technique. Includes support for binary, count, and continuous data.
License: GPL (>= 2)
Packaged: 2014-09-15 14:42:51 UTC; lmcda4
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-15 17:05:56

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New package propOverlap with initial version 1.0
Package: propOverlap
Type: Package
Title: Feature (gene) selection based on the Proportional Overlapping Scores
Version: 1.0
Date: 2014-09-15
Author: Osama Mahmoud, Andrew Harrison, Aris Perperoglou, Asma Gul, Zardad Khan, Berthold Lausen
Maintainer: Osama Mahmoud
Description: A package for selecting the most relevant features (genes) in the high-dimensional binary classification problems. The discriminative features are identified using analyzing the overlap between the expression values across both classes. The package includes functions for measuring the proportional overlapping score for each gene avoiding the outliers effect. The used measure for the overlap is the one defined in the "Proportional Overlapping Score (POS)" technique for feature selection. A gene mask which represents a gene's classification power can also be produced for each gene (feature). The set size of the selected genes might be set by the user. The minimum set of genes that correctly classify the maximum number of the given tissue samples (observations) can be also produced.
Depends: R (>= 2.10), Biobase
LazyLoad: yes
License: GPL (>= 2)
Repository: CRAN
Packaged: 2014-09-15 12:28:08 UTC; osama
NeedsCompilation: no
Date/Publication: 2014-09-15 17:06:03

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Package fmsb updated to version 0.5.1 with previous version 0.5.0 dated 2014-08-04

Title: Functions for medical statistics book with some demographic data
Description: Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
Author: Minato Nakazawa
Maintainer: Minato Nakazawa

Diff between fmsb versions 0.5.0 dated 2014-08-04 and 0.5.1 dated 2014-09-15

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New package hot.deck with initial version 1.0
Package: hot.deck
Type: Package
Title: Multiple Hot-deck Imputation
Version: 1.0
Date: 2014-09-03
Author: Skyler Cranmer, Jeff Gill, Natalie Jackson, Andreas Murr, Dave Armstrong
Maintainer: Dave Armstrong
Description: Performs multiple hot-deck imputation of categorical and continuous variables in a data frame.
License: GPL (>= 2)
Depends: R (>= 3.0), mice
Suggests: knitr, mitools, miceadds, Zelig
Packaged: 2014-09-15 14:26:05 UTC; armstrod
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-15 17:06:01

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New package nonnest2 with initial version 0.1-1
Package: nonnest2
Title: Tests of non-nested models
Version: 0.1-1
Author: Ed Merkle and Dongjun You
Maintainer: Dongjun You
Description: Testing non-nested models via theory supplied by Vuong (1989). Includes tests of model distinguishability and of model fit that can be applied to both nested and non-nested models. Also includes functionality to obtain confidence intervals associated with AIC and BIC.
Depends: R (>= 3.0.0)
Imports: CompQuadForm, mvtnorm, sandwich
License: GPL-2 | GPL-3
LazyData: yes
Packaged: 2014-09-15 11:53:15 UTC; Jun
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-15 14:20:59

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Package PerMallows updated to version 1.7 with previous version 1.3 dated 2014-07-03

Title: Permutations and Mallows distributions
Description: This package includes functions to work with the Mallows, Generalized Mallows and Weighted Mallows Models. The considered distances are Kendall's-tau, Cayley, Hamming and Ulam and it includes functions for making inference, sampling and learning such distributions, some of which are novel in the literature. As a by-product, PerMallows also includes operations for permutations, paying special attention in those related with the Kendall's-tau, Cayley, Ulam and Hamming distances and the random generation of permutations.
Author: Ekhine Irurozki
Maintainer: Ekhine Irurozki

Diff between PerMallows versions 1.3 dated 2014-07-03 and 1.7 dated 2014-09-15

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Package rredis updated to version 1.6.9 with previous version 1.6.8 dated 2013-09-17

Title: Redis client for R
Description: An R client for the Redis persistent key-value database available from http://redis.io.
Author: B. W. Lewis
Maintainer: B. W. Lewis

Diff between rredis versions 1.6.8 dated 2013-09-17 and 1.6.9 dated 2014-09-15

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Package investr updated to version 1.1.2 with previous version 1.1.1 dated 2014-09-09

Title: Inverse Estimation/Calibration Functions
Description: Functions to facilitate inverse estimation/calibration in linear, nonlinear, and (linear) mixed 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 1.1.1 dated 2014-09-09 and 1.1.2 dated 2014-09-15

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Package genlasso updated to version 1.3 with previous version 1.2 dated 2014-03-02

Title: Path algorithm for generalized lasso problems
Description: This package computes the solution path for generalized lasso problems. Important use cases are the fused lasso over an arbitrary graph, and trend fitting of any given polynomial order. Specialized implementations for the latter two subproblems are given to improve stability and speed.
Author: Taylor B. Arnold and Ryan J. Tibshirani
Maintainer: Taylor Arnold

Diff between genlasso versions 1.2 dated 2014-03-02 and 1.3 dated 2014-09-15

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Package demography updated to version 1.18 with previous version 1.17 dated 2014-02-01

Title: Forecasting mortality, fertility, migration and population data
Description: Functions for demographic analysis including lifetable calculations; Lee-Carter modelling; functional data analysis of mortality rates, fertility rates, net migration numbers; and stochastic population forecasting.
Author: Rob J Hyndman with contributions from Heather Booth, Leonie Tickle and John Maindonald.
Maintainer: Rob J Hyndman

Diff between demography versions 1.17 dated 2014-02-01 and 1.18 dated 2014-09-15

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New package binequality with initial version 0.6.1
Package: binequality
Type: Package
Title: Methods for Analyzing Binned Income Data
Version: 0.6.1
Date: 2014-09-14
Author: Samuel V. Scarpino, Paul von Hippel, and Igor Holas
Maintainer: Samuel V. Scarpino
Description: Methods for model selection, model averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation, etc, on binned income data where the topmost bin is right-censored. We provide both a non-parametric method, termed the bounded midpoint estimator (BME), which assigns cases to their bin midpoints; except for the censored bins, where cases are assigned to an income estimated by fitting a Pareto distribution. Because the usual Pareto estimate can be inaccurate or undefined, especially in small samples, we implement a bounded Pareto estimate that yields much better results. We also provide a parametric approach, which fits distributions from the generalized beta (GB) family. Because some GB distributions can have poor fit or undefined estimates, we fit 10 GB-family distributions and use multimodel inference to obtain definite estimates from the best-fitting distributions. We also provide binned income data from all United States of America school districts, counties, and states.
License: GPL (>= 3.0)
LazyLoad: yes
Depends: R (>= 2.10), gamlss (>= 4.2.7), gamlss.cens (>= 4.2.7), gamlss.dist (>= 4.3.0)
Imports: survival (>= 2.37-7), ineq (>= 0.2-11)
Packaged: 2014-09-14 22:50:02 UTC; scarpino
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-15 07:27:50

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Sun, 14 Sep 2014

Package Ryacas updated to version 0.2-12.1 with previous version 0.2-11 dated 2011-09-07

Title: R interface to the yacas computer algebra system
Description: An interface to the yacas computer algebra system.
Author: Rob Goedman , Gabor Grothendieck , Søren Højsgaard , Ayal Pinkus
Maintainer: G. Grothendieck

Diff between Ryacas versions 0.2-11 dated 2011-09-07 and 0.2-12.1 dated 2014-09-14

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Package netweavers updated to version 1.1 with previous version 1.0 dated 2013-06-24

Title: NetWeAvers: Weighted Averages for Networks
Description: This package summarizes quantified peptide data, fits linear models on and performs network analysis for proteomics mass spectrometry data.
Author: Elizabeth McClellan Ribble
Maintainer: Elizabeth Ribble

Diff between netweavers versions 1.0 dated 2013-06-24 and 1.1 dated 2014-09-14

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 9 files changed, 21 insertions(+), 16 deletions(-)

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Package MissingDataGUI updated to version 0.2-2 with previous version 0.2-0 dated 2014-03-20

Title: A GUI for Missing Data Exploration
Description: Provides numeric and graphical summaries for the missing values from both categorical and quantitative variables. A variety of imputation methods are applied, including the univariate imputations like fixed or random values, multivariate imputations like the nearest neighbors and multiple imputations, and imputations conditioned on a categorical variable.
Author: Xiaoyue Cheng, Dianne Cook, Heike Hofmann
Maintainer: Xiaoyue Cheng

Diff between MissingDataGUI versions 0.2-0 dated 2014-03-20 and 0.2-2 dated 2014-09-14

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 MissingDataGUI-0.2-2/MissingDataGUI/NEWS                          |    7 
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 25 files changed, 458 insertions(+), 473 deletions(-)

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Package agop updated to version 0.1-4 with previous version 0.1-3 dated 2013-06-27

Title: Aggregation Operators and Preordered Sets
Description: Tools supporting multi-criteria decision making, including variable number of criteria, by means of aggregation operators and preordered sets. Possible applications include, but are not limited to, scientometrics and bibliometrics.
Author: Marek Gagolewski [aut, cre], Anna Cena [ctb]
Maintainer: Marek Gagolewski

Diff between agop versions 0.1-3 dated 2013-06-27 and 0.1-4 dated 2014-09-14

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 agop-0.1-4/agop/NEWS                           |    6 
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 agop-0.1-4/agop/man/agop-package.Rd            |  176 +++++++++++--------------
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 agop-0.1-4/agop/man/closure_transitive.Rd      |   25 +--
 agop-0.1-4/agop/man/de_transitive.Rd           |   25 +--
 agop-0.1-4/agop/man/get_equivalence_classes.Rd |   32 ++--
 agop-0.1-4/agop/man/get_incomparable_pairs.Rd  |   33 ++--
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 agop-0.1-4/agop/man/pord_weakdom.Rd            |   34 ++--
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 34 files changed, 774 insertions(+), 817 deletions(-)

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Package RH2 updated to version 0.2.3 with previous version 0.1-2.12 dated 2014-03-31

Title: DBI/RJDBC interface to h2 Database
Description: DBI/RJDBC interface to h2 database. h2 version 1.3.175 is included.
Author: G. Grothendieck. Author of h2 is Thomas Mueller.
Maintainer: "David M. Kaplan"

Diff between RH2 versions 0.1-2.12 dated 2014-03-31 and 0.2.3 dated 2014-09-14

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Package RcmdrPlugin.coin updated to version 1.0-22 with previous version 1.0-21 dated 2012-10-30

Title: Rcmdr Coin Plug-In
Description: This package provides a Rcmdr "plug-in" based on coin (Conditional Inference Procedures in a Permutation Test Framework).
Author: Daniel-Corneliu Leucuta
Maintainer: Daniel-Corneliu Leucuta

Diff between RcmdrPlugin.coin versions 1.0-21 dated 2012-10-30 and 1.0-22 dated 2014-09-14

 DESCRIPTION                      |   15 -
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 NAMESPACE                        |    6 
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 16 files changed, 549 insertions(+), 252 deletions(-)

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Package multigroup updated to version 0.4.2 with previous version 0.4.1 dated 2014-09-04

Title: methods for multigroup data analysis
Description: This package includes several methods to study multigroup data, where the same set of variables are measured on different groups of individuals.
Author: Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston Sanchez Questions and comments go to Aida Eslami and Stephanie Bougeard
Maintainer: Aida Eslami

Diff between multigroup versions 0.4.1 dated 2014-09-04 and 0.4.2 dated 2014-09-14

 DESCRIPTION                |   13 
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 33 files changed, 1757 insertions(+), 1821 deletions(-)

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Package KernSmooth updated to version 2.23-13 with previous version 2.23-12 dated 2014-03-28

Title: Functions for kernel smoothing for Wand & Jones (1995)
Description: functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) "Kernel Smoothing".
Author: Matt Wand [aut], Brian Ripley [trl, cre, ctb] (R port and updates)
Maintainer: Brian Ripley

Diff between KernSmooth versions 2.23-12 dated 2014-03-28 and 2.23-13 dated 2014-09-14

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 7 files changed, 23 insertions(+), 15 deletions(-)

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Package EDISON updated to version 1.1 with previous version 1.0 dated 2012-07-16

Title: Network Reconstruction and Changepoint Detection
Description: Package EDISON (Estimation of Directed Interactions from Sequences Of Non-homogeneous gene expression) runs an MCMC simulation to reconstruct networks from time series data, using a non-homogeneous, time-varying dynamic Bayesian network. Networks segments and changepoints are inferred concurrently, and information sharing priors provide a reduction of the inference uncertainty.
Author: Frank Dondelinger, Sophie Lebre
Maintainer: Frank Dondelinger

Diff between EDISON versions 1.0 dated 2012-07-16 and 1.1 dated 2014-09-14

 DESCRIPTION                                 |   26 +--
 MD5                                         |  242 ++++++++++++++--------------
 NAMESPACE                                   |   68 +++++++
 R/AcceptableMove.R                          |   75 +++++---
 R/BinoHyperMove.R                           |   29 +++
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 R/CalculateChanges.R                        |   19 ++
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 man/computePx.Rd                            |   78 ++++-----
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 man/convert_nets.Rd                         |   61 +++----
 man/cp.birth.Rd                             |  140 +++++++---------
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 man/cp.shift.Rd                             |  134 ++++++---------
 man/defaultOptions.Rd                       |  104 +++++-------
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 man/generateNetwork.Rd                      |  160 ++++++++----------
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 man/sampleSig2.Rd                           |   77 +++-----
 man/simulateNetwork.Rd                      |  209 +++++++++++-------------
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New package DLMtool with initial version 1.34
Package: DLMtool
Type: Package
Title: Data-Limited Methods Toolkit
Version: 1.34
Date: 2014-09-11
Author: Tom Carruthers
Maintainer: Tom Carruthers
Description: Simulation testing and implementation of data-limited fishery stock assessment methods
License: GPL-2
Depends: R (>= 2.10.0), methods, snowfall, boot, MASS
LazyData: yes
LazyLoad: yes
VignetteBuilder: knitr
Suggests: knitr
Packaged: 2014-09-14 05:06:54 UTC; Tom
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-14 10:12:18

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Package RPMM updated to version 1.20 with previous version 1.10 dated 2012-03-16

Title: Recursively Partitioned Mixture Model
Description: Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models.
Author: E. Andres Houseman, Sc.D. and Devin C. Koestler, Ph.D.
Maintainer: E. Andres Houseman

Diff between RPMM versions 1.10 dated 2012-03-16 and 1.20 dated 2014-09-14

 DESCRIPTION    |   20 ++++---
 MD5            |    8 +--
 R/betaRPMM.R   |  137 ++++++++++++++++++++++++++----------------------------
 R/gaussRPMM.R  |  144 +++++++++++++++++++++++++++------------------------------
 man/glcTree.Rd |    5 +
 5 files changed, 155 insertions(+), 159 deletions(-)

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Package geoR updated to version 1.7-4.1 with previous version 1.7-4 dated 2012-07-05

Title: Analysis of geostatistical data
Description: Geostatistical analysis including traditional, likelihood-based and Bayesian methods.
Author: Paulo J. Ribeiro Jr and Peter J. Diggle
Maintainer: Paulo J. Ribeiro Jr

Diff between geoR versions 1.7-4 dated 2012-07-05 and 1.7-4.1 dated 2014-09-14

 DESCRIPTION     |    7 ++++---
 MD5             |    6 +++---
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 R/geoRdefunct.R |   10 ++++------
 4 files changed, 18 insertions(+), 23 deletions(-)

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Sat, 13 Sep 2014

Package iBATCGH updated to version 1.1 with previous version 1.0 dated 2014-09-02

Title: Integrative Bayesian Analysis of Transcriptomic and CGH data
Description: Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression
Author: Alberto Cassese
Maintainer: Alberto Cassese

Diff between iBATCGH versions 1.0 dated 2014-09-02 and 1.1 dated 2014-09-13

 DESCRIPTION                |    6 +++---
 MD5                        |   16 ++++++++--------
 inst/include/MHXIProbit.h  |    2 +-
 inst/include/MHXImixture.h |    2 +-
 src/MixtureMain.cpp        |    2 +-
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 src/mml.cpp                |    2 +-
 src/omegagamma.cpp         |    2 +-
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 9 files changed, 18 insertions(+), 18 deletions(-)

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Package MASSI (with last version 1.1) was removed from CRAN

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

2013-09-30 1.1
2013-08-20 1.0

Permanent link
Package Lahman updated to version 3.0-1 with previous version 2.0-3 dated 2013-06-01

Title: Sean Lahman's Baseball Database
Description: This package provides the tables from Sean Lahman's Baseball Database as a set of R data.frames. It uses the data on pitching, hitting and fielding performance and other tables from 1871 through 2013, as recorded in the 2014 version of the database.
Author: Michael Friendly [aut, cre], Dennis Murphy [ctb], Martin Monkman [ctb], Chris Dalzell [ctb]
Maintainer: Michael Friendly

Diff between Lahman versions 2.0-3 dated 2013-06-01 and 3.0-1 dated 2014-09-13

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More information about Lahman at CRAN
Permanent link

Package seedy updated to version 0.2 with previous version 0.1 dated 2014-07-10

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

Diff between seedy versions 0.1 dated 2014-07-10 and 0.2 dated 2014-09-13

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Package referenceIntervals updated to version 1.1.1 with previous version 1.1 dated 2014-08-09

Title: Reference Intervals
Description: This is a collection of tools to allow the medical professional to calculate appropriate reference ranges (intervals) with confidence intervals around the limits for diagnostic purposes.
Author: Daniel Finnegan
Maintainer: Daniel Finnegan

Diff between referenceIntervals versions 1.1 dated 2014-08-09 and 1.1.1 dated 2014-09-13

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New package recosystem with initial version 0.2.4
Package: recosystem
Type: Package
Title: Recommender System using Matrix Factorization
Version: 0.2.4
Date: 2014-09-12
Author: Yixuan Qiu, Chih-Jen Lin, Yu-Chin Juan, Yong Zhuang, Wei-Sheng Chin and other contributors. See file AUTHORS for details.
Maintainer: Yixuan Qiu
Description: This package is an R wrapper of the libmf library (http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc.
License: BSD_3_clause + file LICENSE
Copyright: see file COPYRIGHTS
URL: https://github.com/yixuan/recosystem
BugReports: https://github.com/yixuan/recosystem/issues
SystemRequirements: C++11
Depends: methods
Imports: Rcpp (>= 0.11.0)
Suggests: knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
Packaged: 2014-09-12 20:52:34 UTC; qyx
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-13 08:01:57

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Package phyloland updated to version 1.3 with previous version 1.2 dated 2014-09-12

Title: Modelling Competitive Exclusion and Limited Dispersal in a Statistical Phylogeographic Framework
Description: Phyloland package models a space colonization process mapped onto a phylogeny, it aims at estimating limited dispersal and ecological competitive exclusion in a Bayesian MCMC statistical phylogeographic framework (please refer to phyloland-package help for details.)
Author: Louis Ranjard, Marie Paturel
Maintainer: Louis Ranjard

Diff between phyloland versions 1.2 dated 2014-09-12 and 1.3 dated 2014-09-13

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Permanent link

Package ONETr updated to version 1.0 with previous version 0.1-1 dated 2014-07-07

Title: Efficient authenticated interaction with the O*NET API.
Description: This package provides a series of functions designed to enable users to easily search and interact with occupational data from the O*NET API . The package produces parsed and listed XML data for custom interactions, or pre-packaged functions for easy extraction of specific data (e.g., Knowledge, Skills, Abilities, Work Styles, etc.).
Author: Eric Knudsen
Maintainer: Eric Knudsen

Diff between ONETr versions 0.1-1 dated 2014-07-07 and 1.0 dated 2014-09-13

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Permanent link

Package HH updated to version 3.1-5 with previous version 3.0-4 dated 2014-03-11

Title: Statistical Analysis and Data Display: Heiberger and Holland
Description: Support software for Statistical Analysis and Data Display (First Edition, Springer, ISBN 0-387-40270-5, 2004) and (Second Edition, Springer, ISBN x-xxx-xxxxx-x, anticipated 2015) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger

Diff between HH versions 3.0-4 dated 2014-03-11 and 3.1-5 dated 2014-09-13

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More information about HH at CRAN
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Package geepack updated to version 1.2-0 with previous version 1.1-6 dated 2012-01-27

Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can also handle clustered categorical responses.
Author: Søren Højsgaard, , Ulrich Halekoh , Jun Yan ,
Maintainer: Søren Højsgaard

Diff between geepack versions 1.1-6 dated 2012-01-27 and 1.2-0 dated 2014-09-13

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Fri, 12 Sep 2014

Package CorReg updated to version 0.15.6 with previous version 0.15.0 dated 2014-07-15

Title: Linear regression based on linear structure between covariates
Description: Linear regression based on a recursive structural equation model (explicit correlations) found by a MCMC algorithm. It permits to face highly correlated covariates. Variable selection is included (by lasso, elasticnet, etc.). It also provides some graphical tools for basic statistics.
Author: Clement THERY [aut, cre], Christophe BIERNACKI [ctb], Gaetan LORIDANT [ctb], Florian WATRIN [ctb], Quentin GRIMONPREZ [ctb], Vincent KUBICKI [ctb], Samuel BLANCK [ctb], Jeremie KELLNER [ctb]
Maintainer: Clement THERY

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Permanent link

New package treatSens with initial version 1.0
Package: treatSens
Type: Package
Title: Sensitivity analysis for causal inference
Version: 1.0
Date: 2014-09-02
Author: Nicole Bohme Carnegie, Masataka Harada, Jennifer Hill
Maintainer: "Nicole Bohme Carnegie"
Depends: R (>= 3.1.0)
Suggests: doParallel, foreach
Description: Utilities to investigate sensitivity to unmeasured confounding in parametric models with either binary or continuous treatment.
License: GPL-2
LazyLoad: yes
LazyData: yes
Packaged: 2014-09-12 17:24:24 UTC; carnegin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-12 20:27:07

More information about treatSens at CRAN
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Package partykit updated to version 0.8-2 with previous version 0.8-1 dated 2014-09-08

Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and visualizing tree-structured regression and classification models. This unified infrastructure can be used for reading/coercing tree models from different sources (rpart, RWeka, PMML) yielding objects that share functionality for print/plot/predict methods. Furthermore, new and improved reimplementations of conditional inference trees (ctree) and model-based recursive partitioning (mob) from the party package are provided based on the new infrastructure.
Author: Torsten Hothorn [aut, cre], Achim Zeileis [aut]
Maintainer: Torsten Hothorn

Diff between partykit versions 0.8-1 dated 2014-09-08 and 0.8-2 dated 2014-09-12

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Package leafletR updated to version 0.3-0 with previous version 0.2-1 dated 2014-07-09

Title: Interactive web-maps based on the Leaflet JavaScript library
Description: Display your spatial data on interactive web-maps using the open-source JavaScript library Leaflet. The package provides basic web-mapping functionality to combine vector data and online map tiles from different sources.
Author: Christian Graul, with contributions from Francois Guillem
Maintainer: Christian Graul

Diff between leafletR versions 0.2-1 dated 2014-07-09 and 0.3-0 dated 2014-09-12

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 38 files changed, 234 insertions(+), 183 deletions(-)

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Package WhopGenome updated to version 0.9.0 with previous version 0.8.9 dated 2014-08-27

Title: High-speed processing of whole-genome VCF-format variation data, FASTA-format sequence data and several alignments formats.
Description: WhopGenome's provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
Author: Ulrich Wittelsbuerger
Maintainer: Ulrich Wittelsbuerger

Diff between WhopGenome versions 0.8.9 dated 2014-08-27 and 0.9.0 dated 2014-09-12

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 WhopGenome-0.9.0/WhopGenome/src/w_snpmat_int.cpp          |   27 +++++++++++---
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 WhopGenome-0.9.0/WhopGenome/src/w_vcf.cpp                 |   16 ++++----
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 14 files changed, 87 insertions(+), 59 deletions(-)

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Package SpecsVerification updated to version 0.2-0 with previous version 0.1-1 dated 2014-05-02

Title: Forecast verification routines for the SPECS FP7 project
Description: A collection of new forecast verification routines for the SPECS FP7 project. The emphasis is on comparative verification of ensemble forecasts.
Author: Stefan Siegert [aut, cre]
Maintainer: Stefan Siegert

Diff between SpecsVerification versions 0.1-1 dated 2014-05-02 and 0.2-0 dated 2014-09-12

 DESCRIPTION                    |    9 ++---
 MD5                            |   47 +++++++++++++++++++-----------
 NAMESPACE                      |    7 ++++
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Package seewave updated to version 1.7.6 with previous version 1.7.3 dated 2014-01-27

Title: Sound analysis and synthesis
Description: seewave provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur , Thierry Aubin, Caroline Simonis, \cr with contributions of Ethan C. Brown, Camille Desjonqueres, Amandine Gasc, Stefanie LaZerte, Jonathan Lees, Laurent Lellouch, Sandrine Pavoine, Luis J. Villanueva-Rivera, Zev Ross, Carl G. Witthoft.
Maintainer: Jerome Sueur

Diff between seewave versions 1.7.3 dated 2014-01-27 and 1.7.6 dated 2014-09-12

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 25 files changed, 1002 insertions(+), 509 deletions(-)

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Package RhpcBLASctl updated to version 0.14-256 with previous version 0.14-72 dated 2014-03-13

Title: Control the number of threads on BLAS for R
Description: Control the number of threads on BLAS(Aka GotoBLAS, ACML and MKL). -- GotoBLAS(generic) binary for Windows i386 http://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/binary/windows/x86/KATMAI/Rblas.dll GotoBLAS(generic) binary for Windows x64 http://prs.ism.ac.jp/~nakama/SurviveGotoBLAS2/binary/windows/x64/PRESCOTT/Rblas.dll
Author: Junji NAKANO and Eiji NAKAMA
Maintainer: Ei-ji Nakama

Diff between RhpcBLASctl versions 0.14-72 dated 2014-03-13 and 0.14-256 dated 2014-09-12

 ChangeLog   |    4 ++++
 DESCRIPTION |   10 +++++-----
 MD5         |    4 ++--
 3 files changed, 11 insertions(+), 7 deletions(-)

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Package Rhpc updated to version 0.14-256 with previous version 0.14-78 dated 2014-03-22

Title: An R package for High-Performance Computing
Description: Rhpc_lapply, Rhpc_lapplyLB and Rhpc_worker_call using MPI provides better HPC environment on R(works fast on HPC). and this package supports long vector, can deal with slightly big data.
Author: Junji NAKANO and Eiji NAKAMA
Maintainer: Ei-ji Nakama

Diff between Rhpc versions 0.14-78 dated 2014-03-22 and 0.14-256 dated 2014-09-12

 ChangeLog                          |   14 ++
 DESCRIPTION                        |   15 +-
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 NAMESPACE                          |    1 
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 12 files changed, 322 insertions(+), 151 deletions(-)

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Package PReMiuM updated to version 3.0.30 with previous version 3.0.29 dated 2014-09-09

Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: This is a package for Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection.
Author: David I. Hastie , Silvia Liverani , Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi, Sylvia Richardson
Maintainer: Silvia Liverani

Diff between PReMiuM versions 3.0.29 dated 2014-09-09 and 3.0.30 dated 2014-09-12

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 PReMiuM-3.0.30/PReMiuM/src/include/PReMiuMIO.h         |    4 
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 10 files changed, 113 insertions(+), 78 deletions(-)

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New package nettools with initial version 1.0.1
Package: nettools
Type: Package
Title: A Network Comparison Framework
Version: 1.0.1
Date: 2014-09-02
Authors@R: c(person("Michele","Filosi",role=c("aut","cre"), email = "filosi@fbk.eu"), person("Roberto", "Visintainer", role = "aut", email = "visintainer@fbk.eu"), person("Samantha", "Riccadonna", role = "aut", email = "samantha.riccadonna@fmach.it"), person("Giuseppe", "Jurman", role = "ctb", email = "jurman@fbk.eu"), person("Cesare", "Furlanello", role = "ctb", email = "furlan@fbk.eu"))
Maintainer: Michele Filosi
Depends: R (>= 2.14.1), methods
Imports: parallel, rootSolve, dtw, WGCNA, minet, Matrix, minerva, combinat, igraph
Description: A collection of network inference methods for co-expression networks, quantitative network distances and a novel framework for network stability analysis.
License: CC BY-NC-SA 4.0
Packaged: 2014-09-11 10:37:46 UTC; michele
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Samantha Riccadonna [aut], Giuseppe Jurman [ctb], Cesare Furlanello [ctb]
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-12 16:16:26

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Package meta updated to version 3.8-0 with previous version 3.7-1 dated 2014-07-29

Title: Meta-Analysis with R
Description: User-friendly general package providing standard methods for meta-analysis: - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from RevMan 5; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer

Diff between meta versions 3.7-1 dated 2014-07-29 and 3.8-0 dated 2014-09-12

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 57 files changed, 1289 insertions(+), 1156 deletions(-)

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Package Hmisc updated to version 3.14-5 with previous version 3.14-4 dated 2014-04-13

Title: Harrell Miscellaneous
Description: The Hmisc package contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, importing datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX code, and recoding variables.
Author: Frank E Harrell Jr , with contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr

Diff between Hmisc versions 3.14-4 dated 2014-04-13 and 3.14-5 dated 2014-09-12

 DESCRIPTION              |   12 ++---
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Package xtable updated to version 1.7-4 with previous version 1.7-3 dated 2014-03-06

Title: Export tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables
Author: David B. Dahl
Maintainer: David Scott

Diff between xtable versions 1.7-3 dated 2014-03-06 and 1.7-4 dated 2014-09-12

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 17 files changed, 682 insertions(+), 678 deletions(-)

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Package unittest updated to version 1.0-1 with previous version 1.0-0 dated 2014-08-23

Title: TAP-compliant unit testing.
Description: Concise TAP (http://testanything.org/) compliant unit testing package. Authored tests that can be run using CMD check with minimal implementation overhead.
Author: Jamie Lentin [aut], Anthony Hennessey [aut, cre]
Maintainer: Anthony Hennessey

Diff between unittest versions 1.0-0 dated 2014-08-23 and 1.0-1 dated 2014-09-12

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 MD5                          |    8 ++-
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 6 files changed, 60 insertions(+), 47 deletions(-)

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Package spatsurv updated to version 0.9-7 with previous version 0.9-6 dated 2014-07-15

Title: Bayesian spatial survival analysis with parametric proportional hazards models.
Description: an R Package for Bayesian Inference with Spatial Survival Models
Author: Benjamin M. Taylor and Barry S. Rowlingson
Maintainer: Benjamin M. Taylor

Diff between spatsurv versions 0.9-6 dated 2014-07-15 and 0.9-7 dated 2014-09-12

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 man/grid2spix.Rd                           |   11 -
 man/grid2spts.Rd                           |   11 -
 man/gridY.Rd                               |    5 
 man/guess_t.Rd                             |    6 
 man/hasNext.Rd                             |    3 
 man/hasNext.iter.Rd                        |    7 
 man/hazard_PP.Rd                           |    5 
 man/hazardexceedance.Rd                    |   22 +-
 man/hazardpars.Rd                          |   16 --
 man/hessbasehazard.Rd                      |   13 -
 man/hessbasehazard.basehazardspec.Rd       |   12 -
 man/hesscumbasehazard.Rd                   |   13 -
 man/hesscumbasehazard.basehazardspec.Rd    |   15 -
 man/indepGaussianprior.Rd                  |   23 +-
 man/inference.control.Rd                   |   31 +--
 man/invtransformweibull.Rd                 |   13 -
 man/is.burnin.Rd                           |    6 
 man/is.retain.Rd                           |    3 
 man/iteration.Rd                           |    6 
 man/logPosterior.Rd                        |   35 +---
 man/logPosterior_gridded.Rd                |   35 +---
 man/loop.mcmc.Rd                           |    5 
 man/makehamHaz.Rd                          |  100 ++++--------
 man/maxlikparamPHsurv.Rd                   |   13 -
 man/mcmcLoop.Rd                            |   13 -
 man/mcmcPriors.Rd                          |   40 +----
 man/mcmcProgressNone.Rd                    |    3 
 man/mcmcProgressPrint.Rd                   |    3 
 man/mcmcProgressTextBar.Rd                 |    3 
 man/mcmcpars.Rd                            |   13 -
 man/nextStep.Rd                            |    3 
 man/omegapriorGauss.Rd                     |   16 --
 man/plotsurv.Rd                            |   51 ++----
 man/posteriorcov.Rd                        |   33 +---
 man/predict.mcmcspatsurv.Rd                |   43 +----
 man/print.mcmc.Rd                          |    8 -
 man/print.mcmcspatsurv.Rd                  |   21 +-
 man/priorposterior.Rd                      |   27 +--
 man/proposalVariance.Rd                    |   27 +--
 man/proposalVariance_gridded.Rd            |   27 +--
 man/quantile.mcmcspatsurv.Rd               |   21 +-
 man/randompars.Rd                          |   16 --
 man/resetLoop.Rd                           |    3 
 man/setTxtProgressBar2.Rd                  |   12 -
 man/setupHazard.Rd                         |   17 --
 man/simsurv.Rd                             |   42 +----
 man/spatialpars.Rd                         |   16 --
 man/spatsurv-package.Rd                    |   41 +++--
 man/spatsurvVignette.Rd                    |    1 
 man/summary.mcmc.Rd                        |   11 -
 man/summary.mcmcspatsurv.Rd                |   17 +-
 man/surv3d.Rd                              |   30 +--
 man/survival_PP.Rd                         |    5 
 man/survspat.Rd                            |   39 +----
 man/tpowHaz.Rd                             |  105 ++++---------
 man/transformweibull.Rd                    |   13 -
 man/txtProgressBar2.Rd                     |   23 +-
 man/vcov.mcmcspatsurv.Rd                   |   21 +-
 man/weibullHaz.Rd                          |  100 ++++--------
 114 files changed, 990 insertions(+), 1371 deletions(-)

More information about spatsurv at CRAN
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Package SimComp updated to version 2.2 with previous version 1.9.0 dated 2014-02-28

Title: Simultaneous Comparisons for Multiple Endpoints
Description: Simultaneous tests and confidence intervals are provided for one-way experimental designs with one or many normally distributed, primary response variables (endpoints). Differences (Hasler and Hothorn, 2011) or ratios (Hasler and Hothorn, 2012) of means can be considered. Various contrasts can be chosen, unbalanced sample sizes are allowed as well as heterogeneous variances (Hasler and Hothorn, 2008) or covariance matrices (Hasler, 2014).
Author: Mario Hasler
Maintainer: Mario Hasler

Diff between SimComp versions 1.9.0 dated 2014-02-28 and 2.2 dated 2014-09-12

 DESCRIPTION            |   16 +++--------
 MD5                    |   68 +++++++++++++++++++++++++++----------------------
 NAMESPACE              |    4 ++
 R/DfSattDiff.R         |only
 R/DfSattRat.R          |only
 R/SimCiDiff.R          |    5 ++-
 R/SimCiDiffHet.R       |    1 
 R/SimCiDiffHom.R       |    1 
 R/SimCiRat.R           |   29 ++++++++++----------
 R/SimCiRatHet.R        |    1 
 R/SimCiRatHom.R        |    1 
 R/SimTestDiff.R        |    5 ++-
 R/SimTestDiffHet.R     |    5 ++-
 R/SimTestDiffHom.R     |    5 ++-
 R/SimTestRat.R         |   29 ++++++++++----------
 R/SimTestRatHet.R      |    5 ++-
 R/SimTestRatHom.R      |    5 ++-
 R/ermvnorm.R           |    8 ++++-
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 R/print.SimCi.R        |    1 
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 R/summary.SimCi.R      |    1 
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 man/SimCiDiff.Rd       |   40 +++++++++++++++++-----------
 man/SimCiRat.Rd        |   53 +++++++++++++++++++++-----------------
 man/SimComp-package.Rd |   39 ++++++++++++++++++----------
 man/SimTestDiff.Rd     |   38 +++++++++++++++------------
 man/SimTestRat.Rd      |   50 ++++++++++++++++++++----------------
 man/coagulation.Rd     |   12 ++++----
 man/ermvnorm.Rd        |   65 ++++++++++++++++++++++++++++++----------------
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 man/summary.SimTest.Rd |    2 -
 39 files changed, 290 insertions(+), 207 deletions(-)

More information about SimComp at CRAN
Permanent link

Package recosystem (with last version 0.2.3) was removed from CRAN

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

2014-09-11 0.2.3

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Package phyloland updated to version 1.2 with previous version 1.1 dated 2014-08-16

Title: Modelling Competitive Exclusion and Limited Dispersal in a Statistical Phylogeographic Framework
Description: Phyloland package models a space colonization process mapped onto a phylogeny, it aims at estimating limited dispersal and ecological competitive exclusion in a Bayesian MCMC statistical phylogeographic framework (please refer to phyloland-package help for details.)
Author: Louis Ranjard, Marie Paturel
Maintainer: Louis Ranjard

Diff between phyloland versions 1.1 dated 2014-08-16 and 1.2 dated 2014-09-12

 DESCRIPTION                   |    8 ++++----
 MD5                           |    6 +++---
 R/pack_Phylogeo_Functions_g.R |   29 ++++++++++++++++++++++-------
 src/main.c                    |    4 ++--
 4 files changed, 31 insertions(+), 16 deletions(-)

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Package PepPrep updated to version 1.1.0 with previous version 1.0.1 dated 2014-09-04

Title: Insilico peptide mutation, digestion and homologous comparison.
Description: Amino acid exchange based on single nucleotide variant (SNV) information and tryptic digestion on peptide sequence. Searching for homologous by comparison of tryptic digested peptide sequences.
Author: Rafael Dellen
Maintainer: Rafael Dellen

Diff between PepPrep versions 1.0.1 dated 2014-09-04 and 1.1.0 dated 2014-09-12

 ChangeLog                |   11 -
 DESCRIPTION              |    8 
 MD5                      |   12 -
 R/CompHomPep_functions.R |  249 +++++++++++++++-----------
 R/SNVtoPep_functions.R   |  442 ++++++++++++++++++++++++++---------------------
 man/compHomToPepFasta.Rd |   19 +-
 man/snvToPepFasta.Rd     |   21 +-
 7 files changed, 442 insertions(+), 320 deletions(-)

More information about PepPrep at CRAN
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Package MarkedPointProcess (with last version 0.2.22) was removed from CRAN

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

2014-09-09 0.2.22
2013-12-05 0.2.21
2011-10-23 0.2.20
2011-03-02 0.2.17
2010-09-16 0.2.15
2009-11-01 0.2.13
2009-06-29 0.2.11
2008-08-22 0.2.9
2008-03-27 0.2.8
2008-02-19 0.2.7
2008-02-03 0.2.5
2007-12-14 0.2.4
2007-10-04 0.2.3
2006-09-23 0.2.2

Permanent link
Package zCompositions updated to version 1.0.3 with previous version 1.0.2 dated 2014-09-09

Title: Imputation of Zeros and Nondetects in Compositional Data Sets
Description: Principled methods to impute multivariate left-censored data and zeros in compositional data sets
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo

Diff between zCompositions versions 1.0.2 dated 2014-09-09 and 1.0.3 dated 2014-09-12

 DESCRIPTION     |    6 +++---
 MD5             |   12 ++++++------
 NEWS            |    2 +-
 R/multKM.R      |    9 +++++----
 R/splineKM.R    |    7 ++++---
 man/multKM.Rd   |    4 ++--
 man/splineKM.Rd |    5 ++---
 7 files changed, 23 insertions(+), 22 deletions(-)

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Package RGraphics updated to version 2.0-12 with previous version 2.0-9 dated 2014-06-10

Title: Data and Functions from the book R Graphics, Second Edition
Description: Data and Functions from the book R Graphics, Second Edition. There is a function to produce each figure in the book, plus several functions, classes, and methods defined in Chapter 8.
Author: Paul Murrell
Maintainer: Paul Murrell

Diff between RGraphics versions 2.0-9 dated 2014-06-10 and 2.0-12 dated 2014-09-12

 DESCRIPTION                     |   14 
 MD5                             |    9 
 R/figures.R                     |  798 
 inst/extra/capturecomic_moon.ps |only
 inst/extra/comic_moon.ps.xml    |  346 
 inst/extra/tiger.ps.xml         |37165 ++++++++++++++++++++--------------------
 6 files changed, 19327 insertions(+), 19005 deletions(-)

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New package Mobilize with initial version 2.16-4
Package: Mobilize
Type: Package
Title: Mobilize plots and functions
Version: 2.16-4
Date: 2014-09-11
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: Some canned plots and functions designed for the mobilize project. Designed to be called remotely.
License: GPL
Depends: R (>= 2.14), stats, methods, Ohmage
Imports: ggplot2, wordcloud, reshape2
Suggests: XML, maps
Packaged: 2014-09-11 10:24:17 UTC; jeroen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-12 07:53:18

More information about Mobilize at CRAN
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Thu, 11 Sep 2014

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

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

2014-09-11 1.0

Permanent link
Package VennDiagram updated to version 1.6.8 with previous version 1.6.7 dated 2014-07-03

Title: Generate high-resolution Venn and Euler plots
Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros

Diff between VennDiagram versions 1.6.7 dated 2014-07-03 and 1.6.8 dated 2014-09-11

 DESCRIPTION            |    6 ++--
 MD5                    |    8 +++---
 NAMESPACE              |    1 
 R/draw.pairwise.venn.R |   59 +++++++++++++++++++++++++------------------------
 TODO                   |    1 
 5 files changed, 40 insertions(+), 35 deletions(-)

More information about VennDiagram at CRAN
Permanent link

New package lefse with initial version 0.1
Package: lefse
Type: Package
Title: Phylogenetic and Functional Analyses for Ecology
Version: 0.1
Date: 2014-09-04
Author: Nathan G. Swenson
Maintainer: Nathan G. Swenson
Description: Utilizing phylogenetic and functional information for the analyses of ecological datasets. The analyses include methods for quantifying the phylogenetic and functional diversity of assemblages.
License: GPL-2 | GPL-3
Depends: R (>= 2.10)
Imports: ape, picante, geiger, fBasics, SDMTools, vegan
Packaged: 2014-09-05 10:37:55 UTC; nathanswenson
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 21:03:26

More information about lefse at CRAN
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New package GENLIB with initial version 1.0
Package: GENLIB
Type: Package
Title: Genealogical Data Analysis
Version: 1.0
Date: 2012-04-04
Author: Louis Houde, Jean-Francois Lefebvre, Valery Roy-Lagace, Sebastien Lemieux
Maintainer: Marie-Helene Roy-Gagnon
Description: Takes genealogical data frames and calculates different demographic variables such as genetic contribution, kinship, etc...
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 3.0), Rcpp (>= 0.9.10)
Imports: kinship2, methods, bootstrap, Matrix, lattice, quadprog, foreach, parallel, doParallel
LinkingTo: Rcpp
Packaged: 2014-09-11 16:31:06 UTC; sainte-justine\lefjea01
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 21:02:19

More information about GENLIB at CRAN
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Package intsvy updated to version 1.4 with previous version 1.3 dated 2014-03-13

Title: International Assessment Data Manager
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA and PIAAC)
Author: Daniel Caro , Przemyslaw Biecek
Maintainer: Daniel Caro

Diff between intsvy versions 1.3 dated 2014-03-13 and 1.4 dated 2014-09-11

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 intsvy-1.4/intsvy/DESCRIPTION                 |   17 
 intsvy-1.4/intsvy/MD5                         |  164 ++++----
 intsvy-1.4/intsvy/NAMESPACE                   |   83 ++--
 intsvy-1.4/intsvy/R/adj.input.R               |   22 -
 intsvy-1.4/intsvy/R/adj.measlev.R             |   12 
 intsvy-1.4/intsvy/R/is.vlabeled.R             |   24 -
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 intsvy-1.4/intsvy/R/pirls.mean.R              |   52 +-
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 intsvy-1.4/intsvy/R/pirls.reg.R               |   92 ++--
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 intsvy-1.4/intsvy/R/pirls.rho.R               |   62 +--
 intsvy-1.4/intsvy/R/pirls.rho.pv.R            |  146 +++----
 intsvy-1.4/intsvy/R/pirls.select.merge.R      |  486 ++++++++++++-------------
 intsvy-1.4/intsvy/R/pirls.table.R             |   86 ++--
 intsvy-1.4/intsvy/R/pirls.var.label.R         |   82 ++--
 intsvy-1.4/intsvy/R/pisa.ben.pv.R             |  132 +++---
 intsvy-1.4/intsvy/R/pisa.mean.R               |   64 +--
 intsvy-1.4/intsvy/R/pisa.mean.pv.R            |  119 ++++--
 intsvy-1.4/intsvy/R/pisa.reg.R                |   90 ++--
 intsvy-1.4/intsvy/R/pisa.reg.pv.R             |  123 +++---
 intsvy-1.4/intsvy/R/pisa.select.merge.R       |  350 +++++++++---------
 intsvy-1.4/intsvy/R/pisa.table.R              |   98 ++---
 intsvy-1.4/intsvy/R/pisa.var.label.R          |   94 ++--
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 intsvy-1.4/intsvy/R/timss.mean.R              |   52 +-
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 intsvy-1.4/intsvy/R/timss.reg.R               |   92 ++--
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 intsvy-1.4/intsvy/R/timss.rho.R               |   62 +--
 intsvy-1.4/intsvy/R/timss.rho.pv.R            |  146 +++----
 intsvy-1.4/intsvy/R/timss.table.R             |   86 ++--
 intsvy-1.4/intsvy/R/timssg4.select.merge.R    |  500 +++++++++++++-------------
 intsvy-1.4/intsvy/R/timssg4.var.label.R       |   82 ++--
 intsvy-1.4/intsvy/R/timssg8.select.merge.R    |  398 ++++++++++----------
 intsvy-1.4/intsvy/R/timssg8.var.label.R       |   80 ++--
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 intsvy-1.4/intsvy/man/pirls.reg.Rd            |  122 +++---
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 intsvy-1.4/intsvy/man/pirls.rho.Rd            |   98 ++---
 intsvy-1.4/intsvy/man/pirls.rho.pv.Rd         |  102 ++---
 intsvy-1.4/intsvy/man/pirls.select.merge.Rd   |   96 ++--
 intsvy-1.4/intsvy/man/pirls.table.Rd          |   98 ++---
 intsvy-1.4/intsvy/man/pirls.var.label.Rd      |   74 +--
 intsvy-1.4/intsvy/man/pisa.ben.pv.Rd          |   98 ++---
 intsvy-1.4/intsvy/man/pisa.mean.Rd            |  107 ++---
 intsvy-1.4/intsvy/man/pisa.mean.pv.Rd         |  112 +++--
 intsvy-1.4/intsvy/man/pisa.reg.Rd             |   95 ++--
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 intsvy-1.4/intsvy/man/pisa.select.merge.Rd    |  118 +++---
 intsvy-1.4/intsvy/man/pisa.table.Rd           |   96 ++--
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 intsvy-1.4/intsvy/man/timss.mean.Rd           |  106 ++---
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 intsvy-1.4/intsvy/man/timss.reg.Rd            |  100 ++---
 intsvy-1.4/intsvy/man/timss.reg.pv.Rd         |  106 ++---
 intsvy-1.4/intsvy/man/timss.rho.Rd            |   98 ++---
 intsvy-1.4/intsvy/man/timss.rho.pv.Rd         |  102 ++---
 intsvy-1.4/intsvy/man/timss.table.Rd          |  118 +++---
 intsvy-1.4/intsvy/man/timssg4.select.merge.Rd |  100 ++---
 intsvy-1.4/intsvy/man/timssg4.var.label.Rd    |   70 +--
 intsvy-1.4/intsvy/man/timssg8.select.merge.Rd |   96 ++--
 intsvy-1.4/intsvy/man/timssg8.var.label.Rd    |   72 +--
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Package snpEnrichment updated to version 1.4-1 with previous version 1.4-0 dated 2014-02-04

Title: SNPs enrichment analysis
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal)
Author: Mickael Canouil [aut, cre], Loic Yengo [ctb]
Maintainer: Mickael Canouil

Diff between snpEnrichment versions 1.4-0 dated 2014-02-04 and 1.4-1 dated 2014-09-11

 ChangeLog                    |   21 ++++++++-----
 DESCRIPTION                  |    8 ++---
 MD5                          |   38 ++++++++++++------------
 NAMESPACE                    |    4 +-
 R/Global.R                   |   52 ++++++++++++++-------------------
 R/enrichment.R               |   66 +++++++++++++++++++++++++++++++------------
 data/toyEnrichment.RData     |binary
 man/Chromosome-class.Rd      |   28 +++++++++---------
 man/EnrichSNP-class.Rd       |    4 +-
 man/Enrichment-class.Rd      |   12 +++----
 man/compareEnrichment.Rd     |   30 +++++++++----------
 man/excludeSNP-methods.Rd    |    2 -
 man/initFiles.Rd             |   14 ++++-----
 man/mclapply2.Rd             |    4 +-
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 man/readEnrichment.Rd        |   36 +++++++++++------------
 man/snpEnrichment-package.Rd |   44 ++++++++++++++--------------
 man/transcript-dataset.Rd    |    2 -
 man/writeLD.Rd               |   16 +++++-----
 20 files changed, 216 insertions(+), 189 deletions(-)

More information about snpEnrichment at CRAN
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Package knnIndep updated to version 2.0 with previous version 1.0 dated 2014-03-18

Title: Independence tests and benchmarks
Description: This package provides the implementation of an exact formula of the ith nearest neighbour distance distribution and implementations of tests of independence based on that formula. Furthermore the package provides a general framework to benchmark tests of independence.
Author: Sebastian Dümcke
Maintainer: Sebastian Dümcke

Diff between knnIndep versions 1.0 dated 2014-03-18 and 2.0 dated 2014-09-11

 DESCRIPTION               |   10 +++++-----
 MD5                       |   29 ++++++++++++++++++++---------
 NAMESPACE                 |    3 +++
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 R/power.plot.R            |    6 +++++-
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 21 files changed, 63 insertions(+), 35 deletions(-)

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Package glmmLasso updated to version 1.3.3 with previous version 1.3.2 dated 2014-09-10

Title: Variable selection for generalized linear mixed models by L1-penalized estimation
Description: Variable selection for generalized linear mixed models by L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll

Diff between glmmLasso versions 1.3.2 dated 2014-09-10 and 1.3.3 dated 2014-09-11

 DESCRIPTION                        |    8 ++++----
 MD5                                |   14 +++++++-------
 R/glmmLasso.r                      |   15 ++++++++++-----
 R/glmm_final.r                     |    6 ++++--
 R/glmm_final.smooth.r              |    6 ++++--
 R/glmm_final_multi_random.r        |    6 ++++--
 R/glmm_final_multi_random_smooth.r |    6 ++++--
 man/glmmLasso.rd                   |   13 +++++++------
 8 files changed, 44 insertions(+), 30 deletions(-)

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Package pkgKitten updated to version 0.1.2 with previous version 0.1.1 dated 2014-09-10

Title: Create Simple Packages Which Do Not Upset R CMD check
Description: Provides a function kitten() which creates cute little packages which pass R CMD check. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between pkgKitten versions 0.1.1 dated 2014-09-10 and 0.1.2 dated 2014-09-11

 ChangeLog     |    6 ++++++
 DESCRIPTION   |    8 ++++----
 MD5           |    8 ++++----
 R/pkgKitten.R |    2 +-
 inst/NEWS.Rd  |    7 +++++++
 5 files changed, 22 insertions(+), 9 deletions(-)

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Package pbkrtest updated to version 0.4-1 with previous version 0.4-0 dated 2014-08-11

Title: Parametric bootstrap and Kenward Roger based methods for mixed model comparison
Description: Test in linear mixed effects models. Attention is on linear mixed effects models as implemented in the lme4 package. The package implements a parametric bootstrap test The package implements a Kenward-Roger modification of F-tests
Author: Ulrich Halekoh Søren Højsgaard
Maintainer: Søren Højsgaard

Diff between pbkrtest versions 0.4-0 dated 2014-08-11 and 0.4-1 dated 2014-09-11

 pbkrtest-0.4-0/pbkrtest/man/KRinit-modcomp.Rd               |only
 pbkrtest-0.4-1/pbkrtest/ChangeLog                           |   64 +-
 pbkrtest-0.4-1/pbkrtest/DESCRIPTION                         |   10 
 pbkrtest-0.4-1/pbkrtest/MD5                                 |   41 -
 pbkrtest-0.4-1/pbkrtest/NAMESPACE                           |   14 
 pbkrtest-0.4-1/pbkrtest/R/KR-vcovAdj.R                      |  187 ++++---
 pbkrtest-0.4-1/pbkrtest/R/get_ddf_Lb.R                      |  155 +++--
 pbkrtest-0.4-1/pbkrtest/build/vignette.rds                  |binary
 pbkrtest-0.4-1/pbkrtest/data/beets.txt.gz                   |binary
 pbkrtest-0.4-1/pbkrtest/data/budworm.txt.gz                 |binary
 pbkrtest-0.4-1/pbkrtest/inst/doc/pbkrtest-introduction.R    |  311 +++++-------
 pbkrtest-0.4-1/pbkrtest/inst/doc/pbkrtest-introduction.Rnw  |  179 ++----
 pbkrtest-0.4-1/pbkrtest/inst/doc/pbkrtest-introduction.pdf  |binary
 pbkrtest-0.4-1/pbkrtest/man/KRmodcomp.Rd                    |    2 
 pbkrtest-0.4-1/pbkrtest/man/PBmodcomp.Rd                    |    2 
 pbkrtest-0.4-1/pbkrtest/man/PBrefdist.Rd                    |    2 
 pbkrtest-0.4-1/pbkrtest/man/getKR.Rd                        |    2 
 pbkrtest-0.4-1/pbkrtest/man/get_ddf_Lb.Rd                   |   58 +-
 pbkrtest-0.4-1/pbkrtest/man/model2restrictionMatrix.Rd      |    2 
 pbkrtest-0.4-1/pbkrtest/man/pbkrtest-internal.Rd            |    8 
 pbkrtest-0.4-1/pbkrtest/man/vcovAdj.Rd                      |    2 
 pbkrtest-0.4-1/pbkrtest/vignettes/pbkrtest-introduction.Rnw |  179 ++----
 22 files changed, 635 insertions(+), 583 deletions(-)

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New package gapmap with initial version 0.0.1
Package: gapmap
Type: Package
Title: Functions for Drawing Gapped Cluster Heatmap with ggplot2
Version: 0.0.1
URL: https://bitbucket.org/biovizleuven/gapmap/
Date: 2014-09-10
Author: Ryo Sakai
Maintainer: Ryo Sakai
Description: The gap encodes the distance between clusters and improves interpretation of cluster heatmaps. The gaps can be of the same distance based on a height threshold to cut the dendrogram. Another option is to vary the size of gaps based on the distance between clusters.
License: GPL-2 | GPL-3
Depends: ggplot2, grid, reshape2
Suggests: knitr, dendsort
VignetteBuilder: knitr
Packaged: 2014-09-11 10:21:51 UTC; Ryo
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 13:06:15

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New package FRESA.CAD with initial version 1.0
Package: FRESA.CAD
Type: Package
Title: FeatuRE Selection Algorithms for Computer Aided Diagnosis
Version: 1.0
Date: 2014-09-10
Author: Jose Gerardo Tamez-Pena
Maintainer: Jose Gerardo Tamez-Pena
Description: FRESA.CAD provides a set of functions and feature selection algorithms for building Computer Aided Diagnosis Models
License: LGPL (>= 2)
Depends: R (>= 3.0.0),Hmisc,pROC,stringr,miscTools,survival
Suggests: class, cvTools, glmnet, speedglm, gplots, RColorBrewer, nlme, rpart
Packaged: 2014-09-11 12:24:47 UTC; Jose Tamez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 15:08:50

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Package rsubgroup updated to version 0.6 with previous version 0.5 dated 2014-08-06

Title: Subgroup Discovery and Analytics
Description: A collection of efficient and effective tools and algorithms for subgroup discovery and analytics. The package integrates an R interface to the org.vikamine.kernel library of the VIKAMINE system (http://www.vikamine.org) implementing subgroup discovery, pattern mining and analytics in Java.
Author: Martin Atzmueller
Maintainer: Martin Atzmueller

Diff between rsubgroup versions 0.5 dated 2014-08-06 and 0.6 dated 2014-09-11

 DESCRIPTION                    |   12 ++++++------
 MD5                            |   25 +++++++++++++------------
 NEWS                           |only
 R/classes.R                    |   11 +++++++++--
 R/subgroup.R                   |    9 +++++++--
 inst/java/subgroup.jar         |binary
 man/CreateSDTask.Rd            |    2 +-
 man/DiscoverSubgroups.Rd       |   11 +++++++----
 man/DiscoverSubgroupsByTask.Rd |   11 +++++++----
 man/Pattern-class.Rd           |    2 +-
 man/SDTaskConfig-class.Rd      |    3 ++-
 man/ToDataframe.Rd             |    2 +-
 man/as.target.Rd               |    2 +-
 man/subgroup-package.Rd        |    7 +++----
 14 files changed, 58 insertions(+), 39 deletions(-)

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New package lcmm with initial version 1.6.6
Package: lcmm
Type: Package
Title: Estimation of Extended Mixed Models Using Latent Classes and Latent Processes
Version: 1.6.6
Date: 2014-09-10
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima
Description: Functions for the estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
License: GPL (>= 2.0)
Depends: R (>= 2.9.0), survival
LazyLoad: yes
Packaged: 2014-09-10 09:08:05 UTC; vp3
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 11:39:40

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New package gdsfmt with initial version 1.1.0
Package: gdsfmt
Type: Package
Title: R Interface to CoreArray Genomic Data Structure (GDS) files
Version: 1.1.0
Date: 2014-09-10
Depends: R (>= 2.14.0)
Imports: methods
Suggests: parallel, RUnit
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
BugReports: http://github.com/zhengxwen/gdsfmt/issues
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. Data compression and decompression are also supported. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.
License: LGPL-3
URL: http://corearray.sourceforge.net/, http://github.com/zhengxwen/gdsfmt
Packaged: 2014-09-11 06:43:57 UTC; sts
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 12:33:04

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New package recosystem with initial version 0.2.3
Package: recosystem
Type: Package
Title: Recommender System using Matrix Factorization
Version: 0.2.3
Date: 2014-09-08
Authors@R: c(person(given = "Yixuan", family = "Qiu", role = c("aut", "cre"), email = "yixuan.qiu@cos.name"), person(given = "Chih-Jen", family = "Lin", role = c("aut","cph"), comment = "original C++ code"), person(given = "Yu-Chin", family = "Juan", role = c("aut","cph"), comment = "original C++ code"), person(given = "Yong", family = "Zhuang", role = c("aut","cph"), comment = "original C++ code"), person(given = "Wei-Sheng", family = "Chin", role = c("aut","cph"), comment = "original C++ code"))
Maintainer: Yixuan Qiu
Description: This package is an R wrapper of the libmf library (http://www.csie.ntu.edu.tw/~cjlin/libmf/) for recommender system using matrix factorization. It is typically used to approximate an incomplete matrix using the product of two matrices in a latent space. Other common names for this task include "collaborative filtering", "matrix completion", "matrix recovery", etc.
License: BSD_3_clause + file LICENSE
Copyright: see file COPYRIGHTS
URL: https://github.com/yixuan/recosystem
BugReports: https://github.com/yixuan/recosystem/issues
SystemRequirements: C++11
Depends: methods
Imports: Rcpp (>= 0.11.0)
Suggests: knitr
LinkingTo: Rcpp
VignetteBuilder: knitr
Packaged: 2014-09-08 15:06:23 UTC; qyx
Author: Yixuan Qiu [aut, cre], Chih-Jen Lin [aut, cph] (original C++ code), Yu-Chin Juan [aut, cph] (original C++ code), Yong Zhuang [aut, cph] (original C++ code), Wei-Sheng Chin [aut, cph] (original C++ code)
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 10:00:26

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Package RankResponse updated to version 3.1.1 with previous version 3.0.3 dated 2014-04-03

Title: Ranking Responses in a Single Response Question or a Multiple Response Question
Description: Methods for ranking responses of a single response question or a multiple response question
Author: Hsiuying Wang, Yu-Chun Lin
Maintainer: Hsiuying Wang

Diff between RankResponse versions 3.0.3 dated 2014-04-03 and 3.1.1 dated 2014-09-11

 RankResponse-3.0.3/RankResponse/R/rank.LR.R      |only
 RankResponse-3.0.3/RankResponse/man/rank.LR.Rd   |only
 RankResponse-3.1.1/RankResponse/DESCRIPTION      |   10 +-
 RankResponse-3.1.1/RankResponse/MD5              |   32 ++++----
 RankResponse-3.1.1/RankResponse/R/rank.L2R.R     |   35 +--------
 RankResponse-3.1.1/RankResponse/R/rank.LN.R      |   54 ++------------
 RankResponse-3.1.1/RankResponse/R/rank.btmm.R    |    4 -
 RankResponse-3.1.1/RankResponse/R/rank.btnr.R    |    4 -
 RankResponse-3.1.1/RankResponse/R/rank.btqn.R    |    4 -
 RankResponse-3.1.1/RankResponse/R/rank.gs.R      |   72 ++++++++-----------
 RankResponse-3.1.1/RankResponse/R/rank.wald.R    |   85 ++++++++++-------------
 RankResponse-3.1.1/RankResponse/man/rank.L2R.Rd  |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.LN.Rd   |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.btmm.Rd |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.btnr.Rd |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.btqn.Rd |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.gs.Rd   |    4 -
 RankResponse-3.1.1/RankResponse/man/rank.wald.Rd |    4 -
 18 files changed, 125 insertions(+), 203 deletions(-)

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Package rplexos updated to version 0.9.1 with previous version 0.9 dated 2014-08-26

Title: Read and analyze PLEXOS solutions from R
Description: Read and analyze PLEXOS solutions from R
Author: Eduardo Ibanez
Maintainer: Eduardo Ibanez

Diff between rplexos versions 0.9 dated 2014-08-26 and 0.9.1 dated 2014-09-11

 DESCRIPTION           |    8 +--
 MD5                   |   35 +++++++-------
 NAMESPACE             |    3 -
 R/auxiliary.R         |   16 ++++++
 R/globalVariables.R   |    2 
 R/plexos_open.R       |   44 +++++++-----------
 R/process_folder.R    |    2 
 R/process_solution.R  |  111 ++++++++++++++++++++++++++---------------------
 R/query.R             |   67 +++++++++++++++++++++++-----
 man/list_folders.Rd   |    2 
 man/plexos_close.Rd   |    2 
 man/plexos_open.Rd    |    2 
 man/process_folder.Rd |    6 +-
 man/query_config.Rd   |only
 man/query_master.Rd   |    2 
 man/query_property.Rd |    2 
 man/rplexos.Rd        |    2 
 man/valid_columns.Rd  |    2 
 src/process_xml.cpp   |  117 ++++++++++++++++++++++++++++++++------------------
 19 files changed, 261 insertions(+), 164 deletions(-)

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New package rChoiceDialogs with initial version 1.0.6
Package: rChoiceDialogs
Type: Package
Title: rChoiceDialogs collection
Version: 1.0.6
Date: 2014-09-05
Authors@R: c(person("Alex","Lisovich",role=c("aut","cre"),email="alex.lisovich@gmail.com"), person("Roger","Day",role="aut",email="day01@pitt.edu"), person("Sun Microsystems, Inc",role="cph", comment="swing-layout-1.0.4.jar, download from http://www.java2s.com/Code/Jar/s/Downloadswinglayout104jar.htm"))
Description: Collection of portable choice dialog widgets
License: LGPL (>= 2.1)
Depends: rJava, utils
Imports: tcltk
Collate: 'zzz.R' 'rChoiceDialogs-package.R' 'rFileChooser.R' 'rListChooser.R' 'rMiscFunctions.R'
Packaged: 2014-09-10 20:49:54 UTC; alex
Author: Alex Lisovich [aut, cre], Roger Day [aut], Sun Microsystems, Inc [cph] (swing-layout-1.0.4.jar, download from http://www.java2s.com/Code/Jar/s/Downloadswinglayout104jar.htm)
Maintainer: Alex Lisovich
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 07:26:55

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New package OjaNP with initial version 0.9-8
Package: OjaNP
Type: Package
Title: Multivariate Methods Based on the Oja Median and Related Concepts
Version: 0.9-8
Date: 2014-09-10
Author: Daniel Fischer, Jyrki Möttönen, Klaus Nordhausen, Daniel Vogel
Maintainer: Klaus Nordhausen
Depends: R (>= 2.9.0), ICS, ICSNP
Description: The package provides functions for the Oja median, Oja signs and ranks and methods based upon them.
License: GPL (>= 2)
Encoding: latin1
LazyLoad: yes
Packaged: 2014-09-10 09:19:18 UTC; klaus
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-09-11 08:48:28

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

Title: Linear mixed effect model splines for modelling and analysis of time course data
Description: The package implements linear mixed effect model splines for modelling and differential expression for highly dimensional data sets: investNoise for quality control and filterNoise for removing non-informative trajectories; lmmSpline to model time course expression profiles and lmmsDE performs differential expression analysis to identify differential expression between groups, time and/or time x group interaction.
Author: Jasmin Straube, Kim-Anh Le Cao and Emma Huang with contributions of Dominique Gorse
Maintainer: Jasmin Straube

Diff between lmms versions 1.0 dated 2014-06-06 and 1.1 dated 2014-09-11

 DESCRIPTION                   |   16 +++++++++-------
 MD5                           |   39 ++++++++++++++++++++++++---------------
 NAMESPACE                     |    9 +++++++++
 R/AllClasses.R                |   17 +++++++++++++++++
 R/filterNoise-method.R        |only
 R/investNoise-method.R        |only
 R/lmmSpline-method.R          |    4 ++--
 R/lmmsDE-method.R             |    4 ++--
 R/plot.lmmsde-method.R        |   26 +++++++++++++-------------
 R/plot.lmmspline-method.R     |   27 ++++++++++++++-------------
 R/plot.noise-method.R         |only
 R/predict.lmmspline-method.R  |    2 +-
 R/summary.lmmsde-methods.R    |    1 +
 R/summary.lmmspline-methods.R |    1 +
 R/summary.noise-methods.R     |only
 man/filterNoise-methods.Rd    |only
 man/investNoise-methods.Rd    |only
 man/lmmSpline-methods.Rd      |    5 ++---
 man/lmms-package.Rd           |    3 ++-
 man/lmmsDE-methods.Rd         |    5 ++---
 man/noise-class.Rd            |only
 man/plot.lmmsde.Rd            |    4 ++--
 man/plot.noise.Rd             |only
 man/predict.lmmspline.Rd      |    2 +-
 man/summary.noise.Rd          |only
 25 files changed, 102 insertions(+), 63 deletions(-)

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New package funFEM with initial version 1.0
Package: funFEM
Type: Package
Title: Clustering in the Discriminative Functional Subspace
Version: 1.0
Date: 2014-09-06
Author: Charles Bouveyron
Depends: R (>= 2.10), MASS, fda, elasticnet
Maintainer: Charles Bouveyron
Description: The funFEM algorithm (Bouveyron et al., 2014) allows to cluster functional data by modeling the curves within a common and discriminative functional subspace.
License: GPL-2
LazyLoad: yes
Packaged: 2014-09-10 07:52:48 UTC; charles
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-11 07:36:22

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Package DatABEL updated to version 0.9-5 with previous version 0.9-4.1 dated 2014-07-27

Title: file-based access to large matrices stored on HDD in binary format
Description: a package providing an interface to the C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar, Maksim Struchalin
Maintainer: Yurii Aulchenko

Diff between DatABEL versions 0.9-4.1 dated 2014-07-27 and 0.9-5 dated 2014-09-11

 DatABEL-0.9-4.1/DatABEL/CHANGES.LOG                    |only
 DatABEL-0.9-4.1/DatABEL/src/Rstaff.h                   |only
 DatABEL-0.9-5/DatABEL/ChangeLog                        |only
 DatABEL-0.9-5/DatABEL/DESCRIPTION                      |   22 
 DatABEL-0.9-5/DatABEL/MD5                              |  119 -
 DatABEL-0.9-5/DatABEL/NAMESPACE                        |   81 -
 DatABEL-0.9-5/DatABEL/R/DatABEL-package.R              |   32 
 DatABEL-0.9-5/DatABEL/R/apply2dfo.R                    |  406 +++--
 DatABEL-0.9-5/DatABEL/R/apply2dfo_util.R               |  129 +
 DatABEL-0.9-5/DatABEL/R/checkPackageVersionOnCRAN.R    |  130 +
 DatABEL-0.9-5/DatABEL/R/databel.R                      |   16 
 DatABEL-0.9-5/DatABEL/R/databel2matrix.R               |    1 
 DatABEL-0.9-5/DatABEL/R/databel2text.R                 |   13 
 DatABEL-0.9-5/DatABEL/R/databel_class.R                | 1033 ++++++++-------
 DatABEL-0.9-5/DatABEL/R/databel_class_internal.R       |  127 -
 DatABEL-0.9-5/DatABEL/R/extract_text_file_columns.R    |   39 
 DatABEL-0.9-5/DatABEL/R/get_temporary_file_name.R      |   40 
 DatABEL-0.9-5/DatABEL/R/make_empty_fvf.R               |   55 
 DatABEL-0.9-5/DatABEL/R/matrix2databel.R               |   49 
 DatABEL-0.9-5/DatABEL/R/text2databel.R                 |  273 ++--
 DatABEL-0.9-5/DatABEL/R/zzz.R                          |   12 
 DatABEL-0.9-5/DatABEL/build                            |only
 DatABEL-0.9-5/DatABEL/inst/doc/intro_DatABEL.R         |only
 DatABEL-0.9-5/DatABEL/inst/doc/intro_DatABEL.pdf       |binary
 DatABEL-0.9-5/DatABEL/man/DatABEL-package.Rd           |   29 
 DatABEL-0.9-5/DatABEL/man/apply2dfo.Rd                 |  100 -
 DatABEL-0.9-5/DatABEL/man/checkPackageVersionOnCRAN.Rd |only
 DatABEL-0.9-5/DatABEL/man/databel-class.Rd             |  212 +--
 DatABEL-0.9-5/DatABEL/man/databel.Rd                   |   16 
 DatABEL-0.9-5/DatABEL/man/databel2matrix.Rd            |   20 
 DatABEL-0.9-5/DatABEL/man/databel2text.Rd              |   21 
 DatABEL-0.9-5/DatABEL/man/extract_text_file_columns.Rd |   15 
 DatABEL-0.9-5/DatABEL/man/get_temporary_file_name.Rd   |   13 
 DatABEL-0.9-5/DatABEL/man/make_empty_fvf.Rd            |   28 
 DatABEL-0.9-5/DatABEL/man/matrix2databel.Rd            |   31 
 DatABEL-0.9-5/DatABEL/man/process_lm_output.Rd         |   25 
 DatABEL-0.9-5/DatABEL/man/text2databel.Rd              |  185 +-
 DatABEL-0.9-5/DatABEL/src/AbstractMatrix.cpp           |   12 
 DatABEL-0.9-5/DatABEL/src/AbstractMatrix.h             |  113 -
 DatABEL-0.9-5/DatABEL/src/AbstractMatrix_R.cpp         |   13 
 DatABEL-0.9-5/DatABEL/src/CastUtils.cpp                |  294 ++--
 DatABEL-0.9-5/DatABEL/src/CastUtils.h                  |  144 +-
 DatABEL-0.9-5/DatABEL/src/FileVector.cpp               | 1159 +++++++++--------
 DatABEL-0.9-5/DatABEL/src/FileVector.h                 |  219 +--
 DatABEL-0.9-5/DatABEL/src/FilteredMatrix.cpp           |  117 +
 DatABEL-0.9-5/DatABEL/src/FilteredMatrix.h             |  173 +-
 DatABEL-0.9-5/DatABEL/src/FilteredMatrix_R.cpp         |   10 
 DatABEL-0.9-5/DatABEL/src/Logger.cpp                   |    7 
 DatABEL-0.9-5/DatABEL/src/Logger.h                     |   30 
 DatABEL-0.9-5/DatABEL/src/RealHandlerWrapper.cpp       |   21 
 DatABEL-0.9-5/DatABEL/src/RealHandlerWrapper.h         |   10 
 DatABEL-0.9-5/DatABEL/src/ReusableFileHandle.cpp       |   31 
 DatABEL-0.9-5/DatABEL/src/ReusableFileHandle.h         |   28 
 DatABEL-0.9-5/DatABEL/src/Rstuff.h                     |only
 DatABEL-0.9-5/DatABEL/src/Transposer.cpp               |  239 ++-
 DatABEL-0.9-5/DatABEL/src/Transposer.h                 |   50 
 DatABEL-0.9-5/DatABEL/src/convert_util.cpp             |  567 ++++----
 DatABEL-0.9-5/DatABEL/src/convert_util.h               |   10 
 DatABEL-0.9-5/DatABEL/src/dautil.cpp                   |    2 
 DatABEL-0.9-5/DatABEL/src/dautil.h                     |    2 
 DatABEL-0.9-5/DatABEL/src/frutil.cpp                   |  243 +--
 DatABEL-0.9-5/DatABEL/src/frutil.h                     |   88 -
 DatABEL-0.9-5/DatABEL/src/iterator.cpp                 |    4 
 DatABEL-0.9-5/DatABEL/src/iterator_functions.cpp       |    2 
 64 files changed, 3742 insertions(+), 3118 deletions(-)

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Wed, 10 Sep 2014

New package saery with initial version 1.0
Package: saery
Type: Package
Title: Small Area Estimation for Rao and Yu Model
Version: 1.0
Date: 2014-09-10
Author: Maria Dolores Esteban Lefler, Domingo Morales Gonzalez, Agustin Perez Martin
Maintainer: Agustin Perez Martin
Description: A complete set of functions to calculate several EBLUP (Empirical Best Linear Unbiased Predictor) estimators and their mean squared errors. All estimators are based on an area-level linear mixed model introduced by Rao and Yu in 1994 (see documentation). The REML method is used for fitting this model.
License: GPL-2
LazyData: true
Packaged: 2014-09-10 20:48:45 UTC; agus
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 23:18:02

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Package RcmdrPlugin.IPSUR updated to version 0.2-1 with previous version 0.2-0 dated 2014-08-29

Title: An IPSUR Plugin for the R Commander
Description: This package is an R Commander plugin that accompanies IPSUR, an Introduction to Probability and Statistics Using R.
Author: G. Jay Kerns [aut, cre], Theophilus Boye [ctb], Tyler Drombosky [ctb]
Maintainer: G. Jay Kerns

Diff between RcmdrPlugin.IPSUR versions 0.2-0 dated 2014-08-29 and 0.2-1 dated 2014-09-10

 DESCRIPTION                      |    8 ++++----
 MD5                              |    6 +++---
 inst/etc/menus.txt               |   36 ++++++++++++++++++------------------
 man/RcmdrPlugin.IPSUR-package.Rd |    6 +++---
 4 files changed, 28 insertions(+), 28 deletions(-)

More information about RcmdrPlugin.IPSUR at CRAN
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Package glmmLasso updated to version 1.3.2 with previous version 1.3.1 dated 2014-07-10

Title: Variable selection for generalized linear mixed models by L1-penalized estimation
Description: Variable selection for generalized linear mixed models by L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll

Diff between glmmLasso versions 1.3.1 dated 2014-07-10 and 1.3.2 dated 2014-09-10

 DESCRIPTION                        |    8 
 MD5                                |   18 
 R/glmmLasso.r                      |  896 ++++++++++++++++++-------------------
 R/glmm_final.r                     |    9 
 R/glmm_final.smooth.r              |    6 
 R/glmm_final_multi_random.r        |    6 
 R/glmm_final_multi_random_smooth.r |   14 
 R/logLik.glmmLasso.r               |    8 
 demo/glmmLasso-soccer.r            |   49 +-
 man/glmmLasso.rd                   |   38 -
 10 files changed, 521 insertions(+), 531 deletions(-)

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Package cgam updated to version 1.2 with previous version 1.1 dated 2014-04-16

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) may be used to select the best combination of variables and shapes. This package depends on the R package coneproj.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao

Diff between cgam versions 1.1 dated 2014-04-16 and 1.2 dated 2014-09-10

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 NAMESPACE          |    2 
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 27 files changed, 1793 insertions(+), 414 deletions(-)

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Package segmented updated to version 0.5-0.0 with previous version 0.4-0.0 dated 2014-07-11

Title: Segmented relationships in regression models with breakpoints/changepoints estimation
Description: Given a regression 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 0.4-0.0 dated 2014-07-11 and 0.5-0.0 dated 2014-09-10

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 segmented-0.5-0.0/segmented/MD5                      |   45 +++++++++----------
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 segmented-0.5-0.0/segmented/NEWS                     |   13 +++++
 segmented-0.5-0.0/segmented/R/confint.segmented.R    |    2 
 segmented-0.5-0.0/segmented/R/davies.test.r          |    4 -
 segmented-0.5-0.0/segmented/R/intercept.r            |    5 --
 segmented-0.5-0.0/segmented/R/plot.segmented.R       |   13 +++--
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 segmented-0.5-0.0/segmented/R/summary.segmented.R    |   18 +++++++
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 segmented-0.5-0.0/segmented/man/seg.control.Rd       |   12 ++++-
 segmented-0.5-0.0/segmented/man/seg.lm.fit.Rd        |   25 ++++++++--
 segmented-0.5-0.0/segmented/man/segmented-package.Rd |   12 +++--
 segmented-0.5-0.0/segmented/man/segmented.Rd         |   42 +++++++++++++++--
 26 files changed, 234 insertions(+), 84 deletions(-)

More information about segmented at CRAN
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Package GGMselect updated to version 0.1-9 with previous version 0.1-8 dated 2013-12-12

Title: Gaussian Graphs Models selection
Description: GGMselect is a package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: Annie Bouvier

Diff between GGMselect versions 0.1-8 dated 2013-12-12 and 0.1-9 dated 2014-09-10

 DESCRIPTION               |    8 ++---
 MD5                       |   57 +++++++++++++++++++++---------------------
 NAMESPACE                 |    2 +
 NEWS                      |   17 ++++++++++--
 R/MyFamily.R              |   13 +++++----
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 man/GGMselect-package.Rd  |   14 +++++-----
 man/selectQE.Rd           |   14 +++++-----
 src/Makevars              |    5 ++-
 src/boucle.f              |    2 -
 src/critQE.c              |    5 ++-
 tests/bsch.Rout.save      |    8 ++---
 tests/penInf.Rout.save    |    8 ++---
 tests/raj.Rout.save       |   54 ++++++++++++++++++++--------------------
 tests/sh9.2012.Rout.save  |    8 ++---
 tests/shPUR.Rout.save     |    8 ++---
 tests/test1Fast.Rout.save |    8 ++---
 tests/test1QE.Rout.save   |   44 ++++++++++++++++----------------
 tests/test2Fast.Rout.save |    8 ++---
 tests/test2QE.Rout.save   |   26 +++++++++----------
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 tests/test4Fast.R         |    2 -
 tests/test4Fast.Rout.save |   10 +++----
 tests/test4QE.Rout.save   |   38 ++++++++++++++--------------
 tests/test5Fast.Rout.save |    8 ++---
 tests/test6Fast.Rout.save |    8 ++---
 tests/test7Fast.Rout.save |    8 ++---
 tests/testMyFam.Rout.save |    8 ++---
 30 files changed, 239 insertions(+), 222 deletions(-)

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New package Ohmage with initial version 2.11-4
Package: Ohmage
Type: Package
Title: R Client for Ohmage 2 server
Version: 2.11-4
Date: 2014-09-10
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
Description: R Client for Ohmage 2 server. Implements basic R functions to retrieve and process data.
License: GPL
Depends: R (>= 2.14), stats, methods
Imports: RCurl, RJSONIO
Suggests: XML
Packaged: 2014-09-10 13:00:58 UTC; jeroen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 15:14:12

More information about Ohmage at CRAN
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Package caTools updated to version 1.17.1 with previous version 1.17 dated 2014-04-21

Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
Description: Contains several basic utility functions including: moving (rolling, running) window statistic functions, read/write for GIF and ENVI binary files, fast calculation of AUC, LogitBoost classifier, base64 encoder/decoder, round-off-error-free sum and cumsum, etc.
Author: Jarek Tuszynski
Maintainer: Harutyun Khachatryan

Diff between caTools versions 1.17 dated 2014-04-21 and 1.17.1 dated 2014-09-10

 DESCRIPTION  |   10 ++---
 MD5          |    6 +--
 R/runfunc.R  |  103 +++++++++++++++++++++++++++++------------------------------
 R/sumexact.R |   10 ++---
 4 files changed, 63 insertions(+), 66 deletions(-)

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Package pkgKitten updated to version 0.1.1 with previous version 0.1.0 dated 2014-06-13

Title: Create Simple Packages Which Do Not Upset R CMD check
Description: Provides a function kitten() which create cute little packages which pass R CMD check. This sets it apart from package.skeleton() which it calls, and which leaves imperfect files behind. As this is not exactly helpful for beginners, kitten() offers an alternative.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel

Diff between pkgKitten versions 0.1.0 dated 2014-06-13 and 0.1.1 dated 2014-09-10

 ChangeLog                         |   13 +++++++++
 DESCRIPTION                       |   20 +++++++-------
 MD5                               |   12 ++++----
 NAMESPACE                         |    3 +-
 R/pkgKitten.R                     |   54 ++++++++++++++++++++++++++++----------
 inst/NEWS.Rd                      |only
 man/kitten.Rd                     |    4 +-
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 8 files changed, 75 insertions(+), 31 deletions(-)

More information about pkgKitten at CRAN
Permanent link

New package ForwardSearch with initial version 1.0
Package: ForwardSearch
Type: Package
Title: Forward Search using asymptotic theory
Version: 1.0
Date: 2014-09-10
Author: Bent Nielsen
Maintainer: Bent Nielsen
URL: http://users.ox.ac.uk/~nuff0078/
Description: Forward Search analysis of time series regressions. Implements the asymptotic theory developed in Johansen and Nielsen (2013, 2014).
License: GPL-3
Depends: robustbase
Packaged: 2014-09-10 11:19:57 UTC; Nielsen
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 13:56:09

More information about ForwardSearch at CRAN
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Package sjPlot updated to version 1.5 with previous version 1.4.3 dated 2014-08-14

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 1.4.3 dated 2014-08-14 and 1.5 dated 2014-09-10

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New package RImpala with initial version 0.1.4
Package: RImpala
Version: 0.1.4
Date: 2014-09-10
Title: R and Impala
Author: Vijay Raajaa, Austin Chungath Vincent, Sachin Sudarshana, Vikas Raguttahalli
Maintainer: Vijay Raajaa
Contact: Austin Chungath Vincent ,Vikas Raguttahalli , Sachin Sudarshana
Description: RImpala facilitates the connection and execution of distributed queries using Cloudera Impala, which is a massively parallel processing (MPP) SQL query engine that runs natively in Apache Hadoop. Impala supports jdbc integration which RImpala utilizes to establish the connection between R and Impala.
Depends: R (>= 2.7.0), rJava (>= 0.5-0)
SystemRequirements: Java (>= 1.5)
License: GPL-3
Packaged: 2014-09-10 08:47:33 UTC; root
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 11:43:20

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New package RDML with initial version 0.4-2
Package: RDML
Type: Package
Title: Importing real-time thermo cycler (qPCR) data from RDML format files
Version: 0.4-2
LazyData: true
Date: 2014-09-10
Description: Imports real-time thermo cycler (qPCR) data from RDML format files and transforms to the appropriate formats of the 'qpcR' and 'chipPCR' packages.
Authors@R: c( person("Konstantin A.", "Blagodatskikh", email = "k.blag@yandex.ru", role = c("cre", "aut")), person("Stefan", "Roediger", email = "stefan.roedigier@hs-lausitz.de", role = "aut"), person("Michal", "Burdukiewicz", email = "michalburdukiewicz@gmail.com", role = "aut"))
License: GPL (>= 2)
URL: https://github.com/kablag/RDML
Depends: XML (>= 3.98-1.1)
Imports: chipPCR (>= 0.0.8-1)
Suggests: qpcR (>= 1.3-9)
Packaged: 2014-09-10 08:55:14 UTC; kablag
Author: Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 11:38:16

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Package catR updated to version 3.2 with previous version 3.1 dated 2014-06-04

Title: Procedures to generate IRT adaptive tests (CAT)
Description: The catR package allows the generation of response patterns under computerized adaptive testing (CAT) framework, with the choice of several starting rules, next item selection routines, stopping rules and ability estimators. Control methods for item exposure and content balancing are also included.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis

Diff between catR versions 3.1 dated 2014-06-04 and 3.2 dated 2014-09-10

 DESCRIPTION       |    8 
 MD5               |   12 -
 NEWS              |   36 +++
 R/MEI.R           |    2 
 R/eapEst.R        |    2 
 R/genPolyMatrix.R |    2 
 R/randomCAT.R     |  523 +++++++++++++++++++++++++++++-------------------------
 7 files changed, 336 insertions(+), 249 deletions(-)

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Package synbreed updated to version 0.10-2 with previous version 0.10-1 dated 2014-09-02

Title: Framework for the analysis of genomic prediction data using R
Description: The package was developed within the Synbreed project for synergistic plant and animal breeding (www.synbreed.tum.de). It contains a collection of functions required for genomic prediction in both plant and animal breeding. This covers data processing, data visualization and analysis. All functions are embedded within the framework of a single, unified data object. The implementation is flexible with respect to a wide range of data formats. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Hans-Juergen Auinger, Theresa Albrecht, Chris-Carolin Schoen with contributions by Larry Schaeffer, Malena Erbe, Ulrike Ober, Christian Reimer, Yvonne Badke and Peter VandeHaar
Maintainer: Valentin Wimmer

Diff between synbreed versions 0.10-1 dated 2014-09-02 and 0.10-2 dated 2014-09-10

 DESCRIPTION                 |   12 ++++++------
 MD5                         |    6 +++---
 R/codeGeno.r                |   18 +++++++++++++++++-
 R/plot.relationshipMatrix.r |   24 +++++++++++++++++++-----
 4 files changed, 45 insertions(+), 15 deletions(-)

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Package dismo updated to version 1.0-5 with previous version 0.9-3 dated 2013-12-15

Title: Species distribution modeling
Description: Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans

Diff between dismo versions 0.9-3 dated 2013-12-15 and 1.0-5 dated 2014-09-10

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 dismo-1.0-5/dismo/R/Mahalanobis.predict.R |   22 
 dismo-1.0-5/dismo/R/biogeomancer.R        |    6 
 dismo-1.0-5/dismo/R/check.R               |    2 
 dismo-1.0-5/dismo/R/circles.R             |    2 
 dismo-1.0-5/dismo/R/circularArea.R        |    2 
 dismo-1.0-5/dismo/R/diversity.R           |   10 
 dismo-1.0-5/dismo/R/gbif.R                |   61 
 dismo-1.0-5/dismo/R/gbm.fixed.R           |   11 
 dismo-1.0-5/dismo/R/gbm.holdout.R         |   31 
 dismo-1.0-5/dismo/R/gbm.interactions.R    |    6 
 dismo-1.0-5/dismo/R/gbm.perspec.R         |    6 
 dismo-1.0-5/dismo/R/gbm.plot.R            |   25 
 dismo-1.0-5/dismo/R/gbm.plot.fits.R       |    6 
 dismo-1.0-5/dismo/R/gbm.simplify.R        |  342 -
 dismo-1.0-5/dismo/R/gbm.step.R            |  693 +-
 dismo-1.0-5/dismo/R/gbm.utils.R           |   69 
 dismo-1.0-5/dismo/R/geoIDW.R              |    6 
 dismo-1.0-5/dismo/R/geocode.R             |    9 
 dismo-1.0-5/dismo/R/gmap.R                |    2 
 dismo-1.0-5/dismo/R/kfold.R               |    5 
 dismo-1.0-5/dismo/R/maxent.R              |   14 
 dismo-1.0-5/dismo/R/maxent.predict.R      |    9 
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 dismo-1.0-5/dismo/R/voronoiHull.R         |    8 
 dismo-1.0-5/dismo/build/vignette.rds      |binary
 dismo-1.0-5/dismo/inst/doc/brt.R          |   32 
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 dismo-1.0-5/dismo/inst/doc/brt.pdf        |binary
 dismo-1.0-5/dismo/inst/doc/sdm.R          |  183 
 dismo-1.0-5/dismo/inst/doc/sdm.Rnw        |  144 
 dismo-1.0-5/dismo/inst/doc/sdm.pdf        | 7634 +++++++++++++++---------------
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 dismo-1.0-5/dismo/man/gmap.Rd             |    6 
 dismo-1.0-5/dismo/man/randomPoints.Rd     |    3 
 dismo-1.0-5/dismo/vignettes/brt.Rnw       |   34 
 dismo-1.0-5/dismo/vignettes/sdm.Rnw       |  144 
 46 files changed, 4985 insertions(+), 4738 deletions(-)

More information about dismo at CRAN
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Package bstats (with last version 1.1-11-5) was removed from CRAN

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

2014-05-04 1.1-11-5
2014-01-23 1.1-11-4
2013-11-26 1.1-11-1
2013-09-08 1.1-9-8
2013-08-07 1.1-8-8
2011-12-04 1.0-12-3
2011-11-18 1.0-11-17
2011-11-15 1.0-2
2011-11-10 1.0-1
2011-11-02 0.01-4

Permanent link
Package Sim.DiffProc updated to version 2.9 with previous version 2.8 dated 2014-08-19

Title: Simulation of Diffusion Processes
Description: The package Sim.DiffProc is an object created in R environment for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum

Diff between Sim.DiffProc versions 2.8 dated 2014-08-19 and 2.9 dated 2014-09-10

 DESCRIPTION                 |   10 
 MD5                         |   50 +-
 NAMESPACE                   |   61 ++-
 NEWS                        |    4 
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 R/utils.R                   |   94 +++++
 R/zzz.r                     |    4 
 demo/Sim.DiffProc.R         |   19 +
 inst/doc/FitSDE.Rnw         |    7 
 inst/doc/FitSDE.pdf         |binary
 inst/doc/Introduction.R     |    6 
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 man/bridgesde3d.Rd          |   80 ++--
 man/plot2d.Rd               |    1 
 tests/bridgesde.R           |   13 
 vignettes/Core_FitSDE.tex   |  208 +++++++++++
 vignettes/FitSDE.Rnw        |    7 
 vignettes/Introduction.Rnw  |   12 
 vignettes/SDEs.Rnw          |   15 
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Package mmcm updated to version 1.2-5 with previous version 1.2-4 dated 2013-01-20

Title: Modified Maximum Contrast Method
Description: This package provides an implementation of modified maximum contrast methods and the maximum contrast method. This version supports functions mmcm.mvt, mcm.mvt that gives P-value by using randomized quasi-Monte Carlo method from pmvt function of package mvtnorm, and mmcm.resamp that gives P-value by using the permutation method.
Author: Kengo NAGASHIMA and Yasunori SATO
Maintainer: Kengo NAGASHIMA

Diff between mmcm versions 1.2-4 dated 2013-01-20 and 1.2-5 dated 2014-09-10

 DESCRIPTION         |   23 ++---
 MD5                 |   26 ++---
 NAMESPACE           |    5 -
 NEWS                |    6 +
 R/mcm.mvt.R         |    4 
 R/mmcm.mvt.R        |    3 
 R/mmcm.resamp.R     |    5 -
 R/package.R         |    3 
 R/print.mmcm.R      |    5 -
 man/mcm.mvt.Rd      |  175 +++++++++++++++++++++-------------------
 man/mmcm-package.Rd |   55 ++++--------
 man/mmcm.mvt.Rd     |  190 +++++++++++++++++++++++--------------------
 man/mmcm.resamp.Rd  |  226 ++++++++++++++++++++++++++--------------------------
 man/print.mmcm.Rd   |   34 ++-----
 14 files changed, 379 insertions(+), 381 deletions(-)

More information about mmcm at CRAN
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