Fri, 24 Oct 2014

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

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

2013-10-15 1.0

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Package WRS2 updated to version 0.2-0 with previous version 0.1-0 dated 2014-10-03

Title: Wilcox Robust Estimation and Testing.
Description: A user-friendly version of Wilcox' robust statistics functions (WRS package on GitHub). It implements robust tests for ANOVA and ANCOVA as described in R. Wilcox (2012) 'Introduction to Robust Estimation and Hypothesis Testing'.
Author: Patrick Mair [cre, aut], Felix Schoenbrodt [aut], Rand Wilcox [aut]
Maintainer: Patrick Mair

Diff between WRS2 versions 0.1-0 dated 2014-10-03 and 0.2-0 dated 2014-10-24

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 NAMESPACE             |    8 ++++++--
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More information about WRS2 at CRAN
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Package spocc updated to version 0.2.2 with previous version 0.2.0 dated 2014-08-06

Title: R Interface to Many Species Occurrence Data Sources.
Description: A programmatic interface to many species occurrence data sources, including GBIF, USGS's BISON, iNaturalist, Berkeley Ecoinformatics Engine eBird, AntWeb, and more as they sources become easily available.
Author: Scott Chamberlain [aut, cre], Karthik Ram [aut], Ted Hart [aut]
Maintainer: Scott Chamberlain

Diff between spocc versions 0.2.0 dated 2014-08-06 and 0.2.2 dated 2014-10-24

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 67 files changed, 1206 insertions(+), 679 deletions(-)

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New package PHENIX with initial version 1.0
Package: PHENIX
Type: Package
Title: Phenotypic Integration Index
Version: 1.0
Date: 2014-10-15
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares
Imports: ppcor
Encoding: UTF-8
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might overestimate the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) and a bootstrapping method to test the significance of both integration indices.
License: GPL (>= 2)
Packaged: 2014-10-23 20:33:24 UTC; ajesusmp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-24 07:51:38

More information about PHENIX at CRAN
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New package P2C2M with initial version 0.5
Package: P2C2M
Type: Package
Title: Posterior Predictive Checks of Coalescent Models
Version: 0.5
Date: 2014-10-23
Author: Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl
Depends: R (>= 3.0.0)
Imports: ape (>= 3.1-4), apTreeshape (>= 1.4-5), ggplot2 (>= 1.0.0), rPython (>= 0.0-5), stringr (>= 0.6.2)
Suggests: genealogicalSorting (>= 0.92), phybase (>= 1.3.1), Rmpi (>= 0.6-5), xtermStyle (>= 2.2-4)
Description: P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST and *BEAST, respectively. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is necessary.
License: GPL (>= 2)
OS_type: unix
NeedsCompilation: yes (automatic)
SystemRequirements: Python (= 2.7)
Packaged: 2014-10-23 06:55:27 UTC; michael
Repository: CRAN
Date/Publication: 2014-10-24 07:51:37

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Thu, 23 Oct 2014

Package splitstackshape updated to version 1.4.2 with previous version 1.4.0 dated 2014-10-13

Title: Stack and Reshape Datasets After Splitting Concatenated Values
Description: Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions splits such data into separate cells. The package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced"---something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.
Author: Ananda Mahto
Maintainer: Ananda Mahto

Diff between splitstackshape versions 1.4.0 dated 2014-10-13 and 1.4.2 dated 2014-10-23

 DESCRIPTION                          |    8 +++----
 MD5                                  |   40 +++++++++++++++++++----------------
 NAMESPACE                            |    2 +
 NEWS                                 |   14 ++++++++++++
 R/Stacked.R                          |    3 +-
 R/cSplit.R                           |   27 +++++++++++++++++++----
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More information about splitstackshape at CRAN
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Package rtkpp updated to version 0.8.3 with previous version 0.8.2 dated 2014-10-21

Title: STK++ Integration To R Using Rcpp
Description: STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later.
Author: Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb]
Maintainer: Serge Iovleff

Diff between rtkpp versions 0.8.2 dated 2014-10-21 and 0.8.3 dated 2014-10-23

 src/makefile                                                                                                          |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/DESCRIPTION                                                               |   11 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/MD5                                                                       |   82 ++--
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterCategorical.R                                                    |   10 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterDiagGaussian.R                                                   |   61 ++-
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterGamma.R                                                          |    7 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/ClusterModelNames.R                                                     |   12 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/R/IClusterModel.R                                                         |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/cleanup                                                                   |    2 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/makefile                                                             |   14 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Arrays/src/makefile                                         |    4 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Clustering/src/makefile                                     |    4 
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 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/DManager/src/STK_DataHandler.cpp                            |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Regress/src/makefile                                        |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Rtkpp/include/STK_RDataHandler.h                            |   14 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Rtkpp/include/STK_RcppMatrix.h                              |   18 +
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Rtkpp/include/STK_RcppVector.h                              |   18 +
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/inst/projects/Sdk/src/makefile                                            |    4 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/clusterCategorical.Rd                                                 |   12 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/clusterDiagGaussian.Rd                                                |    9 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/clusterGamma.Rd                                                       |    7 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/diagGaussianNames.Rd                                                  |   38 --
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/man/gammaNames.Rd                                                         |   36 --
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/Makevars                                                              |   22 -
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/STK_ClusterFacade.cpp                                                 |    2 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/STK_ClusterLauncher.cpp                                               |  167 +++++-----
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/STK_RDataHandler.cpp                                                  |    2 
 tmp/cranberry21822d5a0c3b/rtkpp-0.8.3/rtkpp/src/clusterMixture.cpp                                                    |    2 
 41 files changed, 408 insertions(+), 291 deletions(-)

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New package rsml with initial version 1.0
Package: rsml
Type: Package
Title: Root System Markup Language (RSML) file processing
Version: 1.0
Date: 2014-07-22
Author: Guillaume Lobet
Maintainer: Guillaume Lobet
Description: Read and analyse Root System Markup Language (RSML) files.
License: GPL-2
Imports: XML,rgl
Packaged: 2014-10-23 14:10:40 UTC; guillaumelobet
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-23 17:25:08

More information about rsml at CRAN
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Package leafletR updated to version 0.3-1 with previous version 0.3-0 dated 2014-09-12

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 0.3-0 dated 2014-09-12 and 0.3-1 dated 2014-10-23

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Package sgof updated to version 2.1.1 with previous version 2.1 dated 2014-07-11

Title: Multiple hypothesis testing
Description: This package implements six different methods for multiple testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez.
Maintainer: Irene Castro Conde

Diff between sgof versions 2.1 dated 2014-07-11 and 2.1.1 dated 2014-10-23

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Package sld updated to version 0.3 with previous version 0.2.1 dated 2014-08-15

Title: Estimation and Use of the Quantile-Based Skew Logistic Distribution
Description: The skew logistic distribution is a quantile-defined generalisation of the logistic distribution (van Staden and King 2015). Provides random numbers, quantiles, probabilities, densities and density quantiles for the distribution. It provides Quantile-Quantile plots and method of L-Moments estimation (including asymptotic standard errors) for the distribution.
Author: Robert King , Paul van Staden
Maintainer: Robert King

Diff between sld versions 0.2.1 dated 2014-08-15 and 0.3 dated 2014-10-23

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 DESCRIPTION   |   16 ++++++++++------
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 12 files changed, 112 insertions(+), 40 deletions(-)

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Package CAMAN updated to version 0.72 with previous version 0.71 dated 2014-08-09

Title: Finite Mixture Models and meta-analysis tools - based on C.A.MAN
Description: Tools for the analysis of finite semiparametric mixtures. These are useful when data is heterogeneous, e.g. in pharmacokinetics or meta-analysis. The NPMLE and VEM algorithms (flexible support size) and EM algorithms (fixed support size) are provided for univariate and bivariate data
Author: Peter Schlattmann , Johannes Hoehne, Maryna Verba
Maintainer: Philipp Doebler

Diff between CAMAN versions 0.71 dated 2014-08-09 and 0.72 dated 2014-10-23

 DESCRIPTION |   14 +++++++-------
 MD5         |    2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

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New package matR with initial version 0.9
Package: matR
Type: Package
Title: Metagenomics Analysis Tools for R
Authors@R: c (person ("Daniel", "Braithwaite", role = c ("aut", "cre"), email = "contact.dtb@gmail.com"), person ("Kevin", "Keegan", role = "aut", email = "keegan@mcs.anl.gov"), person (c ("University", "of"), "Chicago", role = "cph"))
Version: 0.9
Depends: R (>= 2.10), MGRASTer, BIOM.utils, graphics, stats, utils
Imports:
Suggests: RJSONIO, qvalue, ecodist, gplots, scatterplot3d
URL: https://github.com/MG-RAST/matR/
Date: 2014-10-22
Description: An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. matR integrates easily with other R packages and non-R software.
License: BSD_2_clause + file LICENSE
Copyright: University of Chicago
LazyData: yes
Collate: utils.R biom-ext.R client.R graphics.R analysis-support.R analysis-misc.R distx.R rowstats.R transform.R boxplot.R princomp.R image.R init.R
Packaged: 2014-10-23 07:39:09 UTC; dan
Author: Daniel Braithwaite [aut, cre], Kevin Keegan [aut], University of Chicago [cph]
Maintainer: Daniel Braithwaite
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-23 11:50:13

More information about matR at CRAN
Permanent link

Package IsingFit updated to version 0.3.0 with previous version 0.2.0 dated 2014-04-23

Title: Fitting Ising models using the eLasso method
Description: This network estimation procedure eLasso, which is based on the Ising model, combines l1-regularized logistic regression with model selection based on the Extended Bayesian Information Criterion (EBIC). EBIC is a fit measure that identifies relevant relationships between variables. The resulting network consists of variables as nodes and relevant relationships as edges. Can deal with binary data.
Author: Claudia van Borkulo, Sacha Epskamp, with contributions from Alexander Robitzsch
Maintainer: Claudia van Borkulo

Diff between IsingFit versions 0.2.0 dated 2014-04-23 and 0.3.0 dated 2014-10-23

 DESCRIPTION             |    8 -
 MD5                     |    8 -
 R/IsingFit.R            |  206 ++++++++++++++++++++++++++----------------------
 man/isingfit-package.rd |    6 -
 man/isingfit.rd         |   10 +-
 5 files changed, 131 insertions(+), 107 deletions(-)

More information about IsingFit at CRAN
Permanent link

Package spatstat updated to version 1.39-0 with previous version 1.38-1 dated 2014-08-28

Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley , Rolf Turner and Ege Rubak , with substantial contributions of code by Kasper Klitgaard Berthelsen; Abdollah Jalilian; Marie-Colette van Lieshout; Dominic Schuhmacher; and Rasmus Waagepetersen. Additional contributions by Q.W. Ang; S. Azaele; M. Baddeley; C. Beale; M. Bell; R. Bernhardt; T. Bendtsen; A. Bevan; B. Biggerstaff; L. Bischof; R. Bivand; J.M. Blanco Moreno; F. Bonneu; J. Burgos; S. Byers; Y.M. Chang; J.B. Chen; I. Chernayavsky; Y.C. Chin; B. Christensen; J.-F. Coeurjolly; R. Corria Ainslie; M. de la Cruz; P. Dalgaard; S. Das; P.J. Diggle; P. Donnelly; I. Dryden; S. Eglen; O. Flores; E.D. Ford; P. Forbes; S. Frank; J. Franklin; N. Funwi-Gabga; O. Garcia; A. Gault; M. Genton; S. Ghalandarayeshi; J. Gilbey; J. Goldstick; P. Grabarnik; C. Graf; U. Hahn; A. Hardegen; M. Hering; M.B. Hansen; M. Hazelton; J. Heikkinen; K. Hornik; P. Hunziker; R. Ihaka; A. Jammalamadaka; R. John-Chandran; D. Johnson; M. Khanmohammadi; M. Kuhn; J. Laake; F. Lavancier; T. Lawrence; R.A. Lamb; J. Lee; G.P. Leser; H.T. Li; G. Limitsios; B. Madin; J. Marcus; K. Marchikanti; R. Mark; J. Mateu; P. McCullagh; U. Mehlig; S. Meyer; X.C. Mi; L. De Middeleer; R.K. Milne; J. Moller; E. Mudrak; G.M. Nair; N. Nava; L.S. Nielsen; F. Nunes; J.R. Nyengaard; J. Oehlschlaegel; T. Onkelinx; S. O'Riordan; E. Parilov; J. Picka; N. Picard; M. Porter; S. Protsiv; A. Raftery; S. Rakshit; P. Ramon; X. Raynaud, M. Reiter; T.O. Richardson; B.D. Ripley; E. Rosenbaum; B. Rowlingson; J. Rudokas; J. Rudge; C. Ryan; F. Safavimanesh; A. Sarkka; K. Schladitz; S. Schutte; B.T. Scott; G.C. Shen; V. Shcherbakov; I.-M. Sintorn; Y. Song; M. Spiess; M. Stevenson; K. Stucki; M. Sumner; P. Surovy; B. Taylor; T. Thorarinsdottir; B. Turlach; K. Ummer; M. Uppala; A. van Burgel; T. Verbeke; M. Vihtakari; A. Villers; F. Vinatier; H. Wang; H. Wendrock; J. Wild; C. Witthoft; S. Wong; M.E. Zamboni and A. Zeileis.
Maintainer: Adrian Baddeley

Diff between spatstat versions 1.38-1 dated 2014-08-28 and 1.39-0 dated 2014-10-23

 spatstat-1.38-1/spatstat/R/morishita.R              |only
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More information about spatstat at CRAN
Permanent link

Package MRH updated to version 1.1 with previous version 1.0 dated 2014-10-17

Title: Multi-Resolution Estimation of the Hazard Rate
Description: Used on survival data to jointly estimate the hazard rate and the effects of covariates on failure times.
Author: Yolanda Hagar, Yuanting Chen, Vanja Dukic
Maintainer: Yolanda Hagar

Diff between MRH versions 1.0 dated 2014-10-17 and 1.1 dated 2014-10-23

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More information about MRH at CRAN
Permanent link

Package JADE updated to version 1.9-92 with previous version 1.9-91 dated 2013-11-11

Title: JADE and other BSS methods as well as some BSS performance criteria
Description: The package ports JF Cardoso's JADE algorithm as well as his function for joint diagonalization. The package also includes several other blind source separation (BSS) methods, like AMUSE and SOBI, as well as some criteria for performance evaluation of BSS algorithms.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen

Diff between JADE versions 1.9-91 dated 2013-11-11 and 1.9-92 dated 2014-10-23

 DESCRIPTION         |   10 +++++-----
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More information about JADE at CRAN
Permanent link

Package httpuv updated to version 1.3.2 with previous version 1.3.0 dated 2014-04-04

Title: HTTP and WebSocket server library
Description: httpuv provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: RStudio, Inc.
Maintainer: Joe Cheng

Diff between httpuv versions 1.3.0 dated 2014-04-04 and 1.3.2 dated 2014-10-23

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Package highr updated to version 0.4 with previous version 0.3 dated 2013-10-26

Title: Syntax highlighting for R
Description: This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages can be supported via Andre Simon's Highlight package.
Author: Christopher Gandrud [ctb], Qiang Li [ctb], Yixuan Qiu [aut], Yihui Xie [aut, cre]
Maintainer: Yihui Xie

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Wed, 22 Oct 2014

New package sigloc with initial version 0.0.4
Package: sigloc
Version: 0.0.4
Date: 2013-04-23
Title: Signal Location Estimation
Author: Sergey S. Berg
Maintainer: Sergey S. Berg
Depends: R (>= 2.15.3), nleqslv, ellipse
Description: A collection of tools for estimating the location of a transmitter signal from radio telemetry studies using the maximum likelihood estimation (MLE) approach described in Lenth (1981).
License: GPL (>= 2)
URL: http://www.r-project.org
Packaged: 2014-10-22 20:22:57 UTC; Serge
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 23:14:50

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Package RAM updated to version 1.1.0 with previous version 1.0.0 dated 2014-08-21

Title: R for Amplicon-based Metagenomics
Description: This package provides a series of functions to make amplicon-based metagenomic analysis more accessible, and publication-quality plots simple. Amplicon-based (or targeted) metagenomics amplifies and sequences selected DNA regions of environmental samples, but not the entire pool of genetic material, which is referred to as shotgun metagenomics. The amplicon-metagenomics mainly aims at characterizing broad microbiota biodiversity in different environments.
Author: Wen Chen and Joshua Simpson
Maintainer: Wen Chen

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Package MixGHD updated to version 1.1 with previous version 1.0 dated 2014-07-22

Title: Model based clustering, classification and discriminant analysis using the mixture of generalized hyperbolic distributions.
Description: Carries out model-based clustering, classification and discriminant analysis using four different models. The models are all based on the generalized hyperbolic distribution.The first model MGHD is the classical mixture of generalized hyperbolic distributions. The MGHFA is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The MSGHD, mixture of multiple scaled generalized hyperbolic distributions. The MCGHD, mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora, Ryan P. Browne, Brian C. Franczak and Paul D. McNicholas.
Maintainer: Cristina Tortora

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Package JMdesign updated to version 1.1 with previous version 1.0 dated 2014-10-20

Title: Joint Modeling of Longitudinal and Survival Data - Power Calculation
Description: Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix, Sigma_theta, is unknown.
Author: Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim
Maintainer: Shannon T. Holloway

Diff between JMdesign versions 1.0 dated 2014-10-20 and 1.1 dated 2014-10-22

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Package FLSSS updated to version 3.0 with previous version 2.0.1 dated 2014-10-01

Title: Fixed Size Subset Sum Solution
Description: Solve an approximate Subset Sum Problem by introducing a recursive compression algorithm
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu

Diff between FLSSS versions 2.0.1 dated 2014-10-01 and 3.0 dated 2014-10-22

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Package confidence updated to version 1.1-0 with previous version 1.0-0 dated 2014-09-19

Title: Confidence Estimation of Environmental State Classifications
Description: Functions for estimating and reporting multiyear averages and corresponding confidence intervals and distributions. A potential use case is reporting the chemical and ecological status of surface waters according to the European Water Framework Directive.
Author: Willem M. G. M. van Loon [aut, cph], Dennis J. J. Walvoort [aut, cre]
Maintainer: Dennis J. J. Walvoort

Diff between confidence versions 1.0-0 dated 2014-09-19 and 1.1-0 dated 2014-10-22

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New package TDboost with initial version 1.0
Package: TDboost
Title: A Boosted Nonparametric Tweedie Model
Version: 1.0
Date: 2013-10-11
Author: Yi Yang , Wei Qian , Hui Zou
Maintainer: Yi Yang
Depends: R (>= 2.12.0), lattice
Description: A fully nonparametric Tweedie model using the gradient boosting. It is capable of fitting a flexible nonlinear model and capturing interactions among predictors.
LazyData: yes
License: GPL-3
Packaged: 2014-10-22 16:33:11 UTC; emeryyi
NeedsCompilation: yes
Date/Publication: 2014-10-22 20:48:02
Repository: CRAN

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New package glmvsd with initial version 1.0
Package: glmvsd
Type: Package
Title: Variable Selection Deviation (VSD) Measures and Instability Tests for High-dimensional Generalized Linear Models
Version: 1.0
Date: 2014-09-19
Author: Ying Nan , Yi Yang , Yuhong Yang
Maintainer: Yi Yang
Depends: stats, glmnet, ncvreg, MASS
Description: Variable selection deviation measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable.
License: GPL-2
URL: https://github.com/emeryyi/glmvsd
Packaged: 2014-10-22 16:08:33 UTC; emeryyi
Date/Publication: 2014-10-22 20:49:00
NeedsCompilation: no
Repository: CRAN

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Package timeordered updated to version 0.9.7 with previous version 0.9.6 dated 2014-03-10

Title: Time-ordered and time-aggregated network analyses
Description: Methods for incorporating time into network analysis. Construction of time-ordered networks (temporal graphs). Shortest-time and shortest-path-length analyses. Resource spread calculations. Data resampling and rarefaction for null model construction. Reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks. Vector clock latencies. Plotting functionalities.
Author: Benjamin Blonder
Maintainer: Benjamin Blonder

Diff between timeordered versions 0.9.6 dated 2014-03-10 and 0.9.7 dated 2014-10-22

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New package traj with initial version 1.0
Package: traj
Title: Trajectory Analysis
Description: Implements the three step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Version: 1.0
Date: 2014-07-10
Author: Marie-Pierre Sylvestre, Dan Vatnik
Maintainer: Dan Vatnik
License: GPL-2
LazyData: true
Depends: R (>= 3.0.3)
Imports: cluster, psych, pastecs, NbClust, graphics, grDevices, stats, utils, GPArotation
Packaged: 2014-10-22 15:47:16 UTC; Dan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 18:20:51

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Package synbreed updated to version 0.10-3 with previous version 0.10-2 dated 2014-09-10

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 0.10-2 dated 2014-09-10 and 0.10-3 dated 2014-10-22

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Package speedglm updated to version 0.2-1.0 with previous version 0.2 dated 2013-07-24

Title: Fitting Linear and Generalized Linear Models to large data sets.
Description: Fitting LMs and GLMs to large data sets by updating algorithms.
Author: Marco ENEA
Maintainer: Marco ENEA

Diff between speedglm versions 0.2 dated 2013-07-24 and 0.2-1.0 dated 2014-10-22

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New package saeSim with initial version 0.6.0
Package: saeSim
Type: Package
Title: Simulation Tools for Small Area Estimation
Date: 2014-10-22
Version: 0.6.0
Author: Sebastian Warnholz
Maintainer: Sebastian Warnholz
URL: https://wahani.github.io/saeSim
BugReports: https://github.com/wahani/saeSim/issues
Depends: R(>= 3.1), methods
Imports: dplyr(>= 0.2), ggplot2, MASS, spdep, parallel
Suggests: testthat, knitr
Description: Tools for the simulation of data in the context of small area estimation. Combine all steps of your simulation - from data generation over drawing samples to model fitting - in one object. This enables easy modification and combination of different scenarios. You can store your results in a folder or start the simulation in parallel.
License: GPL-3 | file LICENSE
VignetteBuilder: knitr
Packaged: 2014-10-22 12:28:59 UTC; swarnholz
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-10-22 16:04:46

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Package rpf updated to version 0.40 with previous version 0.39 dated 2014-09-22

Title: Response Probability Functions
Description: The purpose of this package is to factor out logic and math common to Item Factor Analysis fitting, diagnostics, and analysis. It is envisioned as core support code suitable for more specialized IRT packages to build upon. Complete access to optimized C functions are made available with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut], Jonathan Weeks [ctb], Li Cai [ctb], Carrie Houts [ctb], Phil Chalmers [ctb]
Maintainer: Joshua Pritikin

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Package BayesFactor updated to version 0.9.9 with previous version 0.9.8 dated 2014-08-29

Title: Computation of Bayes factors for common designs
Description: The BayesFactor package is a suite of functions for computing various Bayes factors for simple designs, including contingency tables, one- and two-sample designs, one-way designs, general ANOVA designs, and linear regression.
Author: Richard D. Morey [aut, cre], Jeffrey N. Rouder [aut], Tahira Jamil [ctb]
Maintainer: Richard D. Morey

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Package BAT updated to version 1.0.1 with previous version 1.0 dated 2014-08-19

Title: Biodiversity Assessment Tools
Description: This package introduces algorithms to assess alpha and beta diversity in all their dimensions (taxon, phylogenetic and functional diversity), whether communities are completely sampled or not. It allows performing a number of analyses based on either species identities or ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso

Diff between BAT versions 1.0 dated 2014-08-19 and 1.0.1 dated 2014-10-22

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Package AutoSEARCH updated to version 1.3 with previous version 1.2 dated 2012-10-11

Title: General-to-Specific (GETS) Model Selection
Description: Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or of a log-ARCH-X model of the error. NOTE: The package has been succeeded by the package gets, also available on the CRAN, which is intended to be more user-friendly, faster and easier to extend. AutoSEARCH will continue to be maintained, but the development focus will switch to gets. Users are therefore encouraged to consider gets instead.
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat

Diff between AutoSEARCH versions 1.2 dated 2012-10-11 and 1.3 dated 2014-10-22

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

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

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

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

More information about lmenssp at CRAN
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Package ParetoPosStable updated to version 1.0.3 with previous version 1.0.2 dated 2014-02-19

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

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

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

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

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

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

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

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

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

More information about indicoio at CRAN
Permanent link

Tue, 21 Oct 2014

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

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

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

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

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

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

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

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

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

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

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

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

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More information about MESS at CRAN
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Package equate updated to version 2.0-3 with previous version 2.0-2 dated 2014-02-22

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

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

 equate-2.0-2/equate/R/smoothing.r                |only
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 equate-2.0-3/equate/R/composite.R                |   13 
 equate-2.0-3/equate/R/equate.R                   |   68 +-
 equate-2.0-3/equate/R/equipercentile.R           |   94 +--
 equate-2.0-3/equate/R/error.R                    |  109 ++--
 equate-2.0-3/equate/R/freqtab.R                  |  553 ++++++++++++++++-------
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 33 files changed, 1987 insertions(+), 923 deletions(-)

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

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

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

 DESCRIPTION                                     |   10 
 MD5                                             |  386 ++++++++++++------------
 NAMESPACE                                       |    1 
 NEWS                                            |   89 +++++
 R/anovaPE.R                                     |   27 +
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 R/cdfCompare.R                                  |    2 
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 197 files changed, 1685 insertions(+), 1156 deletions(-)

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

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

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

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

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

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 43 files changed, 373 insertions(+), 469 deletions(-)

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

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

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

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

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 nhlscrapr-1.8/nhlscrapr/R/convert-html.R              |   28 -
 nhlscrapr-1.8/nhlscrapr/R/integrate.R                 |  421 ++++++++++--------
 nhlscrapr-1.8/nhlscrapr/R/manual-name-fixes.R         |   35 +
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 16 files changed, 464 insertions(+), 256 deletions(-)

More information about nhlscrapr at CRAN
Permanent link

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

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

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

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 MPTinR-1.6.3/MPTinR/MD5                   |   45 +++++++--------
 MPTinR-1.6.3/MPTinR/NAMESPACE             |    1 
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 MPTinR-1.6.3/MPTinR/R/bmpt.fia.R          |   16 ++---
 MPTinR-1.6.3/MPTinR/R/fit.model.R         |    2 
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 MPTinR-1.6.3/MPTinR/R/select.mpt.R        |    7 +-
 MPTinR-1.6.3/MPTinR/man/MPTinR-package.Rd |   10 +--
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 26 files changed, 202 insertions(+), 233 deletions(-)

More information about MPTinR at CRAN
Permanent link

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

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

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

 DESCRIPTION             |   29 ++--
 MD5                     |   37 +++--
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 23 files changed, 834 insertions(+), 590 deletions(-)

More information about GGIR at CRAN
Permanent link

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

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

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

 DESCRIPTION                        |   19 +---
 MD5                                |  144 ++++++++++++++++++-------------------
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 man/plot.nma.Rd                    |    2 
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 man/print.xyz.Rd                   |    2 
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 man/read.pdb.Rd                    |    4 -
 man/read.pdcBD.Rd                  |    3 
 man/read.pqr.Rd                    |    3 
 man/rgyr.Rd                        |    2 
 man/sdENM.Rd                       |    2 
 man/sip.Rd                         |    2 
 man/sse.bridges.Rd                 |    4 -
 man/torsion.pdb.Rd                 |    2 
 man/uniprot.Rd                     |    2 
 man/view.cna.Rd                    |   19 ----
 man/view.dccm.Rd                   |    2 
 man/view.modes.Rd                  |    2 
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 man/write.pdb.Rd                   |    3 
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 tests/testthat/test-aa2mass.R      |    3 
 tests/testthat/test-atom2mass.R    |   31 +++----
 tests/testthat/test-cmap.R         |   10 +-
 tests/testthat/test-core.find.R    |   31 ++++---
 tests/testthat/test-dccm.R         |   13 +--
 tests/testthat/test-deformation.R  |   32 ++++----
 tests/testthat/test-fitting.R      |   62 +++++++++------
 tests/testthat/test-get.pdb.R      |    4 +
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 tests/testthat/test-nma.pdbs.R     |  109 ++++++++++------------------
 tests/testthat/test-overlap.R      |    8 +-
 tests/testthat/test-pca.R          |   34 +++-----
 tests/testthat/test-pdb.annotate.R |    1 
 tests/testthat/test-pdbsplit.R     |    3 
 tests/testthat/test-read.pdb.R     |   46 ++++++++---
 tests/testthat/test-rmsd.R         |   50 +++++++-----
 74 files changed, 451 insertions(+), 416 deletions(-)

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

More information about cdcsis at CRAN
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Package vcf2geno (with last version 2.3) was removed from CRAN

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

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

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

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

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

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

More information about STARSEQ at CRAN
Permanent link

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

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

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

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 RcppParallel-4.3.3/DESCRIPTION                                                   |    8 
 RcppParallel-4.3.3/MD5                                                           | 1147 ++++----
 RcppParallel-4.3.3/NEWS                                                          |    6 
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 RcppParallel-4.3.3/inst/include/tbb/cache_aligned_allocator.h                    |   47 
 RcppParallel-4.3.3/inst/include/tbb/combinable.h                                 |   38 
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 RcppParallel-4.3.3/inst/include/tbb/concurrent_queue.h                           |  268 +
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 RcppParallel-4.3.3/inst/include/tbb/concurrent_vector.h                          |  263 +
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 RcppParallel-4.3.3/inst/include/tbb/internal/_aggregator_impl.h                  |   38 
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 RcppParallel-4.3.3/inst/include/tbb/internal/_concurrent_unordered_impl.h        |  185 +
 RcppParallel-4.3.3/inst/include/tbb/internal/_flow_graph_impl.h                  |  480 ++-
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 RcppParallel-4.3.3/src/Makevars                                                  |    6 
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 RcppParallel-4.3.3/src/tbb/src/tbb/pipeline.cpp                                  |   64 
 RcppParallel-4.3.3/src/tbb/src/tbb/private_server.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/queuing_mutex.cpp                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/queuing_rw_mutex.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/reader_writer_lock.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/recursive_mutex.cpp                           |   53 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler.cpp                                 |   50 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler.h                                   |   83 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler_common.h                            |   84 
 RcppParallel-4.3.3/src/tbb/src/tbb/scheduler_utility.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/semaphore.cpp                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/semaphore.h                                   |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/spin_mutex.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/spin_rw_mutex.cpp                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/task.cpp                                      |   44 
 RcppParallel-4.3.3/src/tbb/src/tbb/task_group_context.cpp                        |   58 
 RcppParallel-4.3.3/src/tbb/src/tbb/task_stream.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_assert_impl.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_main.cpp                                  |   40 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_main.h                                    |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_misc.cpp                                  |   71 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_misc.h                                    |   46 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_misc_ex.cpp                               |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_resource.rc                               |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_statistics.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_statistics.h                              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_thread.cpp                                |   49 
 RcppParallel-4.3.3/src/tbb/src/tbb/tbb_version.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tls.h                                         |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/disable_warnings.h                  |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/internal/ittnotify.h                |  659 ----
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify.h                         |  560 +++
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_config.h                  |  169 -
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_static.c                  |  371 +-
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_static.h                  |   89 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/ittnotify_types.h                   |   42 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/legacy/ittnotify.h                  |   74 
 RcppParallel-4.3.3/src/tbb/src/tbb/tools_api/prototype/ittnotify.h               |  143 -
 RcppParallel-4.3.3/src/tbb/src/tbb/win32-tbb-export.def                          |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/win32-tbb-export.lst                          |   55 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-gcc-tbb-export.def                      |   38 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-gcc-tbb-export.lst                      |   51 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-tbb-export.def                          |   36 
 RcppParallel-4.3.3/src/tbb/src/tbb/win64-tbb-export.lst                          |   55 
 RcppParallel-4.3.3/src/tbb/src/tbb/winrt-tbb-export.lst                          |   39 
 RcppParallel-4.3.3/src/tbb/src/tbb/x86_rtm_rw_mutex.cpp                          |   91 
 RcppParallel-4.3.3/src/tbb/src/tbb/xbox360-tbb-export.def                        |   36 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/Customize.h                             |   43 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/MapMemory.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/Statistics.h                            |   40 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/TypeDefinitions.h                       |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/backend.cpp                             |  235 -
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/backref.cpp                             |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/frontend.cpp                            |  117 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/large_objects.cpp                       |  153 -
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin32-proxy-export.def                  |   39 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin32-tbbmalloc-export.def              |   49 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64-proxy-export.def                  |   39 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64-tbbmalloc-export.def              |   49 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64ipf-proxy-export.def               |   39 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/lin64ipf-tbbmalloc-export.def           |   49 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/mac32-tbbmalloc-export.def              |   44 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/mac64-tbbmalloc-export.def              |   44 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/proxy.cpp                               |  308 +-
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/proxy.h                                 |   67 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/proxy_overload_osx.h                    |only
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/shared_utils.h                          |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbb_function_replacement.cpp            |   48 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbb_function_replacement.h              |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc.cpp                           |  142 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc.rc                            |   38 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc_internal.h                    |  179 -
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/tbbmalloc_internal_api.h                |   40 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win32-gcc-tbbmalloc-export.def          |   48 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win32-tbbmalloc-export.def              |   46 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win64-gcc-tbbmalloc-export.def          |   48 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/win64-tbbmalloc-export.def              |   46 
 RcppParallel-4.3.3/src/tbb/src/tbbmalloc/xbox360-tbbmalloc-export.def            |   46 
 RcppParallel-4.3.3/src/tbb/src/tbbproxy/tbbproxy-windows.asm                     |   36 
 RcppParallel-4.3.3/src/tbb/src/tbbproxy/tbbproxy.cpp                             |   42 
 RcppParallel-4.3.3/src/tbb/src/test/harness.h                                    |   62 
 RcppParallel-4.3.3/src/tbb/src/test/harness_allocator.h                          |  397 ++
 RcppParallel-4.3.3/src/tbb/src/test/harness_assert.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_bad_expr.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_barrier.h                            |   47 
 RcppParallel-4.3.3/src/tbb/src/test/harness_checktype.h                          |   39 
 RcppParallel-4.3.3/src/tbb/src/test/harness_concurrency.h                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_concurrency_tracker.h                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_cpu.h                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_defs.h                               |   80 
 RcppParallel-4.3.3/src/tbb/src/test/harness_dynamic_libs.h                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_eh.h                                 |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_fp.h                                 |only
 RcppParallel-4.3.3/src/tbb/src/test/harness_graph.h                              |  585 +++-
 RcppParallel-4.3.3/src/tbb/src/test/harness_inject_scheduler.h                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_iterator.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_m128.h                               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_memory.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_mic.h                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_report.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_runtime_loader.h                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_task.h                               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_tbb_independence.h                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/harness_test_cases_framework.h               |   39 
 RcppParallel-4.3.3/src/tbb/src/test/harness_tsx.h                                |   63 
 RcppParallel-4.3.3/src/tbb/src/test/test_ScalableAllocator.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_ScalableAllocator_STL.cpp               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_aggregator.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_aligned_space.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_allocator.h                             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_allocator_STL.h                         |   74 
 RcppParallel-4.3.3/src/tbb/src/test/test_assembly.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_atomic.cpp                              |  165 -
 RcppParallel-4.3.3/src/tbb/src/test/test_blocked_range.cpp                       |   46 
 RcppParallel-4.3.3/src/tbb/src/test/test_blocked_range2d.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_blocked_range3d.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_broadcast_node.cpp                      |  208 +
 RcppParallel-4.3.3/src/tbb/src/test/test_buffer_node.cpp                         |   62 
 RcppParallel-4.3.3/src/tbb/src/test/test_cache_aligned_allocator.cpp             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cache_aligned_allocator_STL.cpp         |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cilk_common.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cilk_dynamic_load.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_cilk_interop.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_combinable.cpp                          |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_hash_map.cpp                 |  489 +++
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_lru_cache.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_monitor.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_priority_queue.cpp           |  622 +++-
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_queue.cpp                    |  803 ++++-
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_queue.h                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_queue_whitebox.cpp           |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_unordered_common.h           |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_unordered_map.cpp            |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_unordered_set.cpp            |only
 RcppParallel-4.3.3/src/tbb/src/test/test_concurrent_vector.cpp                   | 1143 +++++---
 RcppParallel-4.3.3/src/tbb/src/test/test_condition_variable.h                    |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_container_move_support.h                |only
 RcppParallel-4.3.3/src/tbb/src/test/test_continue_node.cpp                       |  168 +
 RcppParallel-4.3.3/src/tbb/src/test/test_critical_section.cpp                    |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_dynamic_link.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_eh_algorithms.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_eh_flow_graph.cpp                       |   49 
 RcppParallel-4.3.3/src/tbb/src/test/test_eh_tasks.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_enumerable_thread_specific.cpp          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_examples_common_utility.cpp             |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_fast_random.cpp                         |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_flow_graph.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_flow_graph_whitebox.cpp                 |only
 RcppParallel-4.3.3/src/tbb/src/test/test_fp.cpp                                  |  174 -
 RcppParallel-4.3.3/src/tbb/src/test/test_function_node.cpp                       |  178 +
 RcppParallel-4.3.3/src/tbb/src/test/test_halt.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_handle_perror.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_hw_concurrency.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_indexer_node.cpp                        |  376 ++
 RcppParallel-4.3.3/src/tbb/src/test/test_initializer_list.h                      |  105 
 RcppParallel-4.3.3/src/tbb/src/test/test_inits_loop.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_intrusive_list.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_ittnotify.cpp                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_join_node.cpp                           |  663 +++-
 RcppParallel-4.3.3/src/tbb/src/test/test_lambda.cpp                              |   56 
 RcppParallel-4.3.3/src/tbb/src/test/test_limiter_node.cpp                        |  198 +
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_atexit.cpp                       |  185 -
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_compliance.cpp                   |   44 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_init_shutdown.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_lib_unload.cpp                   |   58 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_overload.cpp                     |  150 -
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_pools.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_pure_c.c                         |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_regression.cpp                   |   76 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_used_by_lib.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_malloc_whitebox.cpp                     |   48 
 RcppParallel-4.3.3/src/tbb/src/test/test_model_plugin.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_multifunction_node.cpp                  |  243 +
 RcppParallel-4.3.3/src/tbb/src/test/test_mutex.cpp                               |   77 
 RcppParallel-4.3.3/src/tbb/src/test/test_mutex_native_threads.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_openmp.cpp                              |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_overwrite_node.cpp                      |   52 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_do.cpp                         |   93 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_for.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_for_each.cpp                   |   96 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_for_vectorization.cpp          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_invoke.cpp                     |   42 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_pipeline.cpp                   |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_reduce.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_scan.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_sort.cpp                       |   92 
 RcppParallel-4.3.3/src/tbb/src/test/test_parallel_while.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_partitioner.h                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_partitioner_whitebox.cpp                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_pipeline.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_pipeline_with_tbf.cpp                   |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_priority_queue_node.cpp                 |   49 
 RcppParallel-4.3.3/src/tbb/src/test/test_queue_node.cpp                          |  360 +-
 RcppParallel-4.3.3/src/tbb/src/test/test_range_based_for.h                       |   44 
 RcppParallel-4.3.3/src/tbb/src/test/test_reader_writer_lock.cpp                  |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_runtime_loader.cpp                      |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_rwm_upgrade_downgrade.cpp               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_semaphore.cpp                           |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_sequencer_node.cpp                      |   46 
 RcppParallel-4.3.3/src/tbb/src/test/test_source_node.cpp                         |  213 +
 RcppParallel-4.3.3/src/tbb/src/test/test_split_node.cpp                          |   43 
 RcppParallel-4.3.3/src/tbb/src/test/test_static_assert.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_std_thread.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tagged_msg.cpp                          |   45 
 RcppParallel-4.3.3/src/tbb/src/test/test_task.cpp                                |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_arena.cpp                          |  236 +
 RcppParallel-4.3.3/src/tbb/src/test/test_task_assertions.cpp                     |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_auto_init.cpp                      |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_enqueue.cpp                        |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_group.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_leaks.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_priority.cpp                       |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_scheduler_init.cpp                 |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_scheduler_observer.cpp             |   39 
 RcppParallel-4.3.3/src/tbb/src/test/test_task_steal_limit.cpp                    |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_condition_variable.cpp              |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_fork.cpp                            |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_header.cpp                          |   92 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_thread.cpp                          |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_tbb_version.cpp                         |   42 
 RcppParallel-4.3.3/src/tbb/src/test/test_thread.h                                |   87 
 RcppParallel-4.3.3/src/tbb/src/test/test_tick_count.cpp                          |   67 
 RcppParallel-4.3.3/src/tbb/src/test/test_tuple.cpp                               |   38 
 RcppParallel-4.3.3/src/tbb/src/test/test_write_once_node.cpp                     |   41 
 RcppParallel-4.3.3/src/tbb/src/test/test_yield.cpp                               |   38 
 578 files changed, 25737 insertions(+), 20735 deletions(-)

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

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

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

 DESCRIPTION                          |    8 ++++----
 MD5                                  |   21 +++++++++++----------
 NEWS                                 |    9 +++++++++
 R/optimizeStrata.R                   |    6 +++---
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 12 files changed, 63 insertions(+), 33 deletions(-)

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

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

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

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 MD5                    |   15 -
 NAMESPACE              |    3 
 NEWS                   |    5 
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More information about RnavGraph at CRAN
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Package jackknifeKME updated to version 1.1 with previous version 1.0 dated 2013-02-24

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

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

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Permanent link

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

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

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

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

More information about openssl at CRAN
Permanent link

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

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

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

 jsonlite-0.9.12/jsonlite/R/asJSON.integer.R             |only
 jsonlite-0.9.13/jsonlite/DESCRIPTION                    |    8 +--
 jsonlite-0.9.13/jsonlite/MD5                            |   40 ++++++++--------
 jsonlite-0.9.13/jsonlite/NAMESPACE                      |    1 
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 24 files changed, 86 insertions(+), 78 deletions(-)

More information about jsonlite at CRAN
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Mon, 20 Oct 2014

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

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

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

 DESCRIPTION           |    6 +++---
 MD5                   |   29 ++++++++++++++++++++++++++---
 R/process_solution.R  |    4 ++--
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 5 files changed, 35 insertions(+), 12 deletions(-)

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

More information about tclust at CRAN
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Package rex updated to version 0.1.1 with previous version 0.1.0 dated 2014-10-14

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

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

 DESCRIPTION                           |   17 ++++--
 MD5                                   |   26 ++++-----
 R/character_class.R                   |   17 +++---
 R/escape.R                            |    6 +-
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 R/rex-mode.R                          |    9 +--
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 tests/testthat/test-match.R           |   95 ++++++++++++++++++++++++++++++++++
 vignettes/log_parsing.Rmd             |   15 ++---
 14 files changed, 217 insertions(+), 71 deletions(-)

More information about rex at CRAN
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Package redcapAPI updated to version 1.0.1 with previous version 1.0 dated 2014-09-15

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

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

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More information about redcapAPI at CRAN
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Package npsp updated to version 0.3-6 with previous version 0.2-4 dated 2013-11-04

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

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

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

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

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

 DESCRIPTION             |   21 ++++++++-------------
 MD5                     |   20 ++++++++++----------
 NAMESPACE               |    1 +
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 man/aft.qp.Rd           |    6 +++---
 man/data.Rd             |    2 +-
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 man/imputeYn.Rd         |    9 ++++-----
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 man/lss.mod.Rd          |    6 +++---
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More information about imputeYn at CRAN
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Package Rook updated to version 1.1-1 with previous version 1.0-9 dated 2013-01-11

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

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

 DESCRIPTION                    |   17 +++++++------
 MD5                            |   21 ++++++++--------
 NAMESPACE                      |    4 +++
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Permanent link

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

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

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

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

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

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 R/icapca.R              |   42 ++-
 man/ica_pca.Rd          |   59 +++-
 src/AIR.h               |   26 +
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 src/random_rotation.c   |   22 +
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 11 files changed, 660 insertions(+), 204 deletions(-)

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

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

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

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 ShrinkCovMat-1.0.2/ShrinkCovMat/R/shrinkcovmat.unequal.R     |    3 -
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Package npmlreg updated to version 0.46-1 with previous version 0.45-5 dated 2014-07-10

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

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

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

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

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

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

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

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

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

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

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Sun, 19 Oct 2014

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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Sat, 18 Oct 2014

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

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

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

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

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

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

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

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

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

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

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 22 files changed, 72 insertions(+), 72 deletions(-)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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