Tue, 10 Dec 2013

Package ExPosition updated to version 2.8.19 with previous version 2.1.3 dated 2013-06-15

Title: Exploratory analysis with the singular value decomposition.
Description: ExPosition is for descriptive (i.e., fixed-effects) multivariate analysis with the singular value decomposition.
Author: Derek Beaton, Cherise R. Chin Fatt, Herve Abdi
Maintainer: Derek Beaton

Diff between ExPosition versions 2.1.3 dated 2013-06-15 and 2.8.19 dated 2013-12-10

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Package xlsx updated to version 0.5.5 with previous version 0.5.1 dated 2013-05-20

Title: Read, write, format Excel 2007 and Excel 97/2000/XP/2003 files
Description: Provide R functions to read/write/format Excel 2007 and Excel 97/2000/XP/2003 file formats.
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu

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Package fTrading updated to version 3010.78 with previous version 2160.77 dated 2012-11-30

Title: Technical Trading Analysis
Description: Environment for teaching "Financial Engineering and Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi

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Package randomForestSRC updated to version 1.4 with previous version 1.3 dated 2013-07-22

Title: Random Forests for Survival, Regression and Classification (RF-SRC)
Description: A unified treatment of Breiman's random forests for survival, regression and classification problems based on Ishwaran and Kogalur's random survival forests (RSF) package. The package runs in both serial and parallel (OpenMP) modes.
Author: Hemant Ishwaran , Udaya B. Kogalur
Maintainer: Udaya B. Kogalur

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Package mRMRe updated to version 2.0.4 with previous version 2.0.3 dated 2013-12-10

Title: R package for parallelized mRMR ensemble feature selection
Description: This package contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with mRMR and a new ensemble mRMR technique.
Author: Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Gianluca Bontempi, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains

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Package lmm updated to version 0.9 with previous version 0.7 dated 2013-09-27

Title: Linear mixed models
Description: Some improved procedures for linear mixed models
Author: Joseph L. Schafer
Maintainer: Jing hua Zhao

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Package iBUGS updated to version 0.1.4 with previous version 0.1.3 dated 2013-03-29

Title: An Interface to WinBUGS/OpenBUGS/JAGS by gWidgets
Description: This package has provided an interface to WinBUGS/OpenBUGS/JAGS via R2WinBUGS and R2jags. Some options will be intelligently guessed, e.g. the path to WinBUGS/OpenBUGS/JAGS and the data/parameter list. Users can specify all the options in a GUI.
Author: Yihui Xie and Jiebiao Wang
Maintainer: Jiebiao Wang

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Package hyperdirichlet updated to version 1.4-9 with previous version 1.4-8 dated 2013-02-11

Title: A generalization of the Dirichlet distribution
Description: A suite of routines for the hyperdirichlet distribution
Author: Robin K.S. Hankin
Maintainer: Robin K. S. Hankin

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Package gsl updated to version 1.9-10 with previous version 1.9-9 dated 2011-09-08

Title: wrapper for the Gnu Scientific Library
Description: An R wrapper for the special functions and quasi random number generators of the Gnu Scientific Library (http://www.gnu.org/software/gsl/). See gsl-package.Rd for details of overall package organization, and Misc.Rd for some functions that are widely used in the package, and some tips on installation.
Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and multimin by Andrew Clausen
Maintainer: Robin K. S. Hankin

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Package conics updated to version 0.3 with previous version 0.2 dated 2012-10-27

Title: Plot Conics
Description: plot conics (ellipses, hyperbolas, parabolas)
Author: Bernard Desgraupes (University of Paris Ouest - Lab Modal'X)
Maintainer: Bernard Desgraupes

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New package binomSamSize with initial version 0.1-3
Package: binomSamSize
Type: Package
Title: Confidence intervals and sample size determination for a binomial proportion under simple random sampling and pooled sampling
Version: 0.1-3
Date: 2013-12-10
Author: Michael Hoehle with contributions by Wei Liu
Maintainer: Michael Hoehle
Depends: binom
Description: A suite of functions to compute confidence intervals and necessary sample sizes for the parameter p of the Bernoulli B(p) distribution under simple random sampling or under pooled sampling. Such computations are e.g. of interest when investigating the incidence or prevalence in populations. The package contains functions to compute coverage probabilities and coverage coefficients of the provided confidence intervals procedures. Sample size calculations are based on expected length.
License: GPL-3
LazyLoad: yes
Encoding: latin1
Packaged: 2013-12-10 21:29:01 UTC; hoehle
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-10 23:04:10

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Permanent link

Package rfisheries updated to version 0.0.6 with previous version 0.0.5 dated 2013-11-13

Title: R interface for fisheries data
Description: A programmatic interface to openfisheries.org. This package is part of the rOpenSci suite (http://ropensci.org)
Author: Karthik Ram [aut, cre], Carl Boettiger [aut], Andrew Dyck [aut]
Maintainer: Karthik Ram

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Package psychomix updated to version 1.1-0 with previous version 1.0-0 dated 2012-05-14

Title: Psychometric Mixture Models
Description: Psychometric mixture models based on flexmix infrastructure. At the moment Rasch mixture models with different parametrizations of the score distribution (saturated vs. mean/variance specification) and Bradley-Terry mixture models are implemented. Both mixture models can be estimated with or without concomitant variables. See vignette("raschmix", package = "psychomix") for details on the Rasch mixture models.
Author: Hannah Frick [aut, cre], Carolin Strobl [aut], Friedrich Leisch [aut], Achim Zeileis [aut]
Maintainer: Hannah Frick

Diff between psychomix versions 1.0-0 dated 2012-05-14 and 1.1-0 dated 2013-12-10

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Package bfp updated to version 0.0-27 with previous version 0.0-25 dated 2012-05-30

Title: Bayesian Fractional Polynomials
Description: The package implements the Bayesian paradigm for fractional polynomial models under the assumption of normally distributed error terms.
Author: Daniel Sabanes Bove
Maintainer: Daniel Sabanes Bove

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Package PopGenome updated to version 1.3.0 with previous version 1.2.6 dated 2013-10-26

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

Diff between PopGenome versions 1.2.6 dated 2013-10-26 and 1.3.0 dated 2013-12-10

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Package MixSim updated to version 1.0-9 with previous version 1.0-8 dated 2012-11-07

Title: Simulating Data to Study Performance of Clustering Algorithms
Description: MixSim allows simulating mixtures of Gaussian distributions with different levels of overlap between mixture components. Pairwise overlap, defined as a sum of two misclassification probabilities, measures the degree of interaction between components and can be readily employed to control the clustering complexity of datasets simulated from mixtures. These datasets can then be used for systematic performance investigation of clustering and finite mixture modeling algorithms. Among other capabilities of MixSim, there are computing the exact overlap for Gaussian mixtures, simulating Gaussian and non-Gaussian data, simulating outliers and noise variables, calculating various measures of agreement between two partitionings, and constructing parallel distribution plots for the graphical display of finite mixture models.
Author: Volodymyr Melnykov [aut, cre], Wei-Chen Chen [aut], Ranjan Maitra [aut]
Maintainer: Volodymyr Melnykov

Diff between MixSim versions 1.0-8 dated 2012-11-07 and 1.0-9 dated 2013-12-10

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Package DataCombine updated to version 0.1.11 with previous version 0.1.10 dated 2013-12-02

Title: R tools for making it easier to combine and clean data sets.
Description: R tools for combining and cleaning data sets, including filling in missing observations with data from another data frame and creating lag/lead variables.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud

Diff between DataCombine versions 0.1.10 dated 2013-12-02 and 0.1.11 dated 2013-12-10

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Package SSsimple updated to version 0.6.2 with previous version 0.6.1 dated 2013-04-02

Title: State space models
Description: Simulate, solve state space models
Author: Dave Zes
Maintainer: Dave Zes

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Package SII updated to version 1.0.3 with previous version 1.0.2 dated 2011-09-02

Title: Calculate ANSI S3.5-1997 Speech Intelligibility Index
Description: This package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), a standard method for computing the intelligibility of speech from acoustical measurements of speech, noise, and hearing thresholds. This package includes data frames corresponding to Tables 1 - 4 in the ANSI standard as well as a function utilizing these tables and user-provided hearing threshold and noise level measurements to compute the SII score. The methods implemented here extend the standard computations to allow calculation of SII when the measured frequencies do not match those required by the standard by applying interpolation to obtain values for the required frequencies -- Development of this package was funded by the Center for Bioscience Education and Technology (CBET) of the Rochester Institute of Technology (RIT).
Author: Gregory R. Warnes
Maintainer: Gregory R. Warnes

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Package missForest updated to version 1.3-1 with previous version 1.3 dated 2012-06-26

Title: Nonparametric Missing Value Imputation using Random Forest
Description: The function 'missForest' in this package is used to impute missing values particularly in the case of mixed-type data. It uses a random forest trained on the observed values of a data matrix to predict the missing values. It can be used to impute continuous and/or categorical data including complex interactions and non-linear relations. It yields an out-of-bag (OOB) imputation error estimate without the need of a test set or elaborate cross-validation.
Author: Daniel J. Stekhoven
Maintainer: Daniel J. Stekhoven

Diff between missForest versions 1.3 dated 2012-06-26 and 1.3-1 dated 2013-12-10

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New package gsscopu with initial version 0.9-1
Package: gsscopu
Version: 0.9-1
Date: 2013-12-9
Title: Copula Density and 2-D Hazard Estimation using Smoothing Splines
Author: Chong Gu
Maintainer: Chong Gu
Depends: R (>= 2.14.0), gss (>= 2.1-0)
Description: A collection of routines for the estimation of copula density and 2-D hazard function using smoothing splines.
License: GPL (>= 2)
Packaged: 2013-12-09 15:17:51 UTC; chong
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-10 16:13:19

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Package gld updated to version 2.2 with previous version 2.0.1 dated 2013-08-31

Title: Estimation and use of the generalised (Tukey) lambda distribution
Description: The generalised lambda distribution, or Tukey lambda distribution, provides a wide variety of shapes with one functional form. This package provides random numbers, quantiles, probabilities, densities for four different parameterisations of the distribution. It provides density function, distribution function and Quantile-Quantile plots. It implements a variety of estimation method for the distribution, including diagnostic plots. Estimation methods include the starship (all 4 parameterisations) and a number of methods for only the FKML parameterisation. These include maximum likelihood, maximum product of spacings, Titterington's method, L moments, Trimmed L moments and Distributional Least Absolutes.
Author: Robert King , Ben Dean
Maintainer: Robert King

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Package tdthap updated to version 1.1-7 with previous version 1.1-6 dated 2013-04-08

Title: TDT tests for extended haplotypes
Description: Transmission/disequilibrium tests for extended marker haplotypes
Author: David Clayton
Maintainer: Jing Hua Zhao

Diff between tdthap versions 1.1-6 dated 2013-04-08 and 1.1-7 dated 2013-12-10

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New package VideoComparison with initial version 0.9-4
Package: VideoComparison
Version: 0.9-4
Date: 2013-12-09
Title: Video comparison tool
Author: Silvia Espinosa, Joaquin Ordieres, Antonio Bello, Jose Maria Perez
Maintainer: Joaquin Ordieres
Depends: R (>= 2.15.2), RJSONIO, RCurl, zoo, stats, pracma, Rcpp (>= 0.10.3)
LinkingTo: Rcpp
Suggests: MASS
Description: It will take the vectors of motion for two videos (coming from a variant of shotdetect code allowing to store detailed motion vectors in json format, for instance) and it will look for comparing taking out the common chunk. Then, provided you have some image's hashes it will compare their signature in order to make up the decision about chunk similarity of two video files.
License: GPL (>= 2)
URL: http://www.r-project.org
Packaged: 2013-12-09 08:58:34 UTC; jmperez
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-12-10 13:41:44

More information about VideoComparison at CRAN
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Package rotations updated to version 0.2 with previous version 0.1 dated 2013-09-09

Title: Tools for Working with Rotation Data
Description: This package implements tools for working with rotational data: it allows simulation from the most commonly used distributions on SO(3), it includes methods for different Bayes, mean and median type estimators for the central orientation of a sample, it provides confidence and credible regions for the central orientation based on those estimators and it includes a novel visualization technique for rotation data.
Author: Bryan Stanfill , Heike Hofmann , Ulrike Genschel
Maintainer: Bryan Stanfill

Diff between rotations versions 0.1 dated 2013-09-09 and 0.2 dated 2013-12-10

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Package PRISMA updated to version 0.2-1 with previous version 0.2-0 dated 2013-04-16

Title: Protocol Inspection and State Machine Analysis
Description: The PRISMA package is capable of loading and processing huge text corpora processed with the sally toolbox (http://www.mlsec.org/sally/). sally acts as a very fast preprocessor which splits the text files into tokens or n-grams. These output files can then be read with the PRISMA package which applies testing-based token selection and has some replicate-aware, highly tuned non-negative matrix factorization and principal component analysis implementation which allows the processing of very big data sets even on desktop machines.
Author: Tammo Krueger, Nicole Kraemer
Maintainer: Tammo Krueger

Diff between PRISMA versions 0.2-0 dated 2013-04-16 and 0.2-1 dated 2013-12-10

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New package pathmox with initial version 0.2.0
Package: pathmox
Type: Package
Title: Pathmox Approach of Segmentation Trees in Partial Least Squares Path Modeling
Version: 0.2.0
Date: 2013-12-09
Authors@R: c( person("Gaston", "Sanchez", email = "gaston.stat@gmail.com", role=c("aut", "cre")), person("Tomas", "Aluja", role=c("aut", "ths")))
Description: pathmox, the cousin package of plspm, provides a very interesting solution for handling segmentation variables in PLS Path Modeling: segmentation trees in PLS Path Modeling.
URL: http://www.gastonsanchez.com
Depends: R (>= 3.0.1), plspm, tester
Suggests: plsdepot
License: GPL-3
LazyLoad: yes
Collate: 'fix.pathmox.R' 'fix.techmox.R' 'pathmox-internal.R' 'pathmox.R' 'plot.bootnodes.R' 'plot.treemox.R' 'plot.treemox.pls.R' 'plspmox.R' 'print.bootnodes.R' 'print.treemox.R' 'print.treemox.pls.R' 'techmox.R' 'treemox.boot.R' 'treemox.pls.R' 'get_fix_xexeloa.R' 'get_nominal_split.R' 'get_ordinal_split.R' 'get_pls_basic.R' 'get_xexeloa.R' 'test_sanchez_aluja.R' 'check_pathmox_args.r'
Packaged: 2013-12-09 18:32:14 UTC; Gaston
Author: Gaston Sanchez [aut, cre], Tomas Aluja [aut, ths]
Maintainer: Gaston Sanchez
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-10 13:34:48

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Package mRMRe updated to version 2.0.3 with previous version 2.0.2 dated 2013-05-23

Title: R package for parallelized mRMR ensemble feature selection
Description: This package contains a set of function to compute mutual information matrices from continuous, categorical and survival variables. It also contains function to perform feature selection with mRMR and a new ensemble mRMR technique.
Author: Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen, Gianluca Bontempi, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains

Diff between mRMRe versions 2.0.2 dated 2013-05-23 and 2.0.3 dated 2013-12-10

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Package kohonen updated to version 2.0.13 with previous version 2.0.12 dated 2013-10-14

Title: Supervised and unsupervised self-organising maps
Description: Supervised and unsupervised self-organising maps
Author: Ron Wehrens
Maintainer: Ron Wehrens

Diff between kohonen versions 2.0.12 dated 2013-10-14 and 2.0.13 dated 2013-12-10

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Package HTSDiff updated to version 1.0.1 with previous version 1.0.0 dated 2013-09-25

Title: Differential analysis of RNA-seq data with Poisson mixture models
Description: This package implements a Poisson mixture model to identify differentially expressed genes from RNA-seq data.
Author: Andrea Rau, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

Diff between HTSDiff versions 1.0.0 dated 2013-09-25 and 1.0.1 dated 2013-12-10

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Package HTSCluster updated to version 2.0.1 with previous version 2.0.0 dated 2013-09-25

Title: Clustering high throughput sequencing (HTS) data
Description: This package implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the ICL criterion is used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau

Diff between HTSCluster versions 2.0.0 dated 2013-09-25 and 2.0.1 dated 2013-12-10

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New package glmx with initial version 0.1-0
Package: glmx
Version: 0.1-0
Date: 2013-12-10
Title: Generalized Linear Models Extended
Authors@R: c(person(given = "Achim", family = "Zeileis", role = c("aut", "cre"), email = "Achim.Zeileis@R-project.org"), person(given = "Roger", family = "Koenker", role = "aut"), person(given = "Philipp", family = "Doebler", role = "aut"))
Description: Extended techniques for generalized linear models (GLMs), especially for binary responses, including parametric links and heteroskedastic latent variables.
Depends: R (>= 2.14.0)
Imports: stats, MASS, Formula, lmtest, sandwich
Suggests: AER, gld, numDeriv, pscl
License: GPL-2 | GPL-3
Packaged: 2013-12-10 11:40:00 UTC; zeileis
Author: Achim Zeileis [aut, cre], Roger Koenker [aut], Philipp Doebler [aut]
Maintainer: Achim Zeileis
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-10 13:11:15

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Package GetoptLong updated to version 0.0.3 with previous version 0.0.2 dated 2013-11-28

Title: Parse command-line arguments
Description: Parsing command-line arguments by Perl module Getopt::Long. It also provides a simple way for variable interpolation in R.
Author: Zuguang Gu
Maintainer: Zuguang Gu

Diff between GetoptLong versions 0.0.2 dated 2013-11-28 and 0.0.3 dated 2013-12-10

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Package CVST updated to version 0.2-1 with previous version 0.2 dated 2013-04-16

Title: Fast Cross-Validation via Sequential Testing
Description: This package implements the fast cross-validation via sequential testing (CVST) procedure. CVST is an improved cross-validation procedure which uses non-parametric testing coupled with sequential analysis to determine the best parameter set on linearly increasing subsets of the data. By eliminating underperforming candidates quickly and keeping promising candidates as long as possible, the method speeds up the computation while preserving the capability of a full cross-validation. Additionally to the CVST the package contains an implementation of the ordinary k-fold cross-validation with a flexible and powerful set of helper objects and methods to handle the overall model selection process. The implementations of the Cochran's Q test with permutations and the sequential testing framework of Wald are generic and can therefore also be used in other contexts.
Author: Tammo Krueger, Mikio Braun
Maintainer: Tammo Krueger

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

Title: Semiparametric Maximum likelihood Method for interactions gene-environment in case-mother control-mother designs
Description: Implements the method of general semiparametric maximum likelihood estimation for logistic models in case-mother control-mother designs.
Author: Moliere Nguile Makao and Alexandre Bureau
Maintainer: Moliere Nguile Makao

Diff between SPmlficmcm versions 1.0 dated 2013-10-11 and 1.1 dated 2013-12-10

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Package rpart updated to version 4.1-4 with previous version 4.1-3 dated 2013-09-02

Title: Recursive Partitioning
Description: Recursive partitioning and regression trees
Author: Terry Therneau [aut], Beth Atkinson [aut], Brian Ripley [aut, trl, cre] (author of R port)
Maintainer: Brian Ripley

Diff between rpart versions 4.1-3 dated 2013-09-02 and 4.1-4 dated 2013-12-10

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Package prim updated to version 1.0.13 with previous version 1.0.12 dated 2011-09-26

Title: Patient Rule Induction Method (PRIM)
Description: PRIM for bump hunting in high-dimensional data
Author: Tarn Duong
Maintainer: Tarn Duong

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New package ICGE with initial version 0.2
Package: ICGE
Version: 0.2
Date: 2011-12-21
Title: Estimation of number of clusters and identification of atypical units
Authors@R: c(person("Itziar", "Irigoien", role = c("aut", "cre"), email = "itziar.irigoien@ehu.es"), person("Concepcion", "Arenas", role = "aut", email="carenas@ub.edu"))
Author: Itziar Irigoien and Conchita Arenas
Maintainer: Itziar Irigoien
Depends: R (>= 2.0.1), MASS, utils, stats, cluster
Description: ICGE is a package that helps to estimate the number of real clusters in data as well as to identify atypical units. The underlying methods are based on distances rather than on unit x variables.
License: GPL (>= 2)
LazyData: yes
Packaged: 2013-12-10 10:58:01 UTC; itziar
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-10 12:34:50

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Package fxregime updated to version 1.0-3 with previous version 1.0-2 dated 2011-11-07

Title: Exchange Rate Regime Analysis
Description: Exchange rate regression and structural change tools for estimating, testing, dating, and monitoring (de facto) exchange rate regimes.
Author: Achim Zeileis [aut, cre], Ajay Shah [ctb], Ila Patnaik [ctb], Anmol Sethy [ctb]
Maintainer: Achim Zeileis

Diff between fxregime versions 1.0-2 dated 2011-11-07 and 1.0-3 dated 2013-12-10

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Package fortunes updated to version 1.5-1 with previous version 1.5-0 dated 2012-04-07

Title: R Fortunes
Description: R Fortunes
Author: Achim Zeileis (R code) and the R community (fortunes). Contributions (fortunes and/or code) by Torsten Hothorn, Peter Dalgaard, Uwe Ligges, Kevin Wright, Martin Maechler, Kjetil Brinchmann Halvorsen, Kurt Hornik, Duncan Murdoch, Andy Bunn, Ray Brownrigg, Roger Bivand, Spencer Graves, Jim Lemon, Christian Kleiber, David L. Reiner, Berton Gunter, Roger Koenker, Charles Berry, Marc Schwartz, Michael Dewey, Ben Bolker, Peter Dunn, Sarah Goslee, Simon Blomberg, Bill Venables, Roland Rau, Thomas Petzoldt, Rolf Turner, Mark Leeds, Emmanuel Charpentier, Chris Evans, Paolo Sonego, Peter Ehlers, Detlef Steuer, Tal Galili, Greg Snow, Brian D. Ripley, Michael Sumner, David Winsemius, Liviu Andronic, Brian Diggs, Matthieu Stigler, Michael Friendly, Dirk Eddelbuettel, Richard M. Heiberger, Patrick Burns, Dieter Menne, Andrie de Vries, Barry Rowlingson, Renaud Lancelot, R. Michael Weylandt, Jon Olav Skoien, Francois Morneau, Antony Unwin, Joshua Wiley, Terry Therneau, Bryan Hanson, Henrik Singmann, Eduard Szoecs.
Maintainer: Achim Zeileis

Diff between fortunes versions 1.5-0 dated 2012-04-07 and 1.5-1 dated 2013-12-10

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Package cloudUtil updated to version 0.1.10 with previous version 0.1.9 dated 2012-03-20

Title: Cloud Util Plots
Description: Provides means of plots for comparing utilization data of compute systems.
Author: Christian Panse , Ermir Qeli
Maintainer: Christian Panse

Diff between cloudUtil versions 0.1.9 dated 2012-03-20 and 0.1.10 dated 2013-12-10

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Package clues (with last version 0.5-0) was removed from CRAN

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

2010-02-03 0.5-0
2009-12-24 0.4.0
2009-11-17 0.3.9
2009-03-17 0.3.2
2009-02-16 0.3.1
2009-02-12 0.2.9

Permanent link
Package bayesGARCH (with last version 1-00.10) was removed from CRAN

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

2011-04-15 1-00.10
2011-02-10 1-00.09
2011-01-04 1-00.08
2010-08-31 1-00.06
2009-11-25 1-00.05
2009-05-11 1-00.04
2008-12-04 1-00.02
2008-06-03 1-00.01

Permanent link
Package AcceptanceSampling (with last version 1.0-2) was removed from CRAN

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

2012-07-02 1.0-2

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Package rsae (with last version 0.1-4) was removed from CRAN

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

2012-01-08 0.1-4
2011-07-25 0.1-3
2011-07-23 0.1-2

Permanent link
Package AdMit (with last version 1-01.06) was removed from CRAN

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

2012-09-08 1-01.06
2012-08-21 1-01.04
2011-02-18 1-01.03.1
2009-08-20 1-01.03
2009-05-11 1-01.02
2009-01-25 1-01.01
2008-12-01 1-00.04
2008-06-11 1-00.02

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Package rmac (with last version 0.9) was removed from CRAN

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

2010-08-31 0.9

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Package int64 (with last version 1.1.2) was removed from CRAN

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

2011-12-02 1.1.2
2011-11-28 1.1.1
2011-11-24 1.1.0
2011-11-20 1.0.0

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Package probemapper (with last version 1.0.0) was removed from CRAN

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

2011-06-19 1.0.0

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

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

2010-03-26 1.0

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Package TreeSim updated to version 1.9.1 with previous version 1.9 dated 2013-06-09

Title: Simulating trees under the birth-death model
Description: The package simulates phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant-rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and number of tips (sim.bd.taxa.age). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa).sim.bd.age (and sim.rateshift.taxa without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot, LTT.plot.gen and LTT.average.root. TreeSim further samples appropriately trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of leaves is first reached (sim.gsa.taxa). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim). (ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa.
Author: Tanja Stadler
Maintainer: Tanja Stadler

Diff between TreeSim versions 1.9 dated 2013-06-09 and 1.9.1 dated 2013-12-10

 DESCRIPTION            |   35 +++++------------------------------
 MD5                    |   11 ++++++-----
 NAMESPACE              |    5 ++---
 R/age.nodes.R          |only
 R/cuttree.R            |   39 +++++++++++++++------------------------
 R/sim2.gsa.R           |   10 +++++-----
 man/TreeSim-package.Rd |    4 ++--
 7 files changed, 35 insertions(+), 69 deletions(-)

More information about TreeSim at CRAN
Permanent link

Package RcppArmadillo updated to version 0.3.930.1 with previous version 0.3.920.3 dated 2013-11-20

Title: Rcpp integration for Armadillo templated linear algebra library
Description: R and Armadillo integration using Rcpp Armadillo is a templated C++ linear algebra library (by Conrad Sanderson) that aims towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. A delayed evaluation approach is employed (during compile time) to combine several operations into one, and to reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. The RcppArmadillo package includes the header files from the templated Armadillo library (currently version 3.920.1). Thus users do not need to install Armadillo itself in order to use RcppArmadillo. This Armadillo integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration. Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel

Diff between RcppArmadillo versions 0.3.920.3 dated 2013-11-20 and 0.3.930.1 dated 2013-12-10

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 RcppArmadillo-0.3.930.1/RcppArmadillo/R/fastLm.R                                             |    5 
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 RcppArmadillo-0.3.930.1/RcppArmadillo/inst/include/armadillo_bits/Base_bones.hpp             |    7 
 RcppArmadillo-0.3.930.1/RcppArmadillo/inst/include/armadillo_bits/Base_meat.hpp              |   18 
 RcppArmadillo-0.3.930.1/RcppArmadillo/inst/include/armadillo_bits/Col_meat.hpp               |   24 
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 RcppArmadillo-0.3.930.1/RcppArmadillo/inst/include/armadillo_bits/Gen_meat.hpp               |   10 
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 RcppArmadillo-0.3.930.1/RcppArmadillo/inst/include/armadillo_bits/Mat_meat.hpp               |  298 ++-
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 136 files changed, 3410 insertions(+), 1544 deletions(-)

More information about RcppArmadillo at CRAN
Permanent link

Package mlegp updated to version 3.1.4 with previous version 3.1.3 dated 2012-12-20

Title: Maximum Likelihood Estimates of Gaussian Processes
Description: Maximum likelihood Gaussian process modeling for univariate and multi-dimensional outputs with diagnostic plots. Contact the maintainer for a package version that implements sensitivity analysis functionality.
Author: Garrett M. Dancik
Maintainer: Garrett M. Dancik

Diff between mlegp versions 3.1.3 dated 2012-12-20 and 3.1.4 dated 2013-12-10

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 27 files changed, 84 insertions(+), 76 deletions(-)

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Package jaatha updated to version 2.2 with previous version 2.1 dated 2013-09-10

Title: A Fast Parameter Estimation Method for Evolutionary Biology
Description: Jaatha is a composite likelihood method for inferring evolutionary parameters using genetic data. Given a model of the evolutionary history of two biological populations as well as SNP data from multiple individuals from each population, it estimates model parameters like the time of separation of both species.
Author: Lisha Mathew, Paul R. Staab and Dirk Metzler
Maintainer: Paul R. Staab

Diff between jaatha versions 2.1 dated 2013-09-10 and 2.2 dated 2013-12-10

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Package hexbin updated to version 1.26.3 with previous version 1.26.2 dated 2013-04-18

Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods.
Author: Dan Carr , ported by Nicholas Lewin-Koh and Martin Maechler
Maintainer: ORPHANED

Diff between hexbin versions 1.26.2 dated 2013-04-18 and 1.26.3 dated 2013-12-10

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Package expm updated to version 0.99-1 with previous version 0.99-0 dated 2012-09-04

Title: Matrix exponential
Description: Computation of the matrix exponential and related quantities.
Author: Vincent Goulet, Christophe Dutang, Martin Maechler, David Firth, Marina Shapira, Michael Stadelmann, expm-developers@lists.R-forge.R-project.org
Maintainer: Martin Maechler

Diff between expm versions 0.99-0 dated 2012-09-04 and 0.99-1 dated 2013-12-10

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Package CCM updated to version 1.1 with previous version 1.0 dated 2011-04-23

Title: Correlation classification method (CCM)
Description: Classification method that classifies a sample according to the class with the maximum mean (or any other function of) correlation between the test and training samples with known classes.
Author: Garrett M. Dancik and Yuanbin Ru
Maintainer: Garrett M. Dancik

Diff between CCM versions 1.0 dated 2011-04-23 and 1.1 dated 2013-12-10

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Package Bessel updated to version 0.5-5 with previous version 0.5-4 dated 2012-03-21

Title: Bessel -- Bessel Functions Computations and Approximations
Description: Bessel Function Computations for complex and real numbers; notably interfacing TOMS 644; approximations for large arguments, experiments, etc.
Author: Martin Maechler
Maintainer: Martin Maechler

Diff between Bessel versions 0.5-4 dated 2012-03-21 and 0.5-5 dated 2013-12-10

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Package sparr updated to version 0.3-4 with previous version 0.3-3 dated 2013-10-08

Title: The sparr package: SPAtial Relative Risk
Description: Provides functions to estimate kernel-smoothed relative risk functions and perform subsequent inference.
Author: T.M. Davies, M.L. Hazelton and J.C. Marshall
Maintainer: Tilman M. Davies

Diff between sparr versions 0.3-3 dated 2013-10-08 and 0.3-4 dated 2013-12-10

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Package RhpcBLASctl updated to version 0.13-344.02 with previous version 0.13-343.05 dated 2013-12-09

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

Diff between RhpcBLASctl versions 0.13-343.05 dated 2013-12-09 and 0.13-344.02 dated 2013-12-10

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Package prettyGraphs updated to version 2.1.5 with previous version 2.0.3 dated 2013-06-12

Title: publication-quality graphics.
Description: prettyGraphs contains simple, crisp graphics. Graphics produced by prettyGraphs are publication-quality.
Author: Derek Beaton
Maintainer: Derek Beaton

Diff between prettyGraphs versions 2.0.3 dated 2013-06-12 and 2.1.5 dated 2013-12-10

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New package corclass with initial version 0.1
Package: corclass
Type: Package
Title: Correlational Class Analysis
Version: 0.1
Date: 2013-11-25
Author: Andrei Boutyline
Maintainer: Andrei Boutyline
Description: Perform a correlational class analysis of the data, resulting in a partition of the data into separate modules.
License: GPL-2
Depends: igraph
Suggests: Cairo
Packaged: 2013-12-10 07:04:09 UTC; ElectricShhh
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-12-10 08:36:54

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Package aylmer updated to version 1.0-11 with previous version 1.0-10 dated 2013-01-21

Title: A generalization of Fisher's exact test
Description: A generalization of Fisher's exact test that allows for structural zeros.
Author: Robin K. S. Hankin (R) and Luke J. West (C++)
Maintainer: Robin K. S. Hankin

Diff between aylmer versions 1.0-10 dated 2013-01-21 and 1.0-11 dated 2013-12-10

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Package AdaptiveSparsity updated to version 1.3 with previous version 1.2 dated 2013-09-19

Title: Adaptive Sparsity Models
Description: Implements Figueiredo EM algorithm for adaptive sparsity (Jeffreys prior) (see Figueiredo, M.A.T.; , "Adaptive sparseness for supervised learning," Pattern Analysis and Machine Intelligence, IEEE Transactions on , vol.25, no.9, pp. 1150- 1159, Sept. 2003) and Wong algorithm for adaptively sparse gaussian geometric models (see Wong, Eleanor, Suyash Awate, and P. Thomas Fletcher. "Adaptive Sparsity in Gaussian Graphical Models." In Proceedings of the 30th International Conference on Machine Learning (ICML-13), pp. 311-319. 2013.)
Author: Kristen Zygmunt, Eleanor Wong, Tom Fletcher
Maintainer: Kristen Zygmunt

Diff between AdaptiveSparsity versions 1.2 dated 2013-09-19 and 1.3 dated 2013-12-10

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