CRANberries

Sat, 25 May 2013

Package profdpm updated to version 3.3 with previous version 3.2 dated 2012-12-25

Title: Profile Dirichlet Process Mixtures
Description: This package facilitates profile inference (inference at the posterior mode) for a class of product partition models (PPM). The Dirichlet process mixture is currently the only available member of this class. These methods search for the maximum posterior (MAP) estimate for the data partition in a PPM.
Author: Matt Shotwell
Maintainer: Matt Shotwell

Diff between profdpm versions 3.2 dated 2012-12-25 and 3.3 dated 2013-05-25

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 profdpm-3.3/profdpm/DESCRIPTION               |    9 +++---
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 profdpm-3.3/profdpm/inst/doc/profdpm.pdf      |binary
 profdpm-3.3/profdpm/man/pci.Rd                |    2 +
 profdpm-3.3/profdpm/man/profBinary.Rd         |    2 +
 profdpm-3.3/profdpm/man/profLinear.Rd         |    2 +
 profdpm-3.3/profdpm/man/profdpm.Rd            |    8 +++--
 profdpm-3.3/profdpm/man/summary.profBinary.Rd |    3 ++
 profdpm-3.3/profdpm/man/summary.profLinear.Rd |    3 ++
 profdpm-3.3/profdpm/src/methods.c             |    2 -
 profdpm-3.3/profdpm/src/pdpmlm.c              |    2 -
 profdpm-3.3/profdpm/src/profBinary.c          |    4 +-
 profdpm-3.3/profdpm/vignettes/profdpm.Rnw     |   35 ++++++++++++--------------
 profdpm-3.3/profdpm/vignettes/profdpm.bib     |    9 +++---
 18 files changed, 81 insertions(+), 66 deletions(-)

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Fri, 24 May 2013

New package msgl with initial version 0.1.1
Package: msgl
Type: Package
Title: High dimensional multiclass classification using sparse group lasso
Version: 0.1.1
Date: 2013-20-05
Author: Martin Vincent (Sparse group lasso), Conrad Sanderson (Armadillo), Jaakko Jarvi (Boost Tuple) and Jens Maurer (Boost Random)
Maintainer: Martin Vincent
Description: Sparse group lasso multiclass classification, suitable for high dimensional problems with many classes (see url). Fast algorithm for solving the multinomial sparse group lasso optimization problem. Use of multiple processors for cross validation and subsampling is supported through OpenMP. The Armadillo C++ library is used as the primary linear algebra engine. Armadillo is licensed under the MPL 2.0 (see url). The Armadillo C++ library is primarily developed at NICTA (Australia) by Conrad Sanderson, with contributions from around the world. Furthermore the package utilize various Boost libraries, in particular the Tuple library by Jaakko Jarvi and the Random library by Jens Maurer. The Boost libraries are licensed under the Boost Software License (see url).
URL: http://arxiv.org/abs/1205.1245 http://arma.sourceforge.net/, http://www.mozilla.org/MPL/2.0/, http://www.boost.org/, http://www.boost.org/users/license.html
License: GPL (>= 2)
LazyLoad: yes
Depends: R (>= 2.13.0), Matrix
Collate: 'msgl_multinomial.R'
Packaged: 2013-05-24 18:52:34 UTC; martin
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-24 21:40:44

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Package bayesPop updated to version 4.0-1 with previous version 3.2-3 dated 2013-04-11

Title: Probabilistic Population Projection
Description: The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy.
Author: Hana Sevcikova, Adrian Raftery
Maintainer: Hana Sevcikova

Diff between bayesPop versions 3.2-3 dated 2013-04-11 and 4.0-1 dated 2013-05-24

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 bayesPop-4.0-1/bayesPop/ChangeLog                                          |   13 
 bayesPop-4.0-1/bayesPop/DESCRIPTION                                        |   14 
 bayesPop-4.0-1/bayesPop/MD5                                                |   76 ---
 bayesPop-4.0-1/bayesPop/R/aggregate.R                                      |   14 
 bayesPop-4.0-1/bayesPop/R/get_outputs.R                                    |   47 +
 bayesPop-4.0-1/bayesPop/R/predict.pop.R                                    |   86 ++-
 bayesPop-4.0-1/bayesPop/data/vwBaseYear2008.txt                            |  236 +++++++++-
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 bayesPop-4.0-1/bayesPop/man/expressions.Rd                                 |    5 
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 bayesPop-4.0-1/bayesPop/man/pop.map.Rd                                     |    2 
 bayesPop-4.0-1/bayesPop/man/predict.pop.Rd                                 |   23 
 bayesPop-4.0-1/bayesPop/man/vwBaseYear.Rd                                  |    1 
 bayesPop-4.0-1/bayesPop/tests/run_tests.R                                  |    3 
 60 files changed, 623 insertions(+), 155 deletions(-)

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Package bayesDem updated to version 2.3-0 with previous version 2.2-1 dated 2013-04-07

Title: Graphical User Interface for bayesTFR, bayesLife and bayesPop
Description: Provides Graphical user interface for the packages bayesTFR, bayesLife and bayesPop
Author: Hana Sevcikova
Maintainer: Hana Sevcikova

Diff between bayesDem versions 2.2-1 dated 2013-04-07 and 2.3-0 dated 2013-05-24

 DESCRIPTION             |   12 +++++----
 MD5                     |   28 +++++++++++-----------
 R/bayesDem.R            |    4 +--
 R/bayesDem_ini.R        |    4 ---
 R/e0-mcmc.R             |    6 +++-
 R/e0-predict.R          |    2 -
 R/handlers_and_fncs.R   |   15 +++--------
 R/pop-predict.R         |   17 +++++++------
 R/pop-results.R         |   15 +++++++----
 R/tfr-cont-mcmc.R       |    3 ++
 R/tfr-mcmc.R            |   61 ++++++++++++++++++++++++------------------------
 R/tfr-predict.R         |   51 +++++++++++++++++++++++++---------------
 R/tfr-results.R         |    5 ---
 man/bayesDem-package.Rd |    5 +--
 man/bayesDem.go.Rd      |   11 +++-----
 15 files changed, 130 insertions(+), 109 deletions(-)

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Package contrast updated to version 0.18 with previous version 0.17 dated 2011-12-24

Title: A collection of contrast methods
Description: Contrast methods, in the style of the Design package, for fit objects produced by the lm, glm, gls, and geese functions.
Author: Max Kuhn, contributions from Steve Weston, Jed Wing and James Forester
Maintainer: Max Kuhn

Diff between contrast versions 0.17 dated 2011-12-24 and 0.18 dated 2013-05-24

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Package arules updated to version 1.0-14 with previous version 1.0-13 dated 2013-04-07

Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides interfaces to C implementations of the association mining algorithms Apriori and Eclat by C. Borgelt.
Author: Michael Hahsler, Christian Buchta, Bettina Gruen and Kurt Hornik
Maintainer: Michael Hahsler

Diff between arules versions 1.0-13 dated 2013-04-07 and 1.0-14 dated 2013-05-24

 DESCRIPTION         |    8 ++++----
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 12 files changed, 31 insertions(+), 24 deletions(-)

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New package tlnise with initial version 2.0
Package: tlnise
Depends: R (>= 3.0.0)
Suggests: MASS
Imports: stats
Version: 2.0
Date: 2013-05-24
Title: Two-level normal independent sampling estimation
Author: S-PLUS original by Phil Everson; R port by Roger D. Peng
Maintainer: Roger D. Peng
Description: Functions for two level normal models as described in Everson and Morris (2000). J. R. Statist. Soc. B, 62 prt 2, pp.399--412.
License: GPL-3
URL: http://www.swarthmore.edu/NatSci/peverso1/TLNise/tlnise.htm
Packaged: 2013-05-24 14:37:36 UTC; rdpeng
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-24 18:24:21

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Package migest updated to version 1.3 with previous version 1.2 dated 2013-04-23

Title: Useful R code for the Estimation of Migration
Description: The migest package contains a collection of R functions that are useful to estimate migration when there is missing data. Included is the ffs routine to estimate migration flows from stock data, as well as various other functions to indirectly estimate flows where marginal totals are known. Functions are illustrated with dummy data.
Author: Guy J. Abel
Maintainer: Guy J. Abel

Diff between migest versions 1.2 dated 2013-04-23 and 1.3 dated 2013-05-24

 DESCRIPTION           |    7 ++++---
 MD5                   |   10 +++++-----
 R/ffs.R               |   24 +++++++++++++++++-------
 R/ipf2.R              |    2 ++
 R/ipf3.R              |    3 ++-
 man/migest-package.Rd |    7 +++----
 6 files changed, 33 insertions(+), 20 deletions(-)

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Package lbiassurv updated to version 1.1 with previous version 1.0 dated 2013-03-11

Title: Length-biased correction to survival curve estimation.
Description: The package offers various length-bias corrections to survival curve estimation.
Author: Pierre-Jerome Bergeron and Vahid Partovi Nia
Maintainer: Vahid Partovi Nia

Diff between lbiassurv versions 1.0 dated 2013-03-11 and 1.1 dated 2013-05-24

 DESCRIPTION         |   12 +--
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Package fda updated to version 2.3.6 with previous version 2.3.4 dated 2013-04-21

Title: Functional Data Analysis
Description: These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer. They were ported from earlier versions in Matlab and S-PLUS. An introduction appears in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009) Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. As of this release, the R-Project is no longer distributing the Matlab versions of the functional data analysis functions and sample analyses through the CRAN distribution system. This is due to the pressure placed on storage required in the many CRAN sites by the rapidly increasing number of R packages, of which the fda package is one. The three of us involved in this package have agreed to help out this situation by switching to distributing the Matlab functions and analyses through Jim Ramsay's ftp site at McGill University. To obtain these Matlab files, go to this site using an ftp utility: http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/ There you find a set of .zip files containing the functions and sample analyses, as well as two .txt files giving instructions for installation and some additional information.
Author: J. O. Ramsay , Hadley Wickham , Spencer Graves , Giles Hooker
Maintainer: J. O. Ramsay

Diff between fda versions 2.3.4 dated 2013-04-21 and 2.3.6 dated 2013-05-24

 DESCRIPTION    |   14 
 MD5            |    6 
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 4 files changed, 546 insertions(+), 548 deletions(-)

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New package SparseTSCGM with initial version 1.0
Package: SparseTSCGM
Type: Package
Title: Sparse time series chain graphical models
Version: 1.0
Date: 2013-05-24
Author: Fentaw Abegaz and Ernst Wit
Maintainer: Fentaw Abegaz
Depends: R (>= 3.0.0), glasso, longitudinal, flare, mvtnorm, network
Description: Compute and plot sparse autoregressive coefficient and precision matrices for time series chain graphical models.
License: GPL (>= 3)
LazyLoad: yes
Packaged: 2013-05-24 12:05:56 UTC; P261204
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-24 15:38:46

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Package ORCME updated to version 1.2.1 with previous version 1.2 dated 2012-09-18

Title: Order Restricted Clustering for Microarray Experiments
Description: This package provides clustering of genes with similar dose response (or time course) profiles. It implements the method described by Lin et al. (2012).
Author: Adetayo Kasim, Martin Otava, Tobias Verbeke
Maintainer: Martin Otava

Diff between ORCME versions 1.2 dated 2012-09-18 and 1.2.1 dated 2013-05-24

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New package compositionsGUI with initial version 1.0
Package: compositionsGUI
Type: Package
Title: Graphical User Environment for Compositional Data Analysis
Version: 1.0
Date: 2013-05-14
Author: Jiri Eichler, Karel Hron, Raimon Tolosana-Delgado, Gerald van den Boogaart, Matthias Templ, Peter Filzmoser
Maintainer: Jiri Eichler
Depends: robCompositions, compositions, mvoutlier, robustbase, RGtk2, MASS, nnet, boot
Description: The package provides graphical user interface and teaching tool for compositional data analysis using R. It contains data loading from various sources (external sources, installed R packages), preprocessing (imputation of missing values and rounded zeros), basic summary statistics as well as log-ratio transformations, necessary for a reasonable statistical treatment of compositional data (isometric, centred, additive log-ratio transformations). Further, also statistical methods like outlier detection and principal component analysis, together with the corresponding graphical tools, are provided. Finally, the package contains plotting functions, suitable for compositional data analysis, like ternary and quaternary diagrams, scatterplots of log-ratio transformed data, and diagrams with categorical/continuous covariates.
License: GPL (>= 2)
Packaged: 2013-05-16 20:20:57 UTC; templ
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-24 12:34:41

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Package BSquare updated to version 1.1 with previous version 1.0 dated 2013-05-22

Title: Bayesian Simultaneous Quantile Regression
Description: This package models the quantile process as a function of predictors.
Author: Luke Smith & Brian Reich
Maintainer: Luke Smith

Diff between BSquare versions 1.0 dated 2013-05-22 and 1.1 dated 2013-05-24

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New package Demerelate with initial version 0.8-0
Package: Demerelate
Version: 0.8-0
Date: 2012-05-24
Title: Functions to calculate relatedness on diploid genetic data
Authors@R: c(person("Philipp","Kraemer",role=c("aut", "cre"),email="Philipp.Kraemer@uni-oldenburg.de"),person("Gabriele","Gerlach",role="aut",email="Gabriele.Gerlach@uni-oldenburg.de"))
Author: Philipp Kraemer and Gabriele Gerlach
Maintainer: Philipp Kraemer
Depends: R (>= 2.15.0), fts, mlogit, sfsmisc
Suggests: MASS
Description: Functions to calculate pairwise relatedness on diploid genetic datasets. Different estimators for relatedness can be combined with information on geographical distances. Information on heterozygosity, allele- and genotype diversity as well as genetic F-statistics are provided for each population.
License: GPL (>= 2)
URL: http://www.r-project.org
BugReports: http://Demerelate.bugtracker.url
Packaged: 2013-05-24 08:10:41 UTC; philipp
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-24 10:29:00

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Package bayesLife updated to version 2.0-0 with previous version 1.1-3 dated 2013-04-06

Title: Bayesian Projection of Life Expectancy
Description: Making probabilistic projections of life expectancy for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova, Adrian Raftery; original WinBugs code written by Jennifer Chunn
Maintainer: Hana Sevcikova

Diff between bayesLife versions 1.1-3 dated 2013-04-06 and 2.0-0 dated 2013-05-24

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 bayesLife-2.0-0/bayesLife/ChangeLog                                                       |   18 
 bayesLife-2.0-0/bayesLife/DESCRIPTION                                                     |   12 
 bayesLife-2.0-0/bayesLife/MD5                                                             | 2320 ++++------
 bayesLife-2.0-0/bayesLife/R/plot_functions.R                                              |   33 
 bayesLife-2.0-0/bayesLife/R/projection_fcns.R                                             |   43 
 bayesLife-2.0-0/bayesLife/R/run_mcmc.R                                                    |    4 
 bayesLife-2.0-0/bayesLife/R/wpp_data.R                                                    |   12 
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Permanent link

Package OUwie updated to version 1.34 with previous version 1.33 dated 2013-03-23

Title: Analysis of evolutionary rates in an OU framework
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu , Brian O'Meara
Maintainer: Jeremy Beaulieu

Diff between OUwie versions 1.33 dated 2013-03-23 and 1.34 dated 2013-05-24

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Permanent link

New package twostageTE with initial version 1.0
Package: twostageTE
Type: Package
Title: Two-Stage Threshold Estimation
Version: 1.0
Date: 2013-03-05
Author: Shawn Mankad, George Michailidis, Moulinath Banerjee
Maintainer: Shawn Mankad
Description: Implements a variety of nonparametric methods for computing one-stage and two-stage confidence intervals, as well as point estimates of threshold values.
License: GPL-2
Depends: isotone
Packaged: 2013-05-23 22:28:03 UTC; smankad
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-24 07:38:34

More information about twostageTE at CRAN
Permanent link

Package bayesTFR updated to version 4.0-0 with previous version 3.0-8 dated 2013-04-06

Title: Bayesian Fertility Projection
Description: Making probabilistic projections of total fertility rate for all countries of the world, using a Bayesian hierarchical model.
Author: Hana Sevcikova , Leontine Alkema , Adrian Raftery with code contribution from Bailey Fosdick and Patrick Gerland
Maintainer: Hana Sevcikova

Diff between bayesTFR versions 3.0-8 dated 2013-04-06 and 4.0-0 dated 2013-05-24

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Thu, 23 May 2013

Package visreg updated to version 2.0-0 with previous version 1.2-1 dated 2013-02-21

Title: Visualization of regression models
Description: Provides convenient interface for constructing plots to visualize the fit of regression models arising from a wide variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny

Diff between visreg versions 1.2-1 dated 2013-02-21 and 2.0-0 dated 2013-05-23

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Package RCA updated to version 1.4 with previous version 1.3.2 dated 2013-04-03

Title: Relational Class Analysis
Description: Relational Class Analysis (RCA) is a method for detecting heterogeneity in attitudinal data. (as described in Goldberg A., 2011, Am. J. Soc, 116(5)) . src/ also contains the source files of igraph-C which was written by Gabor.
Author: Amir Goldberg , Gabor Csardi , Jinjian Zhai
Maintainer: Yuan Wang

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Package SKAT updated to version 0.90 with previous version 0.83 dated 2013-05-09

Title: SNP-set (Sequence) Kernel Association Test
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee

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Package MALDIquant updated to version 1.7 with previous version 1.6 dated 2013-03-01

Title: Quantitative Analysis of Mass Spectrometry Data
Description: MALDIquant provides a complete analysis pipeline for MALDI-TOF and other mass spectrometry data. Distinctive features include baseline subtraction methods such as TopHat or SNIP, peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Author: Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb

Diff between MALDIquant versions 1.6 dated 2013-03-01 and 1.7 dated 2013-05-23

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Package mRMRe updated to version 2.0.2 with previous version 2.0.0 dated 2013-04-16

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 mixsmsn updated to version 1.0-8 with previous version 1.0-7 dated 2013-05-02

Title: Fitting finite mixture of scale mixture of skew-normal distributions .
Description: Functions to fit finite mixture of scale mixture of skew-normal (FM-SMSN) distributions.
Author: Marcos Prates , Victor Lachos and Celso Cabral
Maintainer: Marcos Prates

Diff between mixsmsn versions 1.0-7 dated 2013-05-02 and 1.0-8 dated 2013-05-23

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New package InferenceSMR with initial version 1.0
Package: InferenceSMR
Type: Package
Title: Inference about the standardized mortality ratio when evaluating the effect of a screening program on survival.
Version: 1.0
Date: 2013-05-22
Author: Denis Talbot, Thierry Duchesne, Jacques Brisson, Nathalie Vandal
Maintainer: Denis Talbot
Description: The InferenceSMR package provides functions to make inference about the standardized mortality ratio (SMR) when evaluating the effect of a screening program. The package is based on methods described in Sasieni (2003) and Talbot et al. (2011).
License: GPL (>= 2)
Depends: survival
Packaged: 2013-05-23 14:10:09 UTC; Nilidas
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-23 17:41:26

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Package igraph updated to version 0.6.5-2 with previous version 0.6.5-1 dated 2013-02-28

Title: Network analysis and visualization
Description: Routines for simple graphs and network analysis. igraph can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality indices and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi

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Package gamlss updated to version 4.2-4 with previous version 4.2-0 dated 2012-09-29

Title: Generalised Additive Models for Location Scale and Shape.
Description: The library for fitting GAMLSS models.
Author: Mikis Stasinopoulos , Bob Rigby with contributions from Calliope Akantziliotou and Vlasios Voudouris
Maintainer: Mikis Stasinopoulos

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 gamlss-4.2-4/gamlss/man/term.plot.Rd            |  166 +--
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Package fastcluster updated to version 1.1.11 with previous version 1.1.10 dated 2013-05-23

Title: Fast hierarchical clustering routines for R and Python
Description: This is a two-in-one package which provides interfaces to both R and Python. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: “linkage” in the SciPy package “scipy.cluster.hierarchy”, “hclust” in R's “stats” package, and the “flashClust” package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the Python files, see the file INSTALL in the source distribution.
Author: Daniel Müllner, http://math.stanford.edu/~muellner
Maintainer: Daniel Müllner

Diff between fastcluster versions 1.1.10 dated 2013-05-23 and 1.1.11 dated 2013-05-23

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 INSTALL                    |    2 +-
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 inst/doc/fastcluster.pdf   |binary
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 11 files changed, 64 insertions(+), 48 deletions(-)

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Package cplexAPI updated to version 1.2.9 with previous version 1.2.6 dated 2013-01-23

Title: R Interface to C API of IBM ILOG CPLEX
Description: R Interface to C API of IBM ILOG CPLEX, depends on IBM ILOG CPLEX (>= 12.1)
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

Diff between cplexAPI versions 1.2.6 dated 2013-01-23 and 1.2.9 dated 2013-05-23

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 NAMESPACE                 |    5 +
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New package SODC with initial version 1.0
Package: SODC
Type: Package
Title: Optimal Discriminant Clustering(ODC) and Sparse Optimal Discriminant Clustering(SODC)
Version: 1.0
Date: 2013-05-15
Author: Yanhong Wang
Maintainer: Yanhong Wang
Description: To implement two clustering methods, ODC and SODC, for clustering datasets using optimal scoring, can also be used as an dimension reduction tool.
License: GPL-2
Depends: magic,ppls,psych,MASS
Packaged: 2013-05-23 13:34:01 UTC; matyxwx
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-23 15:53:51

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Package RMAWGEN updated to version 1.2.5.5 with previous version 1.2.5.4 dated 2013-04-24

Title: RMAWGEN (R Multi-site Auto-regressive Weather GENerator), a package to generate daily time series of precipitation and temperature from monthly mean values
Description: This package contains S3 and S4 functions for spatial multi-site stochastic generation of daily time series of temperature and precipitation. The implemented tools make use of Vector AutoRegressive models (VARs). The VAR is calibrated by daily instrumental "Gaussianized" time series and then works with monthly time series as input. Bugs/comments/questions/collaboration of any kind are warmly welcome.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano

Diff between RMAWGEN versions 1.2.5.4 dated 2013-04-24 and 1.2.5.5 dated 2013-05-23

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 R/VAR_mod.R                                           |    2 
 R/WhereIs.R                                           |    2 
 R/acvWGEN.R                                           |    2 
 R/adddate.R                                           |    2 
 R/addsuffixes.R                                       |    4 
 R/arch_test.varest2.R                                 |    4 
 R/continuity_ratio.R                                  |    2 
 R/countNAs.R                                          |    2 
 R/covariance.R                                        |    6 
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 83 files changed, 436 insertions(+), 374 deletions(-)

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Package missMDA updated to version 1.7.1 with previous version 1.7 dated 2013-03-30

Title: Handling missing values with/in multivariate data analysis (principal component methods)
Description: Imputation of incomplete continuous or categorical datasets; Missing values are imputed with a principal component analysis (PCA), a multiple correspondence analysis (MCA) model or a multiple factor analysis (MFA) model; Perform multiple imputation with and in PCA
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson

Diff between missMDA versions 1.7 dated 2013-03-30 and 1.7.1 dated 2013-05-23

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Package geigen updated to version 1.1 with previous version 1.0 dated 2013-05-15

Title: Calculate generalized eigenvalues of a matrix pair
Description: Compute generalized eigenvalues and eigenvectors of a pair of matrices, using routines from Lapack (dggev and zggev). Compute the generalized Schur decomposition of a pair of matrices using Lapack routines. In the latter case options for ordering the generalized eigenvalues are provided.
Author: Berend Hasselman
Maintainer: Berend Hasselman

Diff between geigen versions 1.0 dated 2013-05-15 and 1.1 dated 2013-05-23

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Package MPTinR updated to version 1.1.8 with previous version 1.0.1 dated 2013-02-07

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 specified in external files or within an R script in an intuitive syntax. 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 generating from a model for e.g., parametric bootstrap and plot predicted versus observed data.
Author: Henrik Singmann, David Kellen, and Christian Mueller
Maintainer: Henrik Singmann

Diff between MPTinR versions 1.0.1 dated 2013-02-07 and 1.1.8 dated 2013-05-23

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Package metrumrg updated to version 5.49 with previous version 5.45 dated 2013-05-01

Title: Pharmacometric tools for data preparation, modeling, simulation, and reporting
Description: Pharmacometric tools for common data preparation tasks, stratified bootstrap resampling of data sets, NONMEM control stream creation/editing, NONMEM model execution, creation of standard and user-defined diagnostic plots, execution and summary of bootstrap and predictive check results, implementation of simulations from posterior parameter distributions, reporting of output tables and creation of detailed analysis logs.
Author: Tim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Maintainer: Tim Bergsma

Diff between metrumrg versions 5.45 dated 2013-05-01 and 5.49 dated 2013-05-23

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Package glpkAPI updated to version 1.2.7 with previous version 1.2.6 dated 2013-02-12

Title: R Interface to C API of GLPK
Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

Diff between glpkAPI versions 1.2.6 dated 2013-02-12 and 1.2.7 dated 2013-05-23

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Package clpAPI updated to version 1.2.3 with previous version 1.2.2 dated 2013-01-16

Title: R Interface to C API of COIN-OR Clp
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR Clp Version >= 1.12.0
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich

Diff between clpAPI versions 1.2.2 dated 2013-01-16 and 1.2.3 dated 2013-05-23

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More information about clpAPI at CRAN
Permanent link

Package coloc updated to version 2.0 with previous version 1.11 dated 2013-01-25

Title: Colocalisation tests of two genetic traits
Description: Performs the colocalisation tests described in Plagnol et al (2009), Wallace et al (2013) and Giambartolomei et al (2013).
Author: Chris Wallace, with contributions from Claudia Giambartolemei
Maintainer: Chris Wallace

Diff between coloc versions 1.11 dated 2013-01-25 and 2.0 dated 2013-05-23

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Package Haplin updated to version 5.3 with previous version 5.2 dated 2013-05-02

Title: Analyzing case-parent triad and/or case-control data with SNP haplotypes
Description: Haplin performs a genetic association analysis of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. Haplin estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. Haplin also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. Haplin allows special models, like X-inactivation, to be fitted on the X-chromosome.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing

Diff between Haplin versions 5.2 dated 2013-05-02 and 5.3 dated 2013-05-23

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Package timereg updated to version 1.7.6 with previous version 1.7.5 dated 2013-05-02

Title: Flexible regression models for survival data.
Description: Programs for Martinussen and Scheike (2006), `Dynamic Regression Models for Survival Data', Springer Verlag. Plus more recent developments. Additive survival model, semiparametric proportional odds model, cumulative residuals, excess risk models and more. Flexible competing risks regression including GOF-tests. Two-stage frailty modelling. PLS for the additive risk model. Lasso in ahaz package.
Author: Thomas Scheike with contributions from Torben Martinussen and Jeremy Silver
Maintainer: Thomas Scheike

Diff between timereg versions 1.7.5 dated 2013-05-02 and 1.7.6 dated 2013-05-23

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 src/aalen.c              |  104 +++-
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 21 files changed, 993 insertions(+), 755 deletions(-)

More information about timereg at CRAN
Permanent link

Package strvalidator updated to version 0.2.0 with previous version 0.1 dated 2013-03-11

Title: Internal validation of forensic STR kits made easy with strvalidator.
Description: strvalidator provide tools that make it easier to perform an internal validation of a forensic short tandem repeat (STR) kit for human identification. The tools are developed to provide all necessary data to conform with the ENFSI guidelines for internal validation. More information about each function can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson

Diff between strvalidator versions 0.1 dated 2013-03-11 and 0.2.0 dated 2013-05-23

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 99 files changed, 1502 insertions(+), 642 deletions(-)

More information about strvalidator at CRAN
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Package spTimer updated to version 0.7 with previous version 0.6 dated 2013-03-01

Title: Spatio-Temporal Bayesian Modelling Using R
Description: The package is able to fit, spatially predict and temporally forecast large amounts of space-time data using [1] Bayesian Gaussian Process (GP) Models, [2] Bayesian Auto-Regressive (AR) Models, and [3] Bayesian Gaussian Predictive Processes (GPP) based AR Models.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Khandoker Shuvo Bakar

Diff between spTimer versions 0.6 dated 2013-03-01 and 0.7 dated 2013-05-23

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 25 files changed, 305 insertions(+), 219 deletions(-)

More information about spTimer at CRAN
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Package pcrsim updated to version 0.1.1 with previous version 0.1 dated 2013-04-06

Title: Simulation of the forensic DNA process
Description: pcrsim is a package for simulating the forensic DNA process. pcrsim() opens up a graphical user interface which allow the user to enter parameters required for the simulation. Once calibrated the program can be used to: reduce the laboratory work needed for validation of new STR kits, help develop methods for interpretation of DNA evidence, etc. This is a first version which is still experimental and under development.
Author: Oskar Hansson
Maintainer: Oskar Hansson

Diff between pcrsim versions 0.1 dated 2013-04-06 and 0.1.1 dated 2013-05-23

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 12 files changed, 66 insertions(+), 51 deletions(-)

More information about pcrsim at CRAN
Permanent link

Package MKmisc updated to version 0.94 with previous version 0.93 dated 2013-02-17

Title: Miscellaneous Functions from M. Kohl
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl
Maintainer: Matthias Kohl

Diff between MKmisc versions 0.93 dated 2013-02-17 and 0.94 dated 2013-05-23

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More information about MKmisc at CRAN
Permanent link

Package knitcitations updated to version 0.4-7 with previous version 0.4-4 dated 2013-03-18

Title: Citations for knitr markdown files
Description: knitcitations provides the ability to create dynamic citations in which the bibliographic information is pulled from the web rather than having to be entered into a local database such as bibtex ahead of time. Knitcitations is primarily aimed at authoring in the R markdown format, and can provide outputs for web-based authoring such as linked text and tooltips over inline citations. Cite using a DOI, URL, or bibtex file key. See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger

Diff between knitcitations versions 0.4-4 dated 2013-03-18 and 0.4-7 dated 2013-05-23

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More information about knitcitations at CRAN
Permanent link

Package fastcluster updated to version 1.1.10 with previous version 1.1.9 dated 2013-03-17

Diff between fastcluster versions 1.1.9 dated 2013-03-17 and 1.1.10 dated 2013-05-23

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More information about fastcluster at CRAN
Permanent link

Package DCGL updated to version 2.0.1 with previous version 2.0 dated 2013-03-28

Title: Differential Co-expression Analysis and Differential Regulation Analysis of Gene Expression Microarray Data
Description: Functions for 1) gene filtration; 2) link filtration; 3) differential co-expression analysis: DCG (Differential Coexpressed Gene) identification and DCL (Differentially Coexpressed Link) identification; and 4) differential regulation analysis: DRG (Differential Regulated Gene) identification, DRL (Differential Regulated Link) identification, DRL visualization and regulator ranking.
Author: Jing Yang, Hui Yu, Bao-Hong Liu
Maintainer: Bao-Hong Liu

Diff between DCGL versions 2.0 dated 2013-03-28 and 2.0.1 dated 2013-05-23

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More information about DCGL at CRAN
Permanent link

Wed, 22 May 2013

Package phytools updated to version 0.2-70 with previous version 0.2-50 dated 2013-04-20

Title: Phylogenetic Tools for comparative biology (and other things)
Description: phytools provides various functions for phylogenetic analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell

Diff between phytools versions 0.2-50 dated 2013-04-20 and 0.2-70 dated 2013-05-22

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Package wq updated to version 0.3-9 with previous version 0.3-8 dated 2012-09-09

Title: Exploring water quality monitoring data
Description: Functions to assist in the processing and exploration of data from monitoring programs for aquatic ecosystems. The name "wq" stands for "water quality" and reflects a focus on time series data for physical and chemical properties of water, as well as the plankton. The package is intended for programs that sample approximately monthly at discrete stations, a feature of many legacy data sets. Although our emphasis is on aquatic ecosystems, most of the functions should be useful for analysis of similar-frequency time series regardless of the subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby

Diff between wq versions 0.3-8 dated 2012-09-09 and 0.3-9 dated 2013-05-22

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New package SnowballC with initial version 0.5
Package: SnowballC
Type: Package
Version: 0.5
Date: 2013-05-22
Title: Snowball stemmers based on the C libstemmer UTF-8 library
Authors@R: person("Milan", "Bouchet-Valat", email="nalimilan@club.fr", role=c("aut", "cre"))
Description: An R interface to the C libstemmer library that implements Porter's word stemming algorithm for collapsing words to a common root to aid comparison of vocabulary. Currently supported languages are Danish, Dutch, English, Finnish, French, German, Hungarian, Italian, Norwegian, Portuguese, Romanian, Russian, Spanish, Swedish and Turkish.
License: BSD
Copyright: Dr Martin Porter (2001) for the libstemmer C library, and Milan Bouchet-Valat (2013) for the R package contents
URL: https://r-forge.r-project.org/projects/r-temis/
BugReports: https://r-forge.r-project.org/tracker/?group_id=1437
Packaged: 2013-05-22 12:55:04 UTC; milan
Author: Milan Bouchet-Valat [aut, cre]
Maintainer: Milan Bouchet-Valat
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-22 18:27:08

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Package parallelize.dynamic updated to version 0.9-1 with previous version 0.9 dated 2013-05-08

Title: Automate parallelization of function calls by means of dynamic code analysis
Description: Passing a given function name or a call to the parallelize/parallelize_call functions analyses and executes the code, if possible in parallel. Parallel code execution can be performed locally or on remote batch queuing systems.
Author: Stefan Boehringer
Maintainer: Stefan Boehringer

Diff between parallelize.dynamic versions 0.9 dated 2013-05-08 and 0.9-1 dated 2013-05-22

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Package longpower updated to version 1.0-7 with previous version 1.0-4 dated 2013-01-23

Title: Sample size calculations for longitudinal data
Description: The longpower package contains functions for computing power and sample size for linear models of longitudinal data based on the formula due to Liu and Liang (1997) and Diggle et al (2002). Either formula is expressed in terms of marginal model or Generalized Estimating Equations (GEE) parameters. This package contains functions which translate pilot mixed effect model parameters (e.g. random intercept and/or slope) into marginal model parameters so that the formulas of Diggle et al or Liu and Liang formula can be applied to produce sample size calculations for two sample longitudinal designs assuming known variance.
Author: Michael C. Donohue, Anthony C. Gamst, Steven D. Edland
Maintainer: Michael C. Donohue

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New package epibase with initial version 0.1-0
Package: epibase
Version: 0.1-0
Date: 2013/01/11
Title: basic tools for the analysis of disease outbreaks.
Author: {The Hackout team (In alphabetic order: David Aanensen, Marc Baguelin, Paul Birrell, Simon Cauchemez, Anton Camacho, Caroline Colijn, Anne Cori, Xavier Didelot, Ken Eames, Christophe Fraser, Simon Frost, Niel Hens, Joseph Hugues, Thibaut Jombart, Lulla Opatowski, Oliver Ratmann, Samuel Soubeyrand, Marc Suchard, Jacco Wallinga, Rolf Ypma)}
Maintainer: Thibaut Jombart
Suggests: EpiEstim
Depends: R (>= 2.10), methods, MASS, ape, adegenet, network, networkDynamic, ggplot2, ggmap, sna, scales, plyr, reshape2, mapproj, RColorBrewer, knitr
Description: basic tools for the analysis of disease outbreaks.
License: GPL (>= 2)
LazyLoad: yes
VignetteBuilder: knitr
Collate: 'auxClasses.R' 'generics.R' 'obkContacts.R' 'obkSequences.R' 'obkData.R' 'obkData_Accessors.R' 'subset.R' 'obkData_basics.R' 'uniqSequences.R' 'dna2uniqSequences.R' 'make.phylo.R' 'phylo2ggphy.R' 'plotggMST.R' 'plotggphy.R' 'plot.R' 'plotIndividualTimeline.R' 'simuEpi.R' 'utils.R' 'plotGeo.R' 'annotatedTreeReader.R' 'zzz.R' 'epibase.R'
Packaged: 2013-05-22 15:09:24 UTC; thibaut
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-22 18:34:00

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Package diveRsity updated to version 1.5.0 with previous version 1.4.6 dated 2013-04-01

Title: Genetic diversity partition statistics and Informative locus selection using Fst, Gst, Dest(Jost Chao) G'st and In.
Description: diveRsity is a package which allows the calculation of both genetic diversity partition statistics, genetic differentiation statistics and locus informativeness for ancestry assignment. It also provides users with various option to calculate bootstrapped 95% confidence intervals both across loci, for pairwise population comparisons and to plot these results interactively. V1.2 and up provides parallel computing capabilities and pairwise results without bootstrapping. Weir and Cockerham's 1984 F-statistics are now also calculated. Various plotting features are also provided. Chi-square tests of genetic heterogeneity are also provided. Functionality for the calculation of various diversity parameters is also possible for RAD-seq derived SNP data sets containing thousands of marker loci.
Author: Kevin Keenan,
Maintainer: Kevin Keenan

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Package BayesLogit updated to version 0.2-4 with previous version 0.2-2 dated 2013-05-07

Title: Logistic Regression
Description: The BayesLogit package does posterior simulation for binomial and multinomial logistic regression using the Polya-Gamma latent variable technique. This method is fully automatic, exact, and fast. A routine to efficiently sample from the Polya-Gamma class of distributions is included.
Author: Nicholas G. Polson, James G. Scott, and Jesse Windle
Maintainer: Jesse Windle

Diff between BayesLogit versions 0.2-2 dated 2013-05-07 and 0.2-4 dated 2013-05-22

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Package mets updated to version 0.2.3 with previous version 0.2.2 dated 2013-05-21

Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate event history data. Including multivariate cumulative incidence models, and bivariate random effects probit models (Liability models)
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst

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New package BSquare with initial version 1.0
Package: BSquare
Type: Package
Title: Bayesian Simultaneous Quantile Regression
Version: 1.0
Date: 2013-05-04
Author: Luke Smith & Brian Reich
Maintainer: Luke Smith
Depends: quadprog, quantreg, VGAM
Suggests: survival
Description: This package models the quantile process as a function of predictors.
License: GPL (>= 2)
Packaged: 2013-05-23 15:53:32 UTC; smithinger
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-22 17:07:20

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Package adephylo updated to version 1.1-4 with previous version 1.1-3 dated 2012-10-31

Title: adephylo: exploratory analyses for the phylogenetic comparative method.
Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
Author: Thibaut Jombart , Stephane Dray
Maintainer: Thibaut Jombart

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Package SNPRelate updated to version 0.9.14 with previous version 0.9.13 dated 2013-02-26

Title: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)
Description: A High-performance computing toolset for relatedness and principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng

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Package recluster updated to version 2.1 with previous version 1.9 dated 2013-03-29

Title: Solving biasing produced by tied values in cluster analysis.
Description: A high frequency of ties and zero values produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. The recluster package evaluates the magnitude of this bias and computes consensus trees after re-sampling the original row order also applying this algorithm to a multiscale bootstrap procedure.
Author: Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger Vila, Gerard Talavera, Roger H.L. Dennis
Maintainer: Leonardo Dapporto

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Package CompRandFld updated to version 1.0.3 with previous version 1.0.2 dated 2012-04-13

Title: Composite-likelihood based Analysis of Random Fields
Description: The aim of this package is to collect a set of procedures for the analysis of Random Fields by Composite Likelihood methods. Spatial analysis often involves dealing with large dataset. Therefore even simple studies may be too computationally demanding. Composite likelihood based methods are emerging as useful tools for mitigating such computational problems and show satisfactory results when compared with other techniques such as, for example the tapering method. Moreover, composite likelihood (and related quantities) have some good properties similar to those of the standard likelihood.
Author: Simone Padoan , Moreno Bevilacqua
Maintainer: Simone Padoan

Diff between CompRandFld versions 1.0.2 dated 2012-04-13 and 1.0.3 dated 2013-05-22

 CompRandFld-1.0.2/CompRandFld/R/zzz.r                         |only
 CompRandFld-1.0.3/CompRandFld/DESCRIPTION                     |   22 
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Package visualize updated to version 4.1 with previous version 3.0 dated 2013-02-15

Title: Graph Probability Distributions with User Supplied Parameters and Stats.
Description: Graphs the pdf or pmf and highlights what area or probability is present in user defined locations. Visualize is able to provide lower tail, bounded, upper tail, and two tail calculations. Supports strict and equal to inequalities. Also provided on the graph is the mean and variance of the distribution.
Author: James Balamuta
Maintainer: James Balamuta

Diff between visualize versions 3.0 dated 2013-02-15 and 4.1 dated 2013-05-22

 DESCRIPTION                 |   10 ++---
 MD5                         |   50 ++++++++++++++---------------
 R/visualize.continuous.R    |   74 +++++++++++++++++++++++++++++++++-----------
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 26 files changed, 188 insertions(+), 103 deletions(-)

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New package trueskill with initial version 0.1
Package: trueskill
Title: Implementation the TrueSkill algorithm in R
Description: An implementation of the TrueSkill algorithm (Herbrich, R., Minka, T. and Grapel, T) in R; a Bayesian skill rating system with inference by approximate message passing on a factor graph. Used by Xbox to rank gamers and identify appropriate matches. http://research.microsoft.com/en-us/projects/trueskill/default.aspx Current version allows for one player per team. Will update as time permits. Requires R version 3.0 as it is written with Reference Classes. URL: https://github.com/bhoung/trueskill-in-r Acknowledgements to Doug Zongker and Heungsub Lee for their python implementations of the algorithm and for the liberal reuse of Doug's code comments (@dougz and @sublee on github).
Version: 0.1
Author: Brendan Houng
Maintainer: Brendan Houng
License: GPL-3
Depends: R (>= 3.0)
Imports: methods
Collate: 'factorgraph.r' 'init.r' 'competition.r' 'player.r'
Packaged: 2013-05-22 05:32:15 UTC; brendanhoung
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-22 08:00:08

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New package support.BWS with initial version 0.1-0
Package: support.BWS
Type: Package
Title: Basic functions for supporting an implementation of best-worst scaling
Version: 0.1-0
Date: 2013-05-21
Author: Hideo Aizaki
Maintainer: Hideo Aizaki
Description: This package provides three basic functions that support an implementation of object case (Case 1) best-worst scaling: one for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; one for creating a data set suitable for analysis; and one for calculating count-based scores.
License: GPL (>= 2)
Suggests: DoE.base, crossdes, survival
Packaged: 2013-05-21 23:49:34 UTC; user
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-22 07:47:15

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Package PopGenReport updated to version 1.01 with previous version 0.96 dated 2012-11-28

Title: PopGen: A simple way to analyse and visualize population genetic data
Description: This package provides an easy way to analyse population genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber,

Diff between PopGenReport versions 0.96 dated 2012-11-28 and 1.01 dated 2013-05-22

 DESCRIPTION                            |   12 
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New package OPDOE with initial version 1.0-6
Package: OPDOE
Version: 1.0-6
Title: OPtimal Design Of Experiments
Author: Petr Simecek , Juergen Pilz Mingui Wang , Albrecht Gebhardt .
Maintainer: Albrecht Gebhardt
Description: Experimental Design
Depends: orthopolynom, conf.design, mvtnorm, nlme, gmp, crossdes
License: GPL (>= 2)
Packaged: 2013-05-22 05:19:35 UTC; alge
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-22 07:53:44

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Package growcurves updated to version 0.2.3.5 with previous version 0.2.3.4 dated 2013-03-16

Title: Bayesian semi and nonparametric growth curve models that additionally include multiple membership random effects.
Description: Employs a non-parametric formulation for by-subject random effect parameters to borrow strength over a constrained number of repeated measurement waves in a fashion that permits multiple effects per subject. One class of models employs a Dirichlet process (DP) prior for the subject random effects and includes an additional set of random effects that utilize a different grouping factor and are mapped back to clients through a multiple membership weight matrix; e.g. treatment(s) exposure or dosage. A second class of models employs a dependent DP (DDP) prior for the subject random effects that directly incorporates the multiple membership pattern.
Author: Terrance Savitsky
Maintainer: "terrance savitsky"

Diff between growcurves versions 0.2.3.4 dated 2013-03-16 and 0.2.3.5 dated 2013-05-22

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 17 files changed, 274 insertions(+), 160 deletions(-)

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New package cyphid with initial version 1.1
Package: cyphid
Type: Package
Title: Cycle and Phase Identification for mastication data
Version: 1.1
Date: 2013-04-04
Author: Elizabeth Crane
Maintainer: Elizabeth Crane
Depends: fda
Description: This library contains a primary function that divides chewing sequences in cycles and cycles into phases. See get.all.breaks for an example.
License: GPL (>= 2)
LazyLoad: yes
LazyData: yes
Packaged: 2013-05-22 02:56:31 UTC; bcrane
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-22 07:52:43

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Package biom updated to version 0.3.9 with previous version 0.3.8 dated 2013-04-29

Title: An interface package (beta) for the BIOM file format.
Description: This is an R package for interfacing with the BIOM format. Currently in beta form, this package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.
Author: Paul J. McMurdie and the biom-format team http://biom-format.org/
Maintainer: Paul J. McMurdie

Diff between biom versions 0.3.8 dated 2013-04-29 and 0.3.9 dated 2013-05-22

 DESCRIPTION    |   12 ++++++------
 MD5            |    7 ++++---
 R/BIOM-class.R |   32 ++++++++++++++++++--------------
 R/allPackage.R |    2 +-
 inst/NEWS      |only
 5 files changed, 29 insertions(+), 24 deletions(-)

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Tue, 21 May 2013

New package SphericalCubature with initial version 1.0
Package: SphericalCubature
Type: Package
Title: Numerical integration over spheres and balls in n-dimensions; multivariate polar coordinates
Version: 1.0
Date: 2013-05-16
Author: John P. Nolan, American University
Maintainer: John P. Nolan
Depends: R (>= 2.1.15), cubature
Description: This package defines several methods to integrate functions over the unit sphere and ball in n-dimensional Euclidean space. Routines for converting to/from multivariate polar/spherical coordinates are also provided.
License: GPL (>= 2)
Packaged: 2013-05-21 17:56:00 UTC; jpnolan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-21 22:45:58

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Package mets updated to version 0.2.2 with previous version 0.2.1 dated 2013-04-24

Diff between mets versions 0.2.1 dated 2013-04-24 and 0.2.2 dated 2013-05-21

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Package rPlant updated to version 2.7 with previous version 2.3 dated 2013-03-12

Title: R interface to the iPlant Discovery Environment
Description: rPlant is an R interface to the the many computational resources iPlant offers through their RESTful application programming interface. Currently, rPlant functions interact with the iPlant foundational API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using rPlant, users will have to register with the iPlant Collaborative. http://www.iplantcollaborative.org/discover/discovery-environment
Author: Barb Banbury , Kurt Michels , Jeremy M. Beaulieu , Brian O'Meara
Maintainer: Barb Banbury

Diff between rPlant versions 2.3 dated 2013-03-12 and 2.7 dated 2013-05-21

 DESCRIPTION            |   15 --
 MD5                    |   52 +++----
 R/RunClustal.R         |   17 +-
 R/RunMafft.R           |   17 +-
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 27 files changed, 480 insertions(+), 263 deletions(-)

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Package lava updated to version 1.2.1 with previous version 1.2.0 dated 2013-04-24

Title: Linear Latent Variable Models
Description: Estimation and simulation of latent variable models
Author: Klaus K. Holst
Maintainer: Klaus K. Holst

Diff between lava versions 1.2.0 dated 2013-04-24 and 1.2.1 dated 2013-05-21

 lava-1.2.0/lava/simulate.R                   |only
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Package FastImputation updated to version 1.1 with previous version 1.0 dated 2012-04-10

Title: Learn from training data then quickly fill in missing data.
Description: TrainFastImputation uses training data to describe a multivariate normal distribution that the data approximates or can be transformed into approximating and stores this information as an object of class FastImputationPatterns. The FastImputation function uses this FastImputationPatterns object to impute (make a good guess at) missing data in a single line or a whole dataframe of data. This approximates the process used by Amelia [http://gking.harvard.edu/amelia/] but is much faster when filling in values for a single line of data.
Author: Stephen R. Haptonstahl
Maintainer: Stephen R. Haptonstahl

Diff between FastImputation versions 1.0 dated 2012-04-10 and 1.1 dated 2013-05-21

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Package ecp updated to version 1.5.3 with previous version 1.5.2 dated 2013-02-08

Title: Nonparametric Multiple Change Point Analysis of Multivariate Data
Description: This package performs hierarchical change point analysis through the use of U-statistics. Both agglomerative and divisive procedures return the set of change points estimates, and other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James

Diff between ecp versions 1.5.2 dated 2013-02-08 and 1.5.3 dated 2013-05-21

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New package hint with initial version 0.1-0
Package: hint
Type: Package
Title: Tools for hypothesis testing based on Hypergeometric Intersection distributions
Version: 0.1-0
Date: 2013-05-16
Author: Alex T. Kalinka
Maintainer: Alex T. Kalinka
Description: Hypergeometric Intersection distributions are a broad group of distributions that describe the probability of picking intersections when drawing independently from two (or more) urns containing variable numbers of balls belonging to the same n categories.
License: GPL (>= 2)
LazyLoad: yes
Packaged: 2013-05-21 12:17:26 UTC; alexk
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-21 16:51:44

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Package geospacom updated to version 0.5-6 with previous version 0.5-4 dated 2013-03-17

Title: Helper package to facilitate the generation of distance matrices used in the package spacom.
Description: Generates distance matrices from shape files and represents spatially weighted multilevel analysis results (see spacom)
Author: Davide Morselli [aut], Mathieu Cossuta [aut, cre], Till Junge [aut], Sandra Penic [aut], Guy Elcheroth [ctb], Stephanie Glaeser [ctb]
Maintainer: Davide Morselli

Diff between geospacom versions 0.5-4 dated 2013-03-17 and 0.5-6 dated 2013-05-21

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New package gazetools with initial version 3.0
Package: gazetools
Type: Package
Title: Gaze Tools
Version: 3.0
Date: 2013-05-21
Author: Ryan M. Hope
Maintainer: Ryan M. Hope
URL: http://ryanhope.github.io/gazetools
BugReports: https://github.com/RyanHope/gazetools/issues
Description: A collection of tools for processing and classifying eye gaze data.
License: GPL-3
LazyData: true
Enhances: sp, ggplot2
Depends: R (>= 2.14), Matrix, methods,
Imports: rgeos, maptools, deldir, sp, modeest, signal, zoo, Rmisc, reshape, plyr, spatstat, ggplot2
Collate: 'event_ids.R' 'distance2point.R' 'subtendedAngle.R' 'angle2pixels.R' 'local_maxima.R' 'find_peak_ranges.R' 'find_peaks.R' 'pva.R' 'classify.R' 'classify.V.R' 'classify.VA.R' 'classify.VI.R' 'mould.R' 'mouldThreshold.R' 'voronoi.R' 'chull_area.R' 'nni.R' 'bcea.R' 'gridded_rois.R' 'roi_coverage.R' 'gazetools.R' 'extent.R' 'pva-methods.R' 'classify-methods.R' 'mould-methods.R'
Packaged: 2013-05-21 14:11:59 UTC; ryanhope
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-21 16:53:01

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Package exactRankTests updated to version 0.8-25 with previous version 0.8-24 dated 2013-01-12

Title: Exact Distributions for Rank and Permutation Tests
Description: Computes exact conditional p-values and quantiles using an implementation of the Shift-Algorithm by Streitberg & Roehmel.
Author: Torsten Hothorn and Kurt Hornik
Maintainer: Torsten Hothorn

Diff between exactRankTests versions 0.8-24 dated 2013-01-12 and 0.8-25 dated 2013-05-21

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New package SetMethods with initial version 1.0
Package: SetMethods
Type: Package
Title: SetMethods: A Package Companion to "Set-Theoretic Methods for the Social Sciences".
Version: 1.0
Date: 2013-05-17
Author: Mario Quaranta
Maintainer: Mario Quaranta
Description: SetMethods is a package companion to the book by C. Q. Schneider and C. Wagemann "Set-Theoretic Methods for the Social Sciences", Cambridge University Press. It contains some additional functions not present in other packages and data to replicate the examples in the book and in the online appendix.
Depends: lattice, betareg, R (>= 2.14.0)
Imports: lattice, betareg
License: GPL-2
Packaged: 2013-05-21 09:50:30 UTC; mario
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-05-21 14:52:42

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Package fwi.fbp updated to version 1.2 with previous version 1.01 dated 2012-10-30

Title: Fire Weather Index System and Fire Behaviour Prediction System Calculations
Description: This package provides three new functions to calculate the outputs of the two main components of the Canadian Forest Fire Danger Rating System (CFFDRS): the Fire Weather Index (FWI) System and the Fire Behaviour Prediction (FBP) System.
Author: Xianli Wang, Alan Cantin, Marc-Andre Parisien, Mike Wotton, Kerry Anderson, and Mike Flannigan
Maintainer: Alan Cantin

Diff between fwi.fbp versions 1.01 dated 2012-10-30 and 1.2 dated 2013-05-21

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Package copula updated to version 0.999-7 with previous version 0.999-6 dated 2013-05-14

Title: Multivariate Dependence with Copulas
Description: Classes (S4) of commonly used elliptical, Archimedean, extreme value and some more copula families. Methods for density, distribution, random number generation, bivariate dependence measures, perspective and contour plots. Fitting copula models including variance estimates. Independence and serial (univariate and multivariate) independence tests, and other copula related tests. Goodness-of-fit tests for copulas based on multipliers, the parametric bootstrap with several transformation options. Merged former package 'nacopula' for nested Archimedean copulas: Efficient sampling algorithms, various estimators, goodness-of-fit tests and related tools and special functions.
Author: Marius Hofert , Ivan Kojadinovic , Martin Maechler , and Jun Yan
Maintainer: Martin Maechler

Diff between copula versions 0.999-6 dated 2013-05-14 and 0.999-7 dated 2013-05-21

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Package miscFuncs updated to version 1.2-2 with previous version 1.2 dated 2012-06-14

Title: Miscellaneous Useful Functions
Description: LaTeX tables, Kalman filter, web scraping, development tools
Author: Benjamin M. Taylor
Maintainer: Benjamin M. Taylor

Diff between miscFuncs versions 1.2 dated 2012-06-14 and 1.2-2 dated 2013-05-21

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Package DataCombine updated to version 0.1.5 with previous version 0.1.3 dated 2013-05-16

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.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud

Diff between DataCombine versions 0.1.3 dated 2013-05-16 and 0.1.5 dated 2013-05-21

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Package fastICA updated to version 1.2-0 with previous version 1.1-16 dated 2012-05-21

Title: FastICA Algorithms to perform ICA and Projection Pursuit
Description: Implementation of FastICA algorithm to perform Independent Component Analysis (ICA) and Projection Pursuit.
Author: J L Marchini , C Heaton and B D Ripley
Maintainer: Brian Ripley

Diff between fastICA versions 1.1-16 dated 2012-05-21 and 1.2-0 dated 2013-05-21

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Package SharpeR updated to version 0.1306 with previous version 0.1305 dated 2013-05-11

Title: Statistical significance of Sharpe ratio
Description: a collection of tools for analyzing significance of trading strategies, based on the Sharpe ratio and overfit of the same.
Author: Steven E. Pav
Maintainer: Steven E. Pav

Diff between SharpeR versions 0.1305 dated 2013-05-11 and 0.1306 dated 2013-05-21

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New package overlap with initial version 0.1.0
Package: overlap
Type: Package
Title: Estimates of coefficient of overlapping for animal activity patterns
Version: 0.1.0
Date: 2013-05-21
Author: Mike Meredith and Martin Ridout
Maintainer: Mike Meredith
Description: Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
License: GPL (>= 3)
Packaged: 2013-05-21 04:06:09 UTC; MIKE
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-05-21 07:18:59

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Package MasterBayes updated to version 2.50.1 with previous version 2.50 dated 2012-07-15

Title: ML and MCMC Methods for Pedigree Reconstruction and Analysis
Description: The primary aim of MasterBayes is to use MCMC techniques to integrate over uncertainty in pedigree configurations estimated from molecular markers and phenotypic data. Emphasis is put on the marginal distribution of parameters that relate the phenotypic data to the pedigree. All simulation is done in compiled C++ for efficiency.
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield

Diff between MasterBayes versions 2.50 dated 2012-07-15 and 2.50.1 dated 2013-05-21

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Mon, 20 May 2013

Package xlsxjars updated to version 0.5.0 with previous version 0.4.0 dated 2012-04-16

Title: Package required POI jars for the xlsx package
Description: The xlsxjars package collects all the external jars required for the xlxs package. These external jars are quite large in size (15MB) and have a slow release cycle. By separating the Java and R development, the storage footprint on CRAN is reduced. This release corresponds to POI 3.9.
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu

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Package xlsx updated to version 0.5.1 with previous version 0.5.0 dated 2012-09-26

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

Diff between xlsx versions 0.5.0 dated 2012-09-26 and 0.5.1 dated 2013-05-20

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 xlsx-0.5.1/xlsx/R/read.xlsx2.R                                          |    4 
 xlsx-0.5.1/xlsx/R/readColumns.R                                         |    6 
 xlsx-0.5.1/xlsx/R/write.xlsx.R                                          |   12 
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 xlsx-0.5.1/xlsx/inst/tests/test_import.xlsx                             |binary
 xlsx-0.5.1/xlsx/man/Cell.Rd                                             |    6 
 xlsx-0.5.1/xlsx/man/read.xlsx.Rd                                        |   13 
 xlsx-0.5.1/xlsx/man/write.xlsx.Rd                                       |    5 
 xlsx-0.5.1/xlsx/man/xlsx-package.Rd                                     |   15 
 xlsx-0.5.1/xlsx/other/make.package.R                                    |   64 --
 xlsx-0.5.1/xlsx/other/pom.xml                                           |  297 +++++++---
 xlsx-0.5.1/xlsx/other/src/main/java/org/cran/rexcel/RInterface.java     |   12 
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 xlsx-0.5.1/xlsx/other/src/test/java/org/cran/rexcel/TestRCellBlock.java |    1 
 xlsx-0.5.1/xlsx/other/src/test/java/org/cran/rexcel/TestRInterface.java |   24 
 27 files changed, 431 insertions(+), 199 deletions(-)

More information about xlsx at CRAN
Permanent link

New package nloptwrap with initial version 0.5-1
Package: nloptwrap
Type: Package
Title: Wrapper for Package nloptr
Version: 0.5-1
Date: 2013-05-09
Author: Hans W Borchers
Maintainer: HwB
Depends: R (>= 2.11.1), nloptr
Description: Wraps functions in 'nloptr' for easier access and use.
License: LGPL
LazyLoad: yes
LazyData: yes
Repository: CRAN
Repository/R-Forge/Project: optimist
Repository/R-Forge/Revision: 300
Repository/R-Forge/DateTimeStamp: 2013-05-09 15:38:19
Date/Publication: 2013-05-20 22:26:16
Packaged: 2013-05-09 18:15:54 UTC; rforge
NeedsCompilation: no

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Package mgcv updated to version 1.7-23 with previous version 1.7-22 dated 2012-10-15

Title: Mixed GAM Computation Vehicle with GCV/AIC/REML smoothness estimation
Description: Routines for GAMs and other generalized ridge regression with multiple smoothing parameter selection by GCV, REML or UBRE/AIC. Also GAMMs. Includes a gam() function.
Author: Simon Wood
Maintainer: Simon Wood

Diff between mgcv versions 1.7-22 dated 2012-10-15 and 1.7-23 dated 2013-05-20

 DESCRIPTION                            |    7 -
 MD5                                    |   64 +++++-----
 NAMESPACE                              |    2 
 R/bam.r                                |    4 
 R/gam.fit3.r                           |   17 +-
 R/gamm.r                               |    6 
 R/mgcv.r                               |  163 +++++++++++++++-----------
 R/plots.r                              |   28 +++-
 R/smooth.r                             |  124 +++++++++++++-------
 R/soap.r                               |   21 +--
 changeLog                              |   61 ++++++++-
 man/anova.gam.Rd                       |    2 
 man/extract.lme.cov.Rd                 |    1 
 man/formXtViX.Rd                       |   15 ++
 man/formula.gam.Rd                     |   10 +
 man/gam.Rd                             |   14 +-
 man/gam.models.Rd                      |   34 ++---
 man/gam.side.Rd                        |   24 +++
 man/ldTweedie.Rd                       |    4 
 man/mgcv-package.Rd                    |    3 
 man/mroot.Rd                           |    4 
 man/smooth.construct.fs.smooth.spec.Rd |    4 
 man/smooth.construct.tp.smooth.spec.Rd |    6 
 man/smooth.terms.Rd                    |    7 -
 man/summary.gam.Rd                     |   10 -
 man/te.Rd                              |   35 +++--
 src/init.c                             |    2 
 src/mat.c                              |  203 +++++++++++++++++++++++++--------
 src/mgcv.c                             |    2 
 src/mgcv.h                             |    3 
 src/misc.c                             |    2 
 src/soap.c                             |    6 
 src/tprs.c                             |    4 
 33 files changed, 591 insertions(+), 301 deletions(-)

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Package RadialPlotter updated to version 1.6 with previous version 1.5 dated 2013-04-20

Title: Package for statistical age models analysis in optically stimulated luminescence dating
Description: Package for estimating parameters of statistical age models in optically stimulated luminescence dating dynamically.
Author: Peng Jun
Maintainer: Peng Jun

Diff between RadialPlotter versions 1.5 dated 2013-04-20 and 1.6 dated 2013-05-20

 DESCRIPTION                  |    8 
 MD5                          |   25 
 NEWS                         |    3 
 man/EDdata.Rd                |    1 
 man/RadialPlotter-package.Rd |    6 
 man/RadialPlotter.Rd         |    5 
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 src/fdhessian.f90            |  137 ++-
 src/gradient.f90             |   20 
 src/kmeans.f90               |    2 
 src/lbfgsb.f                 | 1560 ++++++++++++++-----------------------------
 src/linpack.f                |only
 src/pnorm.f90                |    8 
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 15 files changed, 675 insertions(+), 1102 deletions(-)

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Package iGenomicViewer (with last version 2.4.8) was removed from CRAN

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

2012-04-06 2.4.8
2009-11-17 2.4.6
2009-10-29 2.4.4
2009-09-18 2.4.2

Permanent link

Package SSDforR updated to version 1.2 with previous version 1.1 dated 2013-04-24

Title: SSD for R to analyze single system data
Description: Package to visually and statistically analyze single system data
Author: Charles Auerbach,PHD Wendy Zeitlin Schudrich,PHD Wurzweiler School of Social Work
Maintainer: Charles Auerbach

Diff between SSDforR versions 1.1 dated 2013-04-24 and 1.2 dated 2013-05-20

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 SSDforR-1.2/SSDforR/R/ABlineD.R           |    6 -
 SSDforR-1.2/SSDforR/R/ABlines.R           |    4 
 SSDforR-1.2/SSDforR/R/ABplot.R            |   12 +-
 SSDforR-1.2/SSDforR/R/ABstat.R            |    6 -
 SSDforR-1.2/SSDforR/R/ABtext.R            |    7 -
 SSDforR-1.2/SSDforR/R/ABtsplot.R          |    8 +
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 SSDforR-1.2/SSDforR/R/Trimline.R          |    5 
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 SSDforR-1.2/SSDforR/man/ABautoacf.Rd      |    3 
 SSDforR-1.2/SSDforR/man/ABautopacf.Rd     |    3 
 SSDforR-1.2/SSDforR/man/ABbinomial.Rd     |    3 
 SSDforR-1.2/SSDforR/man/ABdescrip.Rd      |    3 
 SSDforR-1.2/SSDforR/man/ABiqr.Rd          |    3 
 SSDforR-1.2/SSDforR/man/ABlineD.Rd        |    3 
 SSDforR-1.2/SSDforR/man/ABlines.Rd        |    3 
 SSDforR-1.2/SSDforR/man/ABma.Rd           |    3 
 SSDforR-1.2/SSDforR/man/ABplot.Rd         |    3 
 SSDforR-1.2/SSDforR/man/ABplotm.Rd        |    3 
 SSDforR-1.2/SSDforR/man/ABregres.Rd       |    3 
 SSDforR-1.2/SSDforR/man/ABrf2.Rd          |    3 
 SSDforR-1.2/SSDforR/man/ABrobust.Rd       |    3 
 SSDforR-1.2/SSDforR/man/ABstat.Rd         |    3 
 SSDforR-1.2/SSDforR/man/ABtext.Rd         |    3 
 SSDforR-1.2/SSDforR/man/ABtsplot.Rd       |    3 
 SSDforR-1.2/SSDforR/man/ABttest.Rd        |    3 
 SSDforR-1.2/SSDforR/man/Aregres.Rd        |    3 
 SSDforR-1.2/SSDforR/man/Arimadiff.Rd      |    3 
 SSDforR-1.2/SSDforR/man/Arimama.Rd        |    3 
 SSDforR-1.2/SSDforR/man/Arobust.Rd        |    3 
 SSDforR-1.2/SSDforR/man/Cchart.Rd         |    3 
 SSDforR-1.2/SSDforR/man/Effectsize.Rd     |    3 
 SSDforR-1.2/SSDforR/man/GABrf2.Rd         |    6 -
 SSDforR-1.2/SSDforR/man/GABttest.Rd       |   15 +-
 SSDforR-1.2/SSDforR/man/Gindex.Rd         |    3 
 SSDforR-1.2/SSDforR/man/Gmedian.Rd        |   24 ++--
 SSDforR-1.2/SSDforR/man/IQRbandgraph.Rd   |    5 
 SSDforR-1.2/SSDforR/man/IQRlegend.Rd      |    3 
 SSDforR-1.2/SSDforR/man/IQRline.Rd        |    3 
 SSDforR-1.2/SSDforR/man/PANDlegend.Rd     |    3 
 SSDforR-1.2/SSDforR/man/PEMabove.Rd       |    3 
 SSDforR-1.2/SSDforR/man/PEMbelow.Rd       |    3 
 SSDforR-1.2/SSDforR/man/PNDbelow.Rd       |    3 
 SSDforR-1.2/SSDforR/man/PNDlegend.Rd      |    3 
 SSDforR-1.2/SSDforR/man/Pchart.Rd         |    6 -
 SSDforR-1.2/SSDforR/man/Rchart.Rd         |   24 ++--
 SSDforR-1.2/SSDforR/man/Rchartsd.Rd       |   18 ++-
 SSDforR-1.2/SSDforR/man/SD1.Rd            |    3 
 SSDforR-1.2/SSDforR/man/SD1legend.Rd      |    7 -
 SSDforR-1.2/SSDforR/man/SD2.Rd            |    7 -
 SSDforR-1.2/SSDforR/man/SD2legend.Rd      |    3 
 SSDforR-1.2/SSDforR/man/SDAband.Rd        |    3 
 SSDforR-1.2/SSDforR/man/SPClegend.Rd      |   27 +++-
 SSDforR-1.2/SSDforR/man/SPCline.Rd        |   21 ++-
 SSDforR-1.2/SSDforR/man/Trimline.Rd       |    3 
 SSDforR-1.2/SSDforR/man/XRchart.Rd        |   24 ++--
 SSDforR-1.2/SSDforR/man/Xmrchart.Rd       |    3 
 SSDforR-1.2/SSDforR/man/cdcabove.rd       |only
 SSDforR-1.2/SSDforR/man/cdcbelow.rd       |only
 SSDforR-1.2/SSDforR/man/diffchart.Rd      |    3 
 SSDforR-1.2/SSDforR/man/ird.rd            |    3 
 SSDforR-1.2/SSDforR/man/meanabove.rd      |    7 -
 SSDforR-1.2/SSDforR/man/meanbelow.rd      |    7 -
 SSDforR-1.2/SSDforR/man/medabove.rd       |    7 -
 SSDforR-1.2/SSDforR/man/medbelow.rd       |    3 
 SSDforR-1.2/SSDforR/man/pandabove.rd      |    3 
 SSDforR-1.2/SSDforR/man/pandbelow.rd      |    3 
 SSDforR-1.2/SSDforR/man/pemlegend.rd      |    3 
 SSDforR-1.2/SSDforR/man/plotnum.Rd        |    3 
 SSDforR-1.2/SSDforR/man/pndabove.rd       |    3 
 SSDforR-1.2/SSDforR/man/regabove.Rd       |    3 
 SSDforR-1.2/SSDforR/man/regbelow.Rd       |    3 
 SSDforR-1.2/SSDforR/man/robregabove.Rd    |    3 
 SSDforR-1.2/SSDforR/man/robregbelow.Rd    |    3 
 SSDforR-1.2/SSDforR/man/robustCDCabove.Rd |only
 SSDforR-1.2/SSDforR/man/robustCDCbelow.Rd |only
 SSDforR-1.2/SSDforR/man/sd1bandgraph.rd   |    3 
 SSDforR-1.2/SSDforR/man/sd2bandgraph.rd   |    8 +
 SSDforR-1.2/SSDforR/man/trimabove.Rd      |    3 
 SSDforR-1.2/SSDforR/man/trimbelow.Rd      |    3 
 102 files changed, 399 insertions(+), 237 deletions(-)

More information about SSDforR at CRAN
Permanent link

Package ccems (with last version 1.03) was removed from CRAN

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

2009-06-14 1.03
2009-03-21 1.02
2009-03-14 1.01
2009-03-06 1.0

Permanent link

Package odesolve (with last version 0.9-9) was removed from CRAN

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

2012-03-19 0.9-9
2008-09-16 0.5-20
2008-02-04 0.5-19
2007-10-09 0.5-18
2007-07-18 0.5-7.1
2007-07-18 0.5-17
2006-08-05 0.5-16

Permanent link

Package TreePar (with last version 2.3) was removed from CRAN

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

2012-08-05 2.3
2011-11-02 2.2
2011-08-23 2.1.2
2011-07-23 2.1
2011-05-10 1.4
2011-03-30 1.3
2011-03-21 1.2
2011-01-25 1.1
2010-06-18 1.0

Permanent link

Package Rlabkey updated to version 2.1.122 with previous version 2.1.121 dated 2013-02-14

Title: Data exchange between R and LabKey Server
Description: This package allows an R user to discover, query and modify data in LabKey Server
Author: Peter Hussey
Maintainer: Cory Nathe

Diff between Rlabkey versions 2.1.121 dated 2013-02-14 and 2.1.122 dated 2013-05-20

 Rlabkey-2.1.121/Rlabkey/license                             |only
 Rlabkey-2.1.122/Rlabkey/DESCRIPTION                         |   10 +
 Rlabkey-2.1.122/Rlabkey/MD5                                 |   72 ++++++------
 Rlabkey-2.1.122/Rlabkey/NEWS                                |    3 
 Rlabkey-2.1.122/Rlabkey/R/ifcookie.R                        |   27 +++-
 Rlabkey-2.1.122/Rlabkey/R/labkey.deleteRows.R               |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.getFolders.R               |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.getQueryInfo.R             |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.getQueryLists.R            |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.getSchemas.R               |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.insertRows.R               |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.saveBatch.R                |    2 
 Rlabkey-2.1.122/Rlabkey/R/labkey.selectRows.R               |    9 -
 Rlabkey-2.1.122/Rlabkey/R/labkey.updateRows.R               |    2 
 Rlabkey-2.1.122/Rlabkey/inst/doc/RlabkeyExample.R           |only
 Rlabkey-2.1.122/Rlabkey/inst/doc/RlabkeyExample.pdf         |binary
 Rlabkey-2.1.122/Rlabkey/man/Rlabkey-package.Rd              |    4 
 Rlabkey-2.1.122/Rlabkey/man/getFolderPath.Rd                |    3 
 Rlabkey-2.1.122/Rlabkey/man/getLookups.Rd                   |    9 +
 Rlabkey-2.1.122/Rlabkey/man/getRows.Rd                      |    3 
 Rlabkey-2.1.122/Rlabkey/man/getSchema.Rd                    |    9 +
 Rlabkey-2.1.122/Rlabkey/man/getSession.Rd                   |   30 +++--
 Rlabkey-2.1.122/Rlabkey/man/labkey.deleteRows.Rd            |   25 ++--
 Rlabkey-2.1.122/Rlabkey/man/labkey.executeSql.Rd            |   26 ++--
 Rlabkey-2.1.122/Rlabkey/man/labkey.getDefaultViewDetails.Rd |    3 
 Rlabkey-2.1.122/Rlabkey/man/labkey.getFolders.Rd            |    6 -
 Rlabkey-2.1.122/Rlabkey/man/labkey.getLookupDetails.Rd      |   19 ++-
 Rlabkey-2.1.122/Rlabkey/man/labkey.getSchemas.Rd            |    3 
 Rlabkey-2.1.122/Rlabkey/man/labkey.insertRows.Rd            |   25 ++--
 Rlabkey-2.1.122/Rlabkey/man/labkey.saveBatch.Rd             |   11 +
 Rlabkey-2.1.122/Rlabkey/man/labkey.selectRows.Rd            |   14 +-
 Rlabkey-2.1.122/Rlabkey/man/labkey.updateRows.Rd            |   25 ++--
 Rlabkey-2.1.122/Rlabkey/man/lsFolders.Rd                    |   10 +
 Rlabkey-2.1.122/Rlabkey/man/lsProjects.Rd                   |    3 
 Rlabkey-2.1.122/Rlabkey/man/lsSchemas.Rd                    |    6 -
 Rlabkey-2.1.122/Rlabkey/man/makeFilter.Rd                   |    3 
 Rlabkey-2.1.122/Rlabkey/man/saveResults.Rd                  |   15 +-
 Rlabkey-2.1.122/Rlabkey/src/JSON_parser.h                   |    2 
 38 files changed, 239 insertions(+), 152 deletions(-)

More information about Rlabkey at CRAN
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