CRANberries

CRANberries aggregates information about new and and updated packages from the
CRAN network for R available as this html version and a corresponding RSS feed.
Created and provided by Dirk Eddelbuettel.

Thu, 02 Sep 2010

Package Boruta updated to version 1.3 with previous version 1.2 dated 2010-05-08

Title: Boruta -- a tool for finding significant attributes in information systems
Description: Boruta is a feature selection algorithm based on a randomForest predictor. It selects the full set of all important attributes by comparing original attributes importance with datum importance of their randomised copies.
Author: Algorithm by Witold R. Rudnicki , R implementation by Miron B. Kursa .
Maintainer: Miron B. Kursa

Diff between Boruta versions 1.2 dated 2010-05-08 and 1.3 dated 2010-09-02

 DESCRIPTION   |    8 ++++----
 R/Boruta.R    |   16 ++++++++--------
 inst/CITATION |only
 inst/NEWS     |    6 +++++-
 man/Boruta.Rd |    6 +++++-
 5 files changed, 22 insertions(+), 14 deletions(-)

More information about Boruta at CRAN
Path: /cran/updated | permanent link

Package supclust updated to version 1.0-6 with previous version 1.0-5 dated 2005-05-18

Title: Supervised Clustering of Predictor Variables such as Genes
Description: Methodology for supervised grouping aka "clustering" of potentially many predictor variables, such as genes etc.
Author: Marcel Dettling and Martin Maechler
Maintainer: Martin Maechler

Diff between supclust versions 1.0-5 dated 2005-05-18 and 1.0-6 dated 2010-09-02

 DESCRIPTION               |   25 +++--
 R/pelora-utils.R          |   15 +--
 R/pelora.R                |  159 +++++++++++++++---------------------
 man/coef.pelora.Rd        |   17 ---
 man/dlda.Rd               |   17 ++-
 man/fitted.pelora.Rd      |   18 +---
 man/fitted.wilma.Rd       |   15 ---
 man/margin.Rd             |    2 
 man/pelora.Rd             |    8 -
 man/plot.pelora.Rd        |   16 ---
 man/plot.wilma.Rd         |   25 +----
 man/predict.pelora.Rd     |   20 +---
 man/predict.wilma.Rd      |   24 ++---
 man/print.pelora.Rd       |   21 +---
 man/print.wilma.Rd        |   13 --
 man/score.Rd              |    2 
 man/sign.change.Rd        |    2 
 man/signflip.Rd           |    2 
 man/standardize.genes.Rd  |    2 
 man/summary.pelora.Rd     |   16 ---
 man/summary.wilma.Rd      |   13 --
 man/wilma.Rd              |    4 
 src/pelora.c              |    6 -
 src/wilma.c               |    8 -
 tests/pelora-ex.Rout.save |  138 +++++++++++++++----------------
 tests/wilma-ex.Rout.save  |  202 +++++-----------------------------------------
 26 files changed, 268 insertions(+), 522 deletions(-)

More information about supclust at CRAN
Path: /cran/updated | permanent link

Package soiltexture updated to version 1.01 with previous version 1.0 dated 2010-08-18

Title: Functions for soil texture plot, classification and transformation
Description: "The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle / classification into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Several texture triangles are predefined: USDA; FAO (which is also the triangle for the soil map of Europe); Aisne (France); GEPPA (France); German triangle (Bodenkundliche Kartieranleitung 1994); Soil Survey of England and Wales (UK); Australian triangle; Belgian triangle; Canadian triangle; ISSS triangle; Romanian traingle. The Soil Texture Wizard is initially develloped from the functions 'soil.texture()' from the package 'plotrix' by Jim Lemon et al.
Author: Julien MOEYS , contributions from Wei Shangguan.
Maintainer: Julien MOEYS

Diff between soiltexture versions 1.0 dated 2010-08-18 and 1.01 dated 2010-09-02

 soiltexture-1.0/soiltexture/inst/doc2                                   |only
 soiltexture-1.01/soiltexture/DESCRIPTION                                |   13 -
 soiltexture-1.01/soiltexture/R/soiltexture.R                            |  129 +++++-----
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 soiltexture-1.01/soiltexture/inst/doc/soiltexture_vignette.pdf          |binary
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 soiltexture-1.01/soiltexture/man/soiltexture-package.Rd                 |    4 
 18 files changed, 89 insertions(+), 77 deletions(-)

More information about soiltexture at CRAN
Path: /cran/updated | permanent link

Package scape updated to version 1.1-4 with previous version 1.1-2 dated 2010-09-01

Title: Statistical Catch-at-Age Plotting Environment
Description: Import and plot results from statistical catch-at-age models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson

Diff between scape versions 1.1-2 dated 2010-09-01 and 1.1-4 dated 2010-09-02

 DESCRIPTION               |    8 ++++----
 NEWS                      |    4 ++--
 data/x.cod.R              |    2 +-
 data/x.ling.R             |    2 +-
 data/x.oreo.R             |    2 +-
 data/x.sbw.R              |    2 +-
 inst/doc/Rplots.pdf       |    4 ++--
 inst/doc/dsc-vignette.pdf |binary
 inst/doc/gallery.pdf      |binary
 inst/doc/mymodel.pdf      |binary
 man/plotB.Rd              |    8 ++------
 man/plotCA.Rd             |   10 +++-------
 man/plotCL.Rd             |    8 ++------
 man/plotIndex.Rd          |    8 ++------
 man/plotLA.Rd             |    8 ++------
 man/plotN.Rd              |    8 ++------
 man/plotSel.Rd            |    6 +-----
 17 files changed, 26 insertions(+), 54 deletions(-)

More information about scape at CRAN
Path: /cran/updated | permanent link

Package rggobi updated to version 2.1.16 with previous version 2.1.14 dated 2009-05-10

Title: Interface between R and GGobi
Description: The rggobi package provides a command-line interface to GGobi, an interactive and dynamic graphics package. Rggobi complements GGobi's graphical user interface, providing a way to fluidly transition between analysis and exploration, as well as automating common tasks.
Author: Duncan Temple Lang , Debby Swayne , Hadley Wickham , Michael Lawrence
Maintainer: Hadley Wickham

Diff between rggobi versions 2.1.14 dated 2009-05-10 and 2.1.16 dated 2010-09-02

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 rggobi-2.1.16/rggobi/DESCRIPTION                                 |   11 ++++------
 rggobi-2.1.16/rggobi/R/data.r                                    |    2 +
 rggobi-2.1.16/rggobi/R/datasets.r                                |    6 +++--
 rggobi-2.1.16/rggobi/R/display-tour.r                            |    5 ++--
 rggobi-2.1.16/rggobi/R/display-variables.r                       |    3 +-
 rggobi-2.1.16/rggobi/R/display.r                                 |    1 
 rggobi-2.1.16/rggobi/R/edges.r                                   |    2 +
 rggobi-2.1.16/rggobi/R/ggobi.r                                   |    5 +++-
 rggobi-2.1.16/rggobi/aclocal.m4                                  |    4 +--
 rggobi-2.1.16/rggobi/man/GGobiCall-n1.rd                         |    2 -
 rggobi-2.1.16/rggobi/man/as-RGtkObject-8g.rd                     |    4 +--
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 rggobi-2.1.16/rggobi/man/edges--p8.rd                            |    4 +--
 rggobi-2.1.16/rggobi/man/edges-lk.rd                             |    4 +--
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 rggobi-2.1.16/rggobi/man/get--GGobi-7p.rd                        |    4 +--
 rggobi-2.1.16/rggobi/man/get--GGobiData-9v.rd                    |    8 +++----
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 rggobi-2.1.16/rggobi/man/ggobi-data-set-variable-43.rd           |    4 +--
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 rggobi-2.1.16/rggobi/man/ggobi-display-get-tour-projection-p0.rd |only
 rggobi-2.1.16/rggobi/man/ggobi-display-make-type-3r.rd           |    4 +--
 rggobi-2.1.16/rggobi/man/ggobi-display-set-tour-projection-2n.rd |    4 +--
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 rggobi-2.1.16/rggobi/src/Makevars                                |    4 +--
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 138 files changed, 88 insertions(+), 81 deletions(-)

More information about rggobi at CRAN
Path: /cran/updated | permanent link

Package rJava updated to version 0.8-5 with previous version 0.8-4 dated 2010-04-29

Title: Low-level R to Java interface
Description: Low-level interface to Java VM very much like .C/.Call and friends. Allows creation of objects, calling methods and accessing fields.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between rJava versions 0.8-4 dated 2010-04-29 and 0.8-5 dated 2010-09-02

 DESCRIPTION                                                       |    4 -
 NEWS                                                              |   13 +++
 inst/java/boot/RJavaClassLoader$RJavaObjectInputStream.class      |binary
 inst/java/boot/RJavaClassLoader.class                             |binary
 inst/java/boot/RJavaClassLoader.java                              |   10 ++-
 inst/javadoc/ArrayDimensionException.html                         |    4 -
 inst/javadoc/ArrayWrapper.html                                    |    4 -
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 inst/javadoc/DummyPoint.html                                      |    4 -
 inst/javadoc/FlatException.html                                   |    4 -
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 inst/javadoc/help-doc.html                                        |    4 -
 inst/javadoc/index-all.html                                       |    4 -
 inst/javadoc/index.html                                           |    2 
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 jri/NEWS                                                          |    9 ++
 jri/Rengine.java                                                  |   16 ++--
 jri/src/Rengine.c                                                 |   33 ++++------
 jri/src/jri.h                                                     |    8 +-
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 src/java/RJavaClassLoader.class                                   |binary
 src/java/RJavaClassLoader.java                                    |   10 ++-
 src/rJava.h                                                       |    2 
 52 files changed, 144 insertions(+), 107 deletions(-)

More information about rJava at CRAN
Path: /cran/updated | permanent link

Package gWidgetsWWW updated to version 0.0-21 with previous version 0.0-19 dated 2010-06-19

Title: Toolkit implementation of the gWidgets API for use with web pages
Description: Port of the gWidgets API to program dynamic websites. Can be used with R's dynamic help web server to serve local files. This provides a convenient means to make local GUIs for users without concern for external GUI toolkits. Also, in combination with RApache, http://biostat.mc.vanderbilt.edu/rapache/index.html, this framework can be used to make public websites powered by R. The Ext JavaScript libararies (www.extjs.com) are used to create and manipulate the widgets dynamically.
Author: John Verzani
Maintainer: John Verzani

Diff between gWidgetsWWW versions 0.0-19 dated 2010-06-19 and 0.0-21 dated 2010-09-02

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 gWidgetsWWW-0.0-21/gWidgetsWWW/NAMESPACE                       |    2 
 gWidgetsWWW-0.0-21/gWidgetsWWW/NEWS                            |   12 
 gWidgetsWWW-0.0-21/gWidgetsWWW/R/LocalVersion.R                |  156 +++++++---
 gWidgetsWWW-0.0-21/gWidgetsWWW/R/aaa.R                         |    1 
 gWidgetsWWW-0.0-21/gWidgetsWWW/R/common.R                      |   18 +
 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gcanvas.R                     |    4 
 gWidgetsWWW-0.0-21/gWidgetsWWW/R/gcommandline.R                |    2 
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 gWidgetsWWW-0.0-21/gWidgetsWWW/inst/Examples/ex-clt.R          |   10 
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 gWidgetsWWW-0.0-21/gWidgetsWWW/man/localServerStart.Rd         |    5 
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More information about gWidgetsWWW at CRAN
Path: /cran/updated | permanent link

Package Rserve updated to version 0.6-2 with previous version 0.6-1 dated 2010-05-25

Title: Binary R server
Description: Rserve acts as a socket server (TCP/IP or local sockets) which allows binary requests to be sent to R. Every connection has a separate workspace and working directory. Client-side implementations are available for popular languages such as C/C++ and Java, allowing any application to use facilities of R without the need of linking to R code. Rserve supports remote connection, user authentication and file transfer. A simple R client is included in this package as well.
Author: Simon Urbanek
Maintainer: Simon Urbanek

Diff between Rserve versions 0.6-1 dated 2010-05-25 and 0.6-2 dated 2010-09-02

 DESCRIPTION                                          |    4 
 NEWS                                                 |   31 +
 clients/cxx/Rconnection.cc                           |   62 +++
 clients/cxx/Rconnection.h                            |   35 ++
 clients/cxx/Rsrv.h                                   |    6 
 clients/cxx/configure                                |  293 +++++++++---------
 clients/java-new/Rserve/protocol/REXPFactory.java    |   51 +--
 clients/java-new/Rserve/test/test.java               |   29 +
 configure                                            |  299 +++++++++----------
 src/Makefile.win                                     |   15 
 src/Rserv.c                                          |   81 +++--
 src/Rsrv.h                                           |    6 
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 src/client/cxx/Rconnection.h                         |   35 ++
 src/client/cxx/Rsrv.h                                |    6 
 src/client/cxx/configure                             |  293 +++++++++---------
 src/client/java-new/Rserve/protocol/REXPFactory.java |   51 +--
 src/client/java-new/Rserve/test/test.java            |   29 +
 src/winembed.c                                       |   34 +-
 19 files changed, 900 insertions(+), 522 deletions(-)

More information about Rserve at CRAN
Path: /cran/updated | permanent link

Package spam updated to version 0.23-0 with previous version 0.22-0 dated 2010-06-09

Title: SPArse Matrix
Description: Set of function for sparse matrix algebra. Differences with SparseM/Matrix are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer
Maintainer: Reinhard Furrer

Diff between spam versions 0.22-0 dated 2010-06-09 and 0.23-0 dated 2010-09-02

 DESCRIPTION                               |    8 ++++----
 R/apply.R                                 |    2 +-
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 R/dist.R                                  |    2 +-
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 man/version.Rd                            |    2 +-
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 tests/demo_article-jss.R                  |    2 +-
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 tests/demo_spam.R                         |    2 +-
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 tests/xybind.R                            |    2 +-
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 96 files changed, 198 insertions(+), 186 deletions(-)

More information about spam at CRAN
Path: /cran/updated | permanent link

Package gnumeric updated to version 0.6-1 with previous version 0.5-3 dated 2009-09-18

Title: Read data from files readable by gnumeric
Description: Read data files readable by gnumeric into R. Can read whole sheet or a range, from several file formats, including the native format of gnumeric. Reading is done by using ssconvert (a file converter utility included in the gnumeric distribution http://projects.gnome.org/gnumeric/) to convert the requested part to CSV. From gnumeric files (but not other formats) can list sheet names and sheet sizes or read all sheets.
Author: Karoly Antal .
Maintainer: Karoly Antal

Diff between gnumeric versions 0.5-3 dated 2009-09-18 and 0.6-1 dated 2010-09-02

 DESCRIPTION                 |    8 ++++----
 R/read.gnumeric.R           |   28 +++++++++++++++++++++++-----
 changelog                   |   13 ++++++++++++-
 man/read.gnumeric.sheet.Rd  |   22 +++++++++++++---------
 man/read.gnumeric.sheets.Rd |   13 ++++++++++---
 5 files changed, 62 insertions(+), 22 deletions(-)

More information about gnumeric at CRAN
Path: /cran/updated | permanent link

Package R2Cuba updated to version 1.0-6 with previous version 1.0-5 dated 2010-09-01

Title: Multidimensional Numerical Integration
Description: R2Cuba implements four general-purpose multidimensional integration algorithms: Vegas, Suave, Divonne and Cuhre
Author: The Cuba library has been written by Thomas Hahn (http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was written by Annie Bouvier and Kiên Kiêu
Maintainer: Annie Bouvier

Diff between R2Cuba versions 1.0-5 dated 2010-09-01 and 1.0-6 dated 2010-09-02

 DESCRIPTION           |    9 +++++----
 man/R2Cuba-package.Rd |    7 ++++---
 2 files changed, 9 insertions(+), 7 deletions(-)

More information about R2Cuba at CRAN
Path: /cran/updated | permanent link

Package FBN updated to version 1.5 with previous version 1.4 dated 2010-02-03

Title: FISH Based Normalization and Copy Number inference of SNP microarray data
Description: Normalizes the data from a file containing the raw values of the SNP probes of microarrray data by using the FISH probes and their corresponding CNs.
Author: Adrian Andronache , Luca Agnelli
Maintainer: Adrian Andronache , Luca Agnelli

Diff between FBN versions 1.4 dated 2010-02-03 and 1.5 dated 2010-09-02

 DESCRIPTION            |    8 ++++----
 R/FBNormalization.R    |   38 ++++++++++++++++++++++++++++++--------
 man/FBN-package.Rd     |    4 ++--
 man/FBNormalization.Rd |    6 ++++--
 4 files changed, 40 insertions(+), 16 deletions(-)

More information about FBN at CRAN
Path: /cran/updated | permanent link

Package tau updated to version 0.0-10 with previous version 0.0-9 dated 2010-08-10

Title: Text Analysis Utilities
Description: Utilities for text analysis
Author: Christian Buchta, Kurt Hornik, Ingo Feinerer, David Meyer
Maintainer: Kurt Hornik

Diff between tau versions 0.0-9 dated 2010-08-10 and 0.0-10 dated 2010-09-02

 DESCRIPTION   |    9 +++++----
 R/sysdata.rda |binary
 2 files changed, 5 insertions(+), 4 deletions(-)

More information about tau at CRAN
Path: /cran/updated | permanent link

Package clue updated to version 0.3-35 with previous version 0.3-34 dated 2010-04-27

Title: Cluster ensembles
Description: CLUster Ensembles
Author: Kurt Hornik, with contributions from Walter Boehm
Maintainer: Kurt Hornik

Diff between clue versions 0.3-34 dated 2010-04-27 and 0.3-35 dated 2010-09-02

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 10 files changed, 64 insertions(+), 16 deletions(-)

More information about clue at CRAN
Path: /cran/updated | permanent link

Package latentnet updated to version 2.4-0 with previous version 2.3-0 dated 2010-04-07

Title: Latent position and cluster models for statistical networks
Description: A package to fit and simulate latent position and cluster models for statistical networks.
Author: Pavel N. Krivitsky , Mark S. Handcock , based on original code from "latentnetHRT", and code from other packages of `statnet' project
Maintainer: Pavel N. Krivitsky

Diff between latentnet versions 2.3-0 dated 2010-04-07 and 2.4-0 dated 2010-09-02

 ChangeLog                  |   17 ++++++
 DESCRIPTION                |   12 ++--
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More information about latentnet at CRAN
Path: /cran/updated | permanent link

Package SMCP updated to version 1.1.3 with previous version 1.1.2 dated 2010-08-30

Title: Smoothed minimax concave penalization (SMCP) method for genome-wide association studies.
Description: A package containing functions for genome-wide association studies.
Author: Jin (Gordon) Liu
Maintainer: Jin (Gordon) Liu

Diff between SMCP versions 1.1.2 dated 2010-08-30 and 1.1.3 dated 2010-09-02

 DESCRIPTION |   12 ++++++------
 R/SMCP.R    |    2 +-
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 3 files changed, 14 insertions(+), 15 deletions(-)

More information about SMCP at CRAN
Path: /cran/updated | permanent link

Wed, 01 Sep 2010

Package caret updated to version 4.59 with previous version 4.58 dated 2010-08-29

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn

Diff between caret versions 4.58 dated 2010-08-29 and 4.59 dated 2010-09-01

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 12 files changed, 351 insertions(+), 87 deletions(-)

More information about caret at CRAN
Path: /cran/updated | permanent link

Package seewave updated to version 1.5.9 with previous version 1.5.8 dated 2010-06-15

Title: Time wave analysis and graphical representation
Description: seewave provides functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses.
Author: Jerome Sueur , Thierry Aubin , Caroline Simonis
Maintainer: Jerome Sueur

Diff between seewave versions 1.5.8 dated 2010-06-15 and 1.5.9 dated 2010-09-01

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 21 files changed, 455 insertions(+), 315 deletions(-)

More information about seewave at CRAN
Path: /cran/updated | permanent link

Package scape updated to version 1.1-2 with previous version 1.1-0 dated 2010-08-31

Title: Statistical Catch-at-Age Plotting Environment
Description: Import and plot results from statistical catch-at-age models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson

Diff between scape versions 1.1-0 dated 2010-08-31 and 1.1-2 dated 2010-09-01

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 16 files changed, 6122 insertions(+), 6820 deletions(-)

More information about scape at CRAN
Path: /cran/updated | permanent link

Package pbatR updated to version 2.2-2 with previous version 2.2-0 dated 2009-11-23

Title: P2BAT
Description: This package provides data analysis via the pbat program, and an alternative internal implementation of the power calculations via simulation only. For analysis, this package provides a frontend to the PBAT software, automatically reading in the output from the pbat program and displaying the corresponding figure when appropriate (i.e. PBAT-logrank). It includes support for multiple processes and clusters. For analysis, users must download PBAT (developed by Christoph Lange) and accept it's license, available on the PBAT webpage. Both the data analysis and power calculations have command line and graphical interfaces using tcltk.
Author: Thomas Hoffmann , with contributions from Christoph Lange
Maintainer: Thomas Hoffmann

Diff between pbatR versions 2.2-0 dated 2009-11-23 and 2.2-2 dated 2010-09-01

 DESCRIPTION           |    8 +++----
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 src/kludge.cpp        |   25 ++++++++++++----------
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 8 files changed, 83 insertions(+), 40 deletions(-)

More information about pbatR at CRAN
Path: /cran/updated | permanent link

Package gmt updated to version 1.1-8 with previous version 1.1-7 dated 2010-08-28

Title: Interface between GMT Map-Making Software and R
Description: Interface between the GMT map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The 'gmt' package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.
Author: Arni Magnusson
Maintainer: Arni Magnusson

Diff between gmt versions 1.1-7 dated 2010-08-28 and 1.1-8 dated 2010-09-01

 DESCRIPTION        |    8 ++++----
 NEWS               |    4 ++--
 man/gmt-package.Rd |    2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

More information about gmt at CRAN
Path: /cran/updated | permanent link

Package gRapHD updated to version 0.1.8 with previous version 0.1.7 dated 2010-08-17

Title: Efficient selection of undirected graphical models for high-dimensional datasets
Description: gRapHD is designed for efficient selection of high-dimensional undirected graphical models. The package provides tools for selecting trees, forests and decomposable models minimizing information criteria such as AIC or BIC, and for displaying the independence graphs of the models. It has also some useful tools for analysing graphical structures. It supports the use of discrete, continuous, or both types of variables.
Author: Gabriel Coelho Goncalves de Abreu , Rodrigo Labouriau , David Edwards .
Maintainer: Gabriel Coelho Goncalves de Abreu

Diff between gRapHD versions 0.1.7 dated 2010-08-17 and 0.1.8 dated 2010-09-01

 DESCRIPTION   |    6 ++---
 R/functions.r |   66 +++++++++++++++++++++++++++++++---------------------------
 man/fit.rd    |    7 ++++--
 3 files changed, 44 insertions(+), 35 deletions(-)

More information about gRapHD at CRAN
Path: /cran/updated | permanent link

Package R2Cuba updated to version 1.0-5 with previous version 1.0-4 dated 2010-02-08

Title: Multidimensional Numerical Integration
Description: R2Cuba implements four general-purpose multidimensional integration algorithms: Vegas, Suave, Divonne and Cuhre
Author: The Cuba library has been written by Thomas Hahn (http://wwwth.mppmu.mpg.de/members/hahn); Interface to R was written by Annie Bouvier and Kiên Kiêu
Maintainer: Annie Bouvier

Diff between R2Cuba versions 1.0-4 dated 2010-02-08 and 1.0-5 dated 2010-09-01

 DESCRIPTION           |    8 ++++----
 R/commoncuba.R        |    7 +++++--
 R/cuhre.R             |    3 ++-
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 R/vegas.R             |    3 ++-
 man/R2Cuba-package.Rd |    4 ++--
 man/cuhre.Rd          |    1 +
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 src/cuhre_common.c    |    2 +-
 src/vegas_Vegas.c     |    3 ++-
 tests/kk.Rout.save    |   10 +++++++---
 12 files changed, 30 insertions(+), 18 deletions(-)

More information about R2Cuba at CRAN
Path: /cran/updated | permanent link

Package Epi updated to version 1.1.17 with previous version 1.1.15 dated 2010-06-19

Title: A package for statistical analysis in epidemiology.
Description: Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, including interval censored data and representation of multistate data. Also some useful functions for tabulation and plotting. Contains some epidemiological datasets.
Author: Bendix Carstensen, Martyn Plummer, Esa Laara, Michael Hills et. al.
Maintainer: Bendix Carstensen

Diff between Epi versions 1.1.15 dated 2010-06-19 and 1.1.17 dated 2010-09-01

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 Epi-1.1.15/Epi/man/mstate.Lexis.Rd    |only
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 Epi-1.1.17/Epi/R/MS.boxes.R           |    7 
 Epi-1.1.17/Epi/R/lexis.R              |    9 
 Epi-1.1.17/Epi/R/stack.Lexis.R        |   68 ++---
 Epi-1.1.17/Epi/inst/doc/Follow-up.pdf |  424 ++++++++++++++++------------------
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 Epi-1.1.17/Epi/man/transform.Lexis.Rd |    9 
 12 files changed, 291 insertions(+), 274 deletions(-)

More information about Epi at CRAN
Path: /cran/updated | permanent link

Package DoE.wrapper updated to version 0.8-1 with previous version 0.8 dated 2010-08-10

Title: Wrapper package for design of experiments functionality
Description: This package creates various kinds of designs for (industrial) experiments. It uses, and sometimes enhances, design generation routines from other packages. Initially, response surface designs from package rsm and latin hypercube samples from package lhs have been implemented.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping

Diff between DoE.wrapper versions 0.8 dated 2010-08-10 and 0.8-1 dated 2010-09-01

 DESCRIPTION         |    8 ++++----
 inst/NEWS           |    3 +++
 man/Dopt.augment.Rd |    3 +--
 man/Dopt.design.Rd  |    3 +--
 4 files changed, 9 insertions(+), 8 deletions(-)

More information about DoE.wrapper at CRAN
Path: /cran/updated | permanent link

Package SubpathwayMiner updated to version 3.1 with previous version 3.0 dated 2010-06-01

Title: A software package for annotation and identification of the KEGG pathways.
Description: SubpathwayMiner is an R-based software for flexible pathway identification. (1) SubpathwayMiner can provide users with sub-pathway annotation and identification of metabolic pathways based on enzyme commission (EC) numbers. (2) SubpathwayMiner can provide users with sub-pathway annotation and identification based on KEGG Orthology (KO) identifiers. (3) SubpathwayMiner can provide annotation and identification of entire pathways. (4) SubpathwayMiner can support most of organisms in the KEGG GENE database. (5) Data can be automatically updated on demand by the user. (6) SubpathwayMiner can provide identification of disease related sub-pathways.(new!) The version 3.1 use a new approach to store organism-related data (e.g., gene-enzyme relation data), which make the running time of the function updateOrgAndIdType reduce significantly compared with the old version. Therefore, the environment variables of organisms will be provided no longer for reducing size of the software package. When using this tool, please cite: Li, C., Li, X., Miao, Y., Wang, Q., Jiang, W., Xu, C., Li, J., Han, J., Zhang, F., Gong, B. et al. (2009) SubpathwayMiner: a software package for flexible identification of pathways. Nucleic Acids Res, 37, e131. Full text: http://nar.oxfordjournals.org/cgi/content/full/37/19/e131
Author: Chunquan Li
Maintainer: Chunquan Li

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Path: /cran/updated | permanent link

Package GeneReg updated to version 1.1.2 with previous version 1.1.1 dated 2009-12-14

Title: Construct time delay gene regulatory network
Description: GeneReg is an R package for inferring time delay gene regulatory network using time course gene expression profiles. The main idea of time delay linear model is to fit a linear regression model using a set of putative regulators to estimate the transcription pattern of a specific target gene.
Author: Tao Huang
Maintainer: Tao Huang

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Tue, 31 Aug 2010

Package xts updated to version 0.7-5 with previous version 0.7-4 dated 2010-08-04

Title: Extensible Time Series
Description: Provide for uniform handling of R's different time-based data classes by extending zoo, maximizing native format information preservation and allowing for user level customization and extension, while simplifying cross-class interoperability.
Author: Jeffrey A. Ryan, Josh M. Ulrich
Maintainer: Jeffrey A. Ryan

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Package chron updated to version 2.3-36 with previous version 2.3-35 dated 2010-04-05

Title: Chronological objects which can handle dates and times
Description: Chronological objects which can handle dates and times
Author: S original by David James , R port by Kurt Hornik .
Maintainer: Kurt Hornik

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Package bayesGARCH updated to version 1-00.06 with previous version 1-00.05 dated 2009-11-25

Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t Innovations
Description: This package provides the bayesGARCH function which performs the Bayesian estimation of the GARCH(1,1) model with Student's t innovations.
Author: David Ardia
Maintainer: David Ardia

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Package npde updated to version 1.2.1 with previous version 1.2 dated 2008-04-02

Title: Normalised prediction distribution errors for nonlinear mixed-effect models
Description: Routines to compute normalised prediction distribution errors, a metric designed to evaluate non-linear mixed effect models such as those used in pharmacokinetics and pharmacodynamics
Author: Emmanuelle Comets, Karl Brendel and France Mentré
Maintainer: Emmanuelle Comets

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Package nnc updated to version 1.14 with previous version 1.13 dated 2010-08-30

Title: Nearest Neighbor Autocovariates
Description: Computes nearest neighbor autocovariates
Author: A. I. McLeod and M. S. Islam
Maintainer:

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Package MIfuns updated to version 4.0.18 with previous version 4.0.17 dated 2010-08-31

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 a detailed analysis log.
Author: Metrum Institute (http://metruminstitute.org): Bill Knebel, Leonid Gibianski, Tim Bergsma
Maintainer: Tim Bergsma

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Package scape updated to version 1.1-0 with previous version 1.0-9 dated 2009-04-21

Title: Statistical Catch-at-Age Plotting Environment
Description: Import and plot results from statistical catch-at-age models, used in fisheries stock assessments.
Author: Arni Magnusson
Maintainer: Arni Magnusson

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Package rworldmap updated to version 0.110 with previous version 0.107 dated 2010-02-03

Title: For mapping global data : rworldmap
Description: Enables mapping of country level and gridded user datasets.
Author: , with contributions from Joe Scutt-Phillips, Barry Rowlingson, Roger Bivand & Pru Foster
Maintainer: Andy South

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Package rjags updated to version 2.1.0-7 with previous version 2.1.0-6 dated 2010-07-29

Title: Bayesian graphical models using MCMC
Description: Interface to the JAGS MCMC library
Author: Martyn Plummer
Maintainer: Martyn Plummer

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Package pomp updated to version 0.32-5 with previous version 0.32-1 dated 2010-08-24

Title: Statistical inference for partially observed Markov processes
Description: Inference methods for partially-observed Markov processes
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
Maintainer: Aaron A. King

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Package PairViz updated to version 1.1 with previous version 1.0 dated 2008-10-28

Title: Visualization using Eulerian tours and Hamiltonian decompositions
Description: Eulerian tours and Hamiltonian decompositions of complete graphs are used to ameliorate order effects in statistical graphics.
Author: C.B. Hurley and R.W. Oldford
Maintainer: Catherine Hurley

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More information about PairViz at CRAN
Path: /cran/updated | permanent link

Package modehunt updated to version 1.0.5 with previous version 1.0.4 dated 2009-03-04

Title: Multiscale Analysis for Density Functions
Description: Given independent and identically distributed observations X(1), ..., X(n) from a density f, this package provides five methods to perform a multiscale analysis about f as well as the necessary critical values. The first method, introduced in Duembgen and Walther (2008), provides simultaneous confidence statements for the existence and location of local increases (or decreases) of f, based on all intervals I(all) spanned by any two observations X(j), X(k). The second method approximates the latter approach by using only a subset of I(all) and is therefore computationally much more efficient, but asymptotically equivalent. Omitting the additive correction term Gamma in either method offers another two approaches which are more powerful on small scales and less powerful on large scales, however, not asymptotically minimax optimal anymore. Finally, the block procedure is a compromise between adding Gamma or not, having intermediate power properties. The latter is again asymptotically equivalent to the first and was introduced in Rufibach and Walther (2010).
Author: Kaspar Rufibach and Guenther Walther
Maintainer: Kaspar Rufibach

Diff between modehunt versions 1.0.4 dated 2009-03-04 and 1.0.5 dated 2010-08-31

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More information about modehunt at CRAN
Path: /cran/updated | permanent link

Package OrdFacReg updated to version 1.0.2 with previous version 1.0.1 dated 2009-09-28

Title: Least squares, logistic, and Cox-regression with ordered predictors
Description: In biomedical studies, researchers are often interested in assessing the association between one or more ordinal explanatory variables and an outcome variable, at the same time adjusting for covariates of any type. The outcome variable may be continuous, binary, or represent censored survival times. In the absence of a precise knowledge of the response function, using monotonicity constraints on the ordinal variables improves efficiency in estimating parameters, especially when sample sizes are small. This package implements an active set algorithm that efficiently computes such estimators.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach

Diff between OrdFacReg versions 1.0.1 dated 2009-09-28 and 1.0.2 dated 2010-08-31

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More information about OrdFacReg at CRAN
Path: /cran/updated | permanent link

Package MIfuns updated to version 4.0.17 with previous version 4.0.16 dated 2010-08-28

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 a detailed analysis log.
Author: Metrum Institute (http://metruminstitute.org): Bill Knebel, Leonid Gibianski, Tim Bergsma
Maintainer: Tim Bergsma

Diff between MIfuns versions 4.0.16 dated 2010-08-28 and 4.0.17 dated 2010-08-31

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More information about MIfuns at CRAN
Path: /cran/updated | permanent link

Package GenABEL updated to version 1.6-4 with previous version 1.6-2 dated 2010-08-08

Title: genome-wide SNP association analysis
Description: a package for genome-wide association analysis between quantitative or binary traits and single-nucleiotide polymorphisms (SNPs).
Author: Yurii Aulchenko, Maksim Struchalin
Maintainer: Yurii Aulchenko

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More information about GenABEL at CRAN
Path: /cran/updated | permanent link

Package tkrplot updated to version 0.0-19 with previous version 0.0-18 dated 2008-04-01

Title: TK Rplot
Description: simple mechanism for placing R graphics in a Tk widget
Author: Luke Tierney
Maintainer: Luke Tierney

Diff between tkrplot versions 0.0-18 dated 2008-04-01 and 0.0-19 dated 2010-08-31

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More information about tkrplot at CRAN
Path: /cran/updated | permanent link

Package testthat updated to version 0.3 with previous version 0.2 dated 2010-07-25

Title: Testthat code. Tools to make testing fun :)
Description: A testing package specifically tailored for R that's fun, flexible and easy to set up.
Author: Hadley Wickham
Maintainer: Hadley Wickham

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More information about testthat at CRAN
Path: /cran/updated | permanent link

Package smoothtail updated to version 2.0.0 with previous version 1.1.4 dated 2009-10-15

Title: Smooth Estimation of GPD Shape Parameter
Description: Given independent and identically distributed observations X(1), ..., X(n) from a Generalized Pareto distribution with shape parameter gamma in [-1,0], this package offers several estimates to compute estimates of gamma. The estimates are based on the principle of replacing the order statistics by quantiles of a distribution function based on a log--concave density function. This procedure is justified by the fact that the GPD density is log--concave for gamma in [-1,0].
Author: Kaspar Rufibach and Samuel Mueller
Maintainer: Kaspar Rufibach

Diff between smoothtail versions 1.1.4 dated 2009-10-15 and 2.0.0 dated 2010-08-31

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More information about smoothtail at CRAN
Path: /cran/updated | permanent link

Package paleoTS updated to version 0.3-3 with previous version 0.3-2 dated 2010-05-08

Title: Modeling evolution in paleontological time-series
Description: This package facilitates analysis of paleontological sequences of trait values from an evolving lineage. Functions are provided to fit, using maximum likelihood, evolutionary models including unbiased random walks, directional evolution, stasis, and Ornstein-Uhlenbeck models. Newly added since version (0.3-1) are functions to analyze punctuations and models in which evolutionary dynamics change over the course of a time-series of trait values.
Author: Gene Hunt
Maintainer: Gene Hunt

Diff between paleoTS versions 0.3-2 dated 2010-05-08 and 0.3-3 dated 2010-08-31

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More information about paleoTS at CRAN
Path: /cran/updated | permanent link

Package lossDev updated to version 0.9.4 with previous version 0.9.3 dated 2010-07-06

Title: Robust Loss Development Using MCMC
Description: Loss Development for Insurance Triangles
Author: Christopher W. Laws, Frank A. Schmid
Maintainer: Christopher W. Laws

Diff between lossDev versions 0.9.3 dated 2010-07-06 and 0.9.4 dated 2010-08-31

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More information about lossDev at CRAN
Path: /cran/updated | permanent link

Package fda updated to version 2.2.3 with previous version 2.2.2 dated 2010-06-22

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.
Author: J. O. Ramsay , Hadley Wickham , Spencer Graves , Giles Hooker
Maintainer: J. O. Ramsay

Diff between fda versions 2.2.2 dated 2010-06-22 and 2.2.3 dated 2010-08-31

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More information about fda at CRAN
Path: /cran/updated | permanent link

Package evaluate updated to version 0.3 with previous version 0.1 dated 2010-07-24

Title: Parsing and evaluation tools that provide more details than the default.
Description: Parsing and evaluation tools that make it easy to recreate the command line behaviour of R.
Author: Hadley Wickham
Maintainer: Hadley Wickham

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More information about evaluate at CRAN
Path: /cran/updated | permanent link

Package SPOT updated to version 0.1.1016 with previous version 0.1.888 dated 2010-06-22

Title: Sequential Parameter Optimization
Description: R-Package for Sequential Parameter Optimization Toolbox
Author: T. Bartz-Beielstein with contributions from: J. Ziegenhirt, W. Konen, O. Flasch, P. Koch, M. Zaefferer
Maintainer: O. Flasch

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Mon, 30 Aug 2010

Package vcd updated to version 1.2-9 with previous version 1.2-8 dated 2010-02-08

Title: Visualizing Categorical Data
Description: Visualization techniques, data sets, summary and inference procedures aimed particularly at categorical data. Special emphasis is given to highly extensible grid graphics. The package was inspired by the book "Visualizing Categorical Data" by Michael Friendly.
Author: David Meyer, Achim Zeileis, Kurt Hornik
Maintainer: David Meyer

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Package sets updated to version 1.0-7 with previous version 1.0-6 dated 2010-04-11

Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets, generalizations such as fuzzy sets, multisets, and fuzzy multisets, customizable sets, and intervals.
Author: David Meyer and Kurt Hornik (with contributions by Christian Buchta)
Maintainer: David Meyer

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Package vrmlgen updated to version 1.4.6 with previous version 1.4.4 dated 2010-06-15

Title: Generate 3D visualizations for data exploration on the web
Description: vrmlgen creates 3D scatter and bar plots, visualizations of 3D meshes, parametric functions and height maps in web-formats like the Virtual Reality Markup Language (VRML, filetype .wrl) and the LiveGraphics3D format.
Author: Enrico Glaab
Maintainer:

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Path: /cran/updated | permanent link

Package sn updated to version 0.4-16 with previous version 0.4-15 dated 2010-04-02

Title: The skew-normal and skew-t distributions
Description: Functions for manipulating skew-normal and skew-t probability distributions, and for fitting them to data, in the scalar and in the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini

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Package rrcov updated to version 1.1-00 with previous version 1.0-01 dated 2010-06-21

Title: Scalable Robust Estimators with High Breakdown Point
Description: Robust Location and Scatter Estimation and Robust Multivariate Analysis with High Breakdown Point.
Author: Valentin Todorov
Maintainer: Valentin Todorov

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Package seqinr updated to version 3.0-0 with previous version 2.0-9 dated 2010-03-20

Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for biological sequence (DNA and protein) data. Include also utilities for sequence data management under the ACNUC system.
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and Leonor Palmeira and Simon Penel
Maintainer: Simon Penel

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Package ez updated to version 2.0-0 with previous version 1.6.1 dated 2010-03-21

Title: Easy analysis and visualization of factorial experiments.
Description: This package facilitates easy analysis of factorial experiments, including purely within-Ss designs (a.k.a. "repeated measures"), purely between-Ss designs, and mixed within-and-between-Ss designs. The functions in this package aim to provide simple, intuitive and consistent specification of data analysis and visualization. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Finally, this package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. The bootstrap function obtains predictions either by cell means or by more advanced/powerful mixed effects models, yielding predictions and confidence intervals that may be easily visualized at any level of the experiment's design.
Author: Michael A. Lawrence
Maintainer: Michael A. Lawrence

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Package RcmdrPlugin.qual updated to version 1.0.0 with previous version 0.5.0 dated 2010-04-27

Title: Rcmdr plugin for quality control course
Description: This package provides an Rcmdr "plug-in" based on the Quality control class Stat 4300
Author: Erin Hodgess
Maintainer: Erin Hodgess

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Package spgrass6 updated to version 0.6-20 with previous version 0.6-19 dated 2010-07-24

Title: Interface between GRASS 6 geographical information system and R
Description: Interpreted interface between GRASS 6 geographical information system and R, based on starting R from within the GRASS environment, or running free-standing R in a temporary GRASS location; the package provides facilities for using all GRASS commands from the R command line.
Author: Roger Bivand
Maintainer: Roger Bivand

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Package secr updated to version 1.4.1 with previous version 1.4.0 dated 2010-05-07

Title: Spatially explicit capture-recapture
Description: Estimate animal population density with capture--recapture data from an array of passive detectors (traps). Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford

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Package nnc updated to version 1.13 with previous version 1.12 dated 2010-08-23

Title: Nearest Neighbor Autocovariates
Description: Computes nearest neighbor autocovariates
Author: A. I. McLeod and M. S. Islam
Maintainer:

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Package SMCP updated to version 1.1.2 with previous version 1.1.1 dated 2010-08-26

Title: Smoothed minimax concave penalization (SMCP) method for genome-wide association studies.
Description: A package containing functions that fit the marginalized linear model with SMCP.
Author: Jin (Gordon) Liu
Maintainer: Jin (Gordon) Liu

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Package R.matlab updated to version 1.3.2 with previous version 1.3.1 dated 2010-05-22

Title: Read and write of MAT files together with R-to-Matlab connectivity
Description: This package provides methods to read and write MAT files. It also makes it possible to communicate (evaluate code, send and retrieve objects etc.) with Matlab v6 or higher running locally or on a remote host.
Author: Henrik Bengtsson , Jason Riedy
Maintainer: Henrik Bengtsson

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Sun, 29 Aug 2010

Package modeest updated to version 1.14 with previous version 1.09 dated 2009-05-24

Title: Mode Estimation
Description: This package provides estimators of the mode of univariate unimodal data or univariate unimodal distributions
Author: P. PONCET
Maintainer: P. PONCET

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Package ris updated to version 1.1 with previous version 1.0 dated 2010-02-21

Title: RIS package for bibliographic analysis
Description: Importing RIS-formatted file into a list of Bibtex-like references; checking for duplications; converting references to citEntry objects
Author: Stephanie Kovalchik
Maintainer: Stephanie Kovalchik

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Package raster updated to version 1.4-10 with previous version 1.3-11 dated 2010-08-12

Title: Geographic analysis and modeling with raster data
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functons, as well as map algebra. Processing of very large files is supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans

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Package pgirmess updated to version 1.4.8 with previous version 1.4.7 dated 2010-07-24

Title: Data analysis in ecology
Description: Miscellaneous functions for analysis and display of ecological and spatial data
Author: Patrick Giraudoux
Maintainer: Patrick Giraudoux

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Package earth updated to version 2.4-2 with previous version 2.4-1 dated 2010-08-28

Title: Multivariate Adaptive Regression Spline Models
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is copyrighted and thus not used in the name of the package.)
Author: Stephen Milborrow derived from mda:mars by Trevor Hastie and Rob Tibshirani.
Maintainer: Stephen Milborrow

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Package caret updated to version 4.58 with previous version 4.57 dated 2010-08-26

Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn

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Package bestglm updated to version 0.30 with previous version 0.20 dated 2009-11-01

Title: Best Subset GLM
Description: Best subset glm using AIC, BIC, EBIC, BICq or Cross-Validation. For the normal case, the 'leaps' is used. Otherwise, a slower exhaustive search. The 'xtable' package is needed for vignette 'SimExperimentBICq.Rnw' accompanying this package.
Author: A.I. McLeod and Changjiang Xu
Maintainer: A.I. McLeod

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Sat, 28 Aug 2010

Package phangorn updated to version 1.1-0 with previous version 1.0-2 dated 2010-05-16

Title: Phylogenetic analysis in R
Description: Phylogenetic analysis in R (Estimation of phylogenetic trees and networks using Maximum Likelihood, Maximum Parsimony, Distance methods & Hadamard conjugation)
Author: Klaus Schliep
Maintainer: Klaus Schliep

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Package gmt updated to version 1.1-7 with previous version 1.1-6 dated 2010-08-27

Title: Interface between GMT Map-Making Software and R
Description: Interface between the GMT map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The 'gmt' package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.
Author: Arni Magnusson
Maintainer: Arni Magnusson

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Package geosphere updated to version 1.2-10 with previous version 1.2-7 dated 2010-07-26

Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans, Ed Williams, Chris Vennes
Maintainer: Robert J. Hijmans

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Package earth updated to version 2.4-1 with previous version 2.4-0 dated 2009-11-09

Title: Multivariate Adaptive Regression Spline Models
Description: Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines". (The term "MARS" is copyrighted and thus not used in the name of the package.)
Author: Stephen Milborrow derived from mda:mars by Trevor Hastie and Rob Tibshirani.
Maintainer: Stephen Milborrow

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Package dclone updated to version 1.2-0 with previous version 1.1-0 dated 2010-05-04

Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods with support for JAGS, WinBUGS and OpenBUGS, with support for parallel computing.
Author: Peter Solymos
Maintainer: Peter Solymos

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Package PBSddesolve updated to version 1.08.11 with previous version 1.08.9 dated 2010-04-29

Title: Solver for Delay Differential Equations
Description: This package solves systems of delay differential equations. by interfacing numerical routines written by Simon N. Wood , with contributions by Benjamin J. Cairns . These numerical routines first appeared in Simon Wood's solv95 program. This package includes a vignette and a complete user's guide. 'PBSddesolve' originally appeared on CRAN under the name 'ddesolve'. That version is no longer supported. The current name emphasizes a close association with other PBS packages, particularly 'PBSmodelling'.
Author: Alex Couture-Beil , Jon Schnute , Rowan Haigh
Maintainer: Jon Schnute

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Package MIfuns updated to version 4.0.16 with previous version 3.2.9 dated 2008-11-04

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 a detailed analysis log.
Author: Metrum Institute (http://metruminstitute.org): Bill Knebel, Leonid Gibianski, Tim Bergsma
Maintainer: Tim Bergsma

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Path: /cran/updated | permanent link

Package FitAR updated to version 1.85 with previous version 1.80 dated 2010-08-16

Title: Subset AR Model Fitting
Description: Comprehensive model building function for identification, estimation and diagnostic checking for AR and subset AR models. Two types of subset AR models are supported. One family of subset AR models, denoted by ARp, is formed by taking subet of the original AR coefficients and in the other, denoted by ARz, subsets of the partial autocorrelations are used. The main advantage of the ARz model is its applicability to very large order models.
Author: A.I. McLeod and Ying Zhang
Maintainer: A.I. McLeod

Diff between FitAR versions 1.80 dated 2010-08-16 and 1.85 dated 2010-08-28

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More information about FitAR at CRAN
Path: /cran/updated | permanent link

Package CADStat updated to version 2.2-6 with previous version 2.2-5 dated 2010-04-08

Title: Provides a GUI to several statistical methods useful for causal assessment.
Description: Using JGR, provides a GUI to several statistical methods - scatterplot, boxplot, linear regression, generalized linear regression, quantile, regression, conditional probability calculations, and regression trees.
Author: Lester Yuan, Tom Stockton, Doug Bronson, Pasha Minallah, and Mark Fitzgerald
Maintainer: Lester Yuan

Diff between CADStat versions 2.2-5 dated 2010-04-08 and 2.2-6 dated 2010-08-28

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More information about CADStat at CRAN
Path: /cran/updated | permanent link

Fri, 27 Aug 2010

Package simba updated to version 0.3-2 with previous version 0.3-1 dated 2010-07-25

Title: A Collection of functions for similarity analysis of vegetation data
Description: Besides functions for the calculation of similarity and multiple plot similarity measures with binary data (for instance presence/absence species data) the package contains some simple wrapper functions for reshaping species lists into matrices and vice versa and some other functions for further processing of similarity data (Mantel-like permutation procedures) as well as some other useful stuff for vegetation analysis.
Author: Gerald Jurasinski , with contributions from Vroni Retzer
Maintainer: Gerald Jurasinski

Diff between simba versions 0.3-1 dated 2010-07-25 and 0.3-2 dated 2010-08-27

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More information about simba at CRAN
Path: /cran/updated | permanent link

Package magma updated to version 0.2.2-1 with previous version 0.2.1-3 dated 2010-08-20

Title: Matrix Algebra on GPU and Multicore Architectures
Description: Magma matrix classes and methods for parallel processing of matrix algebra operations. Operations are performed with algorithms developed by the MAGMA research project. MAGMA aims to achieve the fastest possible linear algebra libraries on hybrid multicore CPU and GPU architectures by exploiting their massive parallelism and minimizing communication latencies.
Author: Brian J Smith
Maintainer: Brian J Smith

Diff between magma versions 0.2.1-3 dated 2010-08-20 and 0.2.2-1 dated 2010-08-27

 ChangeLog        |   20 ++++++++++++++++++++
 DESCRIPTION      |    8 ++++----
 INSTALL          |   13 +++++++------
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More information about magma at CRAN
Path: /cran/updated | permanent link

Package gmt updated to version 1.1-6 with previous version 1.1-4 dated 2010-02-17

Title: Interface between GMT Map-Making Software and R
Description: Interface between the GMT map-making software and R, enabling the user to manipulate geographic data within R and call GMT commands to draw and annotate maps in postscript format. The 'gmt' package is about interactive data analysis, rapidly visualizing subsets and summaries of geographic data, while performing statistical analysis in the R console.
Author: Arni Magnusson
Maintainer: Arni Magnusson

Diff between gmt versions 1.1-4 dated 2010-02-17 and 1.1-6 dated 2010-08-27

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More information about gmt at CRAN
Path: /cran/updated | permanent link

Package catR updated to version 1.1 with previous version 1.0 dated 2010-06-14

Title: Procedures to generate IRT adaptive tests (CAT)
Description: The catR package allows the generation of response patterns under computerized adaptive testing (CAT) framework, with the choice of several starting rules, stopping rules and ability estimators.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada)
Maintainer: David Magis

Diff between catR versions 1.0 dated 2010-06-14 and 1.1 dated 2010-08-27

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More information about catR at CRAN
Path: /cran/updated | permanent link

Package ROracleUI updated to version 1.1-3 with previous version 1.0-0 dated 2010-01-23

Title: Convenient Tools for Working with Oracle Databases
Description: Easy-to-use functions to explore Oracle databases and import data into R. User interface for the ROracle package.
Author: Arni Magnusson
Maintainer: Arni Magnusson

Diff between ROracleUI versions 1.0-0 dated 2010-01-23 and 1.1-3 dated 2010-08-27

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More information about ROracleUI at CRAN
Path: /cran/updated | permanent link

Package hts updated to version 1.4 with previous version 1.3 dated 2010-08-19

Title: Hierarchical time series
Description: Methods for analysing and forecasting hierarchical time series.
Author: Rob J Hyndman, Roman A Ahmed, and Han Lin Shang
Maintainer: Han Lin Shang

Diff between hts versions 1.3 dated 2010-08-19 and 1.4 dated 2010-08-27

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More information about hts at CRAN
Path: /cran/updated | permanent link

Package bspec updated to version 1.2 with previous version 1.1 dated 2008-04-29

Title: Bayesian spectral inference
Description: Bayesian inference on the (discrete) power spectrum of time series.
Author: Christian Roever
Maintainer: Christian Roever

Diff between bspec versions 1.1 dated 2008-04-29 and 1.2 dated 2010-08-27

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More information about bspec at CRAN
Path: /cran/updated | permanent link

Package PowerTOST updated to version 0.7-2 with previous version 0.7-1 dated 2010-08-12

Title: Power and Sample size based on two one-sided t-tests (TOST) for bioequivalence studies
Description: Contains functions to calculate power and sample size for various study designs used for bioequivalence studies. See function known.designs() for study designs covered. Moreover the package contains functions for power and sample size based on 'expected' power in case of uncertain (estimated) variability. Added are functions for the power and sample size for the ratio of two means with normally distributed data on the original scale (based on Fieller's confidence ('fiducial') interval).
Author: Detlew Labes
Maintainer: D. Labes

Diff between PowerTOST versions 0.7-1 dated 2010-08-12 and 0.7-2 dated 2010-08-27

 DESCRIPTION              |    8 ++++----
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 6 files changed, 17 insertions(+), 10 deletions(-)

More information about PowerTOST at CRAN
Path: /cran/updated | permanent link

Package xlsx updated to version 0.2.3 with previous version 0.2.2 dated 2010-07-24

Title: Read, write, format Excel 2007 (xlsx) files
Description: Provide R functions to read/write/format Excel 2007 (xlsx) file formats.
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu

Diff between xlsx versions 0.2.2 dated 2010-07-24 and 0.2.3 dated 2010-08-27

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More information about xlsx at CRAN
Path: /cran/updated | permanent link

Package vars updated to version 1.4-8 with previous version 1.4-7 dated 2010-03-01

Title: VAR Modelling
Description: Estimation, lag selection, diagnostic testing, forecasting, causality analysis, forecast error variance decomposition and impulse response functions of VAR models and estimation of SVAR/SVEC models.
Author: Bernhard Pfaff
Maintainer: Bernhard Pfaff

Diff between vars versions 1.4-7 dated 2010-03-01 and 1.4-8 dated 2010-08-27

 DESCRIPTION       |   10 +++++-----
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 4 files changed, 12 insertions(+), 6 deletions(-)

More information about vars at CRAN
Path: /cran/updated | permanent link

Package tweedie updated to version 2.0.5 with previous version 2.0.2 dated 2009-11-17

Title: Tweedie exponential family models
Description: Maximum likelihood computations for Tweedie families.
Author: Peter K Dunn
Maintainer: Peter K Dunn

Diff between tweedie versions 2.0.2 dated 2009-11-17 and 2.0.5 dated 2010-08-27

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More information about tweedie at CRAN
Path: /cran/updated | permanent link

Package rgenoud updated to version 5.7-1 with previous version 5.6-7 dated 2010-06-01

Title: R version of GENetic Optimization Using Derivatives
Description: A genetic algorithm plus derivative optimizer
Author: Walter R. Mebane, Jr. , Jasjeet Singh Sekhon
Maintainer: Jasjeet Singh Sekhon

Diff between rgenoud versions 5.6-7 dated 2010-06-01 and 5.7-1 dated 2010-08-27

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 DESCRIPTION          |    8 ++---
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More information about rgenoud at CRAN
Path: /cran/updated | permanent link

Package mkin updated to version 0.7-8 with previous version 0.7-6 dated 2010-06-09

Title: Routines for fitting kinetic models with one or more state variables to chemical degradation data
Description: Calculation routines based on the FOCUS Kinetics Report (2006). Includes a function for conveniently defining differential equation models, choice of the optimisation methods made available by the FME package (default is a Levenberg-Marquardt variant). Please note that no warranty is implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke
Maintainer: Johannes Ranke

Diff between mkin versions 0.7-6 dated 2010-06-09 and 0.7-8 dated 2010-08-27

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More information about mkin at CRAN
Path: /cran/updated | permanent link

Package maptools updated to version 0.7-37 with previous version 0.7-36 dated 2010-08-12

Title: Tools for reading and handling spatial objects
Description: Set of tools for manipulating and reading geographic data, in particular ESRI shapefiles; C code used from shapelib. It includes binary access to GSHHS shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as PBSmapping, spatstat, maps, RArcInfo, Stata tmap, WinBUGS, Mondrian, and others.
Author: Nicholas J. Lewin-Koh and Roger Bivand, contributions by Edzer J. Pebesma, Eric Archer, Adrian Baddeley, Hans-Jörg Bibiko, Stéphane Dray, David Forrest, Michael Friendly, Patrick Giraudoux, Duncan Golicher, Virgilio Gómez Rubio, Patrick Hausmann, Thomas Jagger, Sebastian P. Luque, Don MacQueen, Andrew Niccolai, Tom Short and Ben Stabler
Maintainer: Roger Bivand

Diff between maptools versions 0.7-36 dated 2010-08-12 and 0.7-37 dated 2010-08-27

 DESCRIPTION |    8 ++++----
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More information about maptools at CRAN
Path: /cran/updated | permanent link

Package logcondens updated to version 2.0.0 with previous version 1.3.5 dated 2009-12-07

Title: Estimate a Log-Concave Probability Density from iid Observations
Description: Given independent and identically distributed observations X(1), ..., X(n), this package allows to compute the maximum likelihood estimator (MLE) of a density as well as a smoothed version of it under the assumption that the density is log-concave, see Rufibach (2007) and Duembgen and Rufibach (2009). The main function of the package is 'logConDens' that allows computation of the log-concave MLE and its smoothed version. In addition, we provide functions to compute (1) the value of the density and distribution function estimates (MLE and smoothed) at a given point (2) the characterizing functions of the estimator, (3) to sample from the estimated distribution, and (5) to compute a two-sample permutation test based on log-concave densities. Finally, two datasets that have been used to illustrate log-concave density estimation are made available.
Author: Kaspar Rufibach and Lutz Duembgen
Maintainer: Kaspar Rufibach

Diff between logcondens versions 1.3.5 dated 2009-12-07 and 2.0.0 dated 2010-08-27

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More information about logcondens at CRAN
Path: /cran/updated | permanent link

Package delftfews updated to version 0.3-38 with previous version 0.3-33 dated 2010-08-13

Title: delftfews R extensions
Description: a collection of timeseries sets handling functions used here at work (Nelen en Schuurmans), initially for the Lizard Scripter.
Author: Mario Frasca , Mich{\` e}l van Leeuwen
Maintainer: Mario Frasca

Diff between delftfews versions 0.3-33 dated 2010-08-13 and 0.3-38 dated 2010-08-27

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More information about delftfews at CRAN
Path: /cran/updated | permanent link

Package clusterCons updated to version 0.6 with previous version 0.5 dated 2010-08-25

Title: Calculate the consensus clustering result from re-sampled clustering experiments with the option of using multiple algorithms and parameter
Description: clusterCons is a package containing functions that generate robustness measures for clusters and cluster membership based on generating consensus matrices from bootstrapped clustering experiments in which a random proportion of rows of the data set are used in each individual clustering. This allows the user to prioritise clusters and the members of clusters based on their consistency in this regime. The functions allow the user to select several algorithms to use in the re-sampling scheme and with any of the parameters that the algorithm would normally take.
Author: Dr. T. Ian Simpson, University of Edinburgh
Maintainer: Dr. T. Ian Simpson

Diff between clusterCons versions 0.5 dated 2010-08-25 and 0.6 dated 2010-08-27

 DESCRIPTION                |    8 ++++----
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 4 files changed, 18 insertions(+), 14 deletions(-)

More information about clusterCons at CRAN
Path: /cran/updated | permanent link

Package cacher updated to version 1.1-1 with previous version 1.1 dated 2009-06-24

Title: Tools for caching and distributing statistical analyses
Description: This package provides tools for caching statistical analyses in key-value databases which can subsequently be distributed over the web.
Author: Roger D. Peng
Maintainer: Roger D. Peng

Diff between cacher versions 1.1 dated 2009-06-24 and 1.1-1 dated 2010-08-27

 DESCRIPTION         |   12 ++++++------
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More information about cacher at CRAN
Path: /cran/updated | permanent link

Package anapuce updated to version 2.2 with previous version 2.1 dated 2009-02-18

Title: Tools for microarray data analysis
Description: This package contains functions for normalisation,differentially analysis of microarray data and others functions implementing recent methods developed by the Statistic and Genom Team from UMR 518 AgroParisTech/INRA Appl. Math. Comput. Sc.
Author: J. Aubert (INRA)
Maintainer: J. Aubert

Diff between anapuce versions 2.1 dated 2009-02-18 and 2.2 dated 2010-08-27

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More information about anapuce at CRAN
Path: /cran/updated | permanent link

Package ProjectTemplate updated to version 0.1-2 with previous version 0.1-1 dated 2010-08-25

Title: Automates the creation of new R statistical analysis projects
Description: The ProjectTemplate package provides a function, create.project(), that automatically builds a directory for a new R project with a clean sub-directory structure and automatic data and library loading tools. The hope is that standardized data loading, automatic importing of best practice packages, integrated unit testing and useful nudges towards keeping a cleanly organized codebase will improve the quality of R coding.
Author: John Myles White
Maintainer: John Myles White

Diff between ProjectTemplate versions 0.1-1 dated 2010-08-25 and 0.1-2 dated 2010-08-27

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 ProjectTemplate-0.1-2/ProjectTemplate/R/load.project.R               |only
 ProjectTemplate-0.1-2/ProjectTemplate/R/run.tests.R                  |only
 ProjectTemplate-0.1-2/ProjectTemplate/README.markdown                |   49 +++++++++-
 ProjectTemplate-0.1-2/ProjectTemplate/TODO                           |    3 
 ProjectTemplate-0.1-2/ProjectTemplate/build_script.sh                |    4 
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/README           |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/TODO             |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/data             |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/diagnostics      |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/doc              |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/graphs           |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/lib              |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/profiling        |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/reports          |only
 ProjectTemplate-0.1-2/ProjectTemplate/inst/defaults/tests            |only
 ProjectTemplate-0.1-2/ProjectTemplate/man/ProjectTemplate-package.Rd |   20 ++--
 ProjectTemplate-0.1-2/ProjectTemplate/man/create.project.Rd          |    6 -
 ProjectTemplate-0.1-2/ProjectTemplate/man/load.project.Rd            |only
 ProjectTemplate-0.1-2/ProjectTemplate/man/run.tests.Rd               |only
 ProjectTemplate-0.1-2/ProjectTemplate/tests/1.R                      |    8 +
 27 files changed, 97 insertions(+), 52 deletions(-)

More information about ProjectTemplate at CRAN
Path: /cran/updated | permanent link

Package GGally updated to version 0.2.2 with previous version 0.2.1 dated 2010-07-30

Title: Extension to ggplot2.
Description: Package contains templates for different plots to be combined into a plot matrix.
Author: Barret Schloerke , Di Cook , Heike Hofmann , and Hadley Wickham
Maintainer: Barret Schloerke

Diff between GGally versions 0.2.1 dated 2010-07-30 and 0.2.2 dated 2010-08-27

 DESCRIPTION                     |    8 ++--
 NAMESPACE                       |    1 
 R/find-combo.r                  |    3 -
 R/gg-plots.r                    |   16 ++++++++-
 R/ggpairs.r                     |   67 ++++++++++++++++++++++++++--------------
 man/Not-Documented              |only
 man/addAndOverwriteAes.Rd       |    6 ++-
 man/eval_ggpair.Rd              |   22 ++++++++-----
 man/find_plot_type.Rd           |   14 +++++---
 man/getPlot.Rd                  |   14 +++++---
 man/get_plot_type.Rd            |   12 ++++---
 man/ggally_barDiag.Rd           |   15 +++++---
 man/ggally_blank.Rd             |   15 ++++++--
 man/ggally_box.Rd               |   14 +++++---
 man/ggally_cor.Rd               |   15 +++++---
 man/ggally_density.Rd           |   21 ++++++++----
 man/ggally_densityDiag.Rd       |   15 +++++---
 man/ggally_denstrip.Rd          |   14 +++++---
 man/ggally_dot.Rd               |   14 +++++---
 man/ggally_dotAndBox.Rd         |   17 ++++++----
 man/ggally_facetdensity.Rd      |   15 +++++---
 man/ggally_facetdensitystrip.Rd |   17 ++++++----
 man/ggally_facethist.Rd         |   15 +++++---
 man/ggally_points.Rd            |   14 +++++---
 man/ggally_ratio.Rd             |   15 ++++++--
 man/ggally_smooth.Rd            |   15 +++++---
 man/ggally_text.Rd              |   24 ++++++++------
 man/ggfluctuation2.Rd           |   23 +++++++++----
 man/ggpairs.Rd                  |   64 +++++++++++++++++++++-----------------
 man/is_blank_plot.Rd            |    6 ++-
 man/make_ggpair_text.Rd         |only
 man/plot_types.Rd               |   13 +++++--
 man/print.ggpairs.Rd            |   12 ++++---
 man/putPlot.Rd                  |   18 ++++++----
 man/vplayout.Rd                 |   12 ++++---
 35 files changed, 370 insertions(+), 196 deletions(-)

More information about GGally at CRAN
Path: /cran/updated | permanent link

Built and running on Debian GNU/Linux using R, littler and blosxom. Last updated on Fri, 27 Aug 2010 at 02:16.