Package ape updated to version 2.2-2 with previous version 2.2-1 dated 2008-07-11

Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Vincent Lefort, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Title: Analyses of Phylogenetics and Evolution
Description: ape provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel's test, computation of minimum spanning tree, the population parameter theta based on various approaches, nucleotide diversity, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood, classifying genes in trees using the Klastorin-Misawa-Tajima approach. Phylogeny estimation can be done with the NJ, BIONJ, ME, and ML methods.

Diff between ape versions 2.2-1 dated 2008-07-11 and 2.2-2 dated 2008-10-09

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 ape-2.2-2/ape/R/mlphylo.R            |    6 -
 ape-2.2-2/ape/R/phymltest.R          |  123 ++++++++++++++---------------------
 ape-2.2-2/ape/R/read.nexus.R         |   18 ++---
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More information about ape at CRAN
Path: /cran/updated | permanent link

Package tgp updated to version 2.1-3 with previous version 2.1-2 dated 2008-04-18

Author: Robert B. Gramacy and Matt A. Taddy
Title: Bayesian treed Gaussian process models
Description: Bayesian nonstationary, semiparametric nonlinear regression and design by treed Gaussian processes with jumps to the limiting linear model (LLM). Special cases also implemented include Bayesian linear models, CART, treed linear models, stationary separable and isotropic Gaussian processes. Provides 1-d and 2-d plotting functions (with projection and slice capabilities) and tree drawing, designed for visualization of tgp-class output. Sensitivity analysis and multi-resolution models are supported, and a limited set of experimental design and adaptive sampling functions are also provided, including ALM, ALC, and expected improvement.

Diff between tgp versions 2.1-2 dated 2008-04-18 and 2.1-3 dated 2008-10-09

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 96 files changed, 141 insertions(+), 109 deletions(-)

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

Package RcmdrPlugin.Export updated to version 0.2-1 with previous version 0.2-0 dated 2008-04-09

Author: Liviu Andronic
Title: Graphically export objects to LaTeX or HTML
Description: This package provides facilities to graphically export Rcmdr output to LaTeX or HTML code. Essentially, at the moment, the plug-in is a graphical front-end to xtable(). It is intended to (1) facilitate exporting Rcmdr output to formats other than ASCII text and (2) provide R novices with an easy to use, easy to access reference on exporting R objects to formats suited for printed output.

Diff between RcmdrPlugin.Export versions 0.2-0 dated 2008-04-09 and 0.2-1 dated 2008-10-09

 DESCRIPTION                       |    8 -
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 5 files changed, 236 insertions(+), 179 deletions(-)

More information about RcmdrPlugin.Export at CRAN
Path: /cran/updated | permanent link

Package mra updated to version 2.2 with previous version 2.1 dated 2008-09-19

Author: Trent McDonald
Title: Analysis of Mark-Recapture data
Description: Analysis of mark-recapture data using covariates. Models implemented: CJS open population; Huggin's closed population.

Diff between mra versions 2.1 dated 2008-09-19 and 2.2 dated 2008-10-09

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 8 files changed, 410 insertions(+), 129 deletions(-)

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

New package bit with initial version 1.0
Package: bit
Type: Package
Title: A class for vectors of 1-bit booleans
Version: 1.0
Date: 2008-09-29
Author: Jens Oehlschlägel
Maintainer: Jens Oehlschlägel
Description: bitmapped vectors of booleans (no NAs), coercion from and to logicals, integers and integer subscripts; fast boolean operators and fast summary statistics. With bit vectors you can store true binary booleans {FALSE,TRUE} at the expense of 1 bit only, on a 32 bit architecture this means factor 32 less RAM and factor 32 more speed on boolean operations. With this speed gain it even pays-off to convert to bit in order to avoid a single boolean operation on logicals or a single set operation on (longer) integer subscripts, the pay-off is dramatic when such components are used more than once. Reading from and writing to bit is approximately as fast as accessing standard logicals - mostly due to R's time for memory allocation. The package allows to work with pre-allocated memory for return values by calling .Call() directly: when evaluating the speed of C-access with pre-allocated vector memory, coping from bit to logical requires only 70% of the time for copying from logical to logical; and copying from logical to bit comes at a performance penalty of 150%.
License: GPL-2
LazyLoad: yes
Encoding: latin1
Packaged: Wed Oct 8 20:20:10 2008; Jens Oehlschlaegel

More information about bit at CRAN
Path: /cran/new | permanent link

New package R2jags with initial version 0.01-11
Package: R2jags
Version: 0.01-11
Date: 2008-10-7
Title: R2jags: A Package for Running jags from R
Author: Yu-Sung Su , Masanao Yajima ,
Maintainer: Yu-Sung Su
Depends: methods, R(>= 2.7.0), coda, R2WinBUGS, rjags(>= 1.0.3)
SystemRequirements: jags (>= 1.0.3)
Description: Using this package to call jags from R.
License: GPL (>= 2)
Packaged: Thu Oct 9 00:16:01 2008; SUYS

More information about R2jags at CRAN
Path: /cran/new | permanent link