[R] CRAN (and crantastic) updates this week

Mon Sep 28 01:39:27 CEST 2009

CRAN (and crantastic) updates this week

New packages
------------

* bdoc (1.0)
  Michael Anderson
  http://crantastic.org/packages/bdoc

  This package contains a function that will classify DNA barcodes as
  well as a few test and reference data sets.

* bdsmatrix (1.0)
  Terry Therneau
  http://crantastic.org/packages/bdsmatrix

  This is a special case of sparse matrices, used by coxme and kinship

* CircSpatial (1.0)
  Bill Morphet
  http://crantastic.org/packages/CircSpatial

  The package is a collection of functions for color continuous high
  resolution images of circular spatial data, circular kriging, and
  simulation of circular random fields.

* cond (1.1-3)
  Alessandra R. Brazzale
  http://crantastic.org/packages/cond

  Higher order likelihood-based inference for logistic and loglinear
  models

* coxme (2.0)
  Terry Therneau
  http://crantastic.org/packages/coxme

  Cox proportional hazards models containing Gaussian random effects,
  also known as frailty models.

* csampling (1.1-3)
  Alessandra R. Brazzale
  http://crantastic.org/packages/csampling

  Monte Carlo conditional inference for the parameters of a linear
  nonnormal regression model

* desire (1.0.5)
  Olaf Mersmann
  http://crantastic.org/packages/desire

  Harrington and Derringer-Suich type desirability functions

* difR (1.0)
  Sebastien Beland
  http://crantastic.org/packages/difR

  The difR package contains several traditional methods to detect DIF in
  dichotomously scored items. Both uniform and non-uniform DIF effects
  can be detected, with methods relying upon item response models or
  not. Some methods deal with more than one focal group.

* DTDA (1.1)
  Carla Moreira
  http://crantastic.org/packages/DTDA

  This package implements different algorithms for analyzing randomly
  truncated data, one-sided and two-sided (i.e. doubly) truncated
  data.

* gRapHD (0.1.0)
  Gabriel Coelho Goncalves de Abreu
  http://crantastic.org/packages/gRapHD

  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.

* IQCC (1.0)
  Emanuel P. Barbosa
  http://crantastic.org/packages/IQCC

  Builds statistical control charts with exact limits for univariate and
  multivariate cases.

* marg (1.1-3)
  Alessandra R. Brazzale
  http://crantastic.org/packages/marg

  Likelihood inference based on higher order approximations for linear
  nonnormal regression models

* MCMChybridGP (2.1)
  Mark J. Fielding
  http://crantastic.org/packages/MCMChybridGP

  Hybrid Markov chain Monte Carlo (MCMC) to simulate from a multimodal
  target distribution.  A Gaussian process approximation makes this
  possible when derivatives are unknown. The Package serves to
  minimize the number of function evaluations in Bayesian calibration
  of computer models using parallel tempering.  It allows replacement
  of the true target distribution in high temperature chains, or
  complete replacement of the target.  Methods used are described in,
  "Efficient MCMC schemes for Bayesian calibration of computer
  models", Fielding, Mark, Nott, David J. and Liong Shie-Yui (2009),
  in preparation. The authors gratefully acknowledge the support &
  contributions of the Singapore-Delft Water Alliance (SDWA).  The
  research presented in this work was carried out as part of the
  SDWA's Multi-Objective Multi-Reservoir Management research programme
  (R-264-001-272).

* nlreg (1.1-3)
  Alessandra R. Brazzale
  http://crantastic.org/packages/nlreg

  Likelihood inference based on higher order approximations for
  nonlinear models with possibly non constant variance

* nnclust (2.1)
  Thomas Lumley
  http://crantastic.org/packages/nnclust

  Finds nearest neighours and the minimum spanning tree for large data
  sets, does clustering using the minimum spanning tree.

* phybase (1.1)
  Liang Liu
  http://crantastic.org/packages/phybase

  This package provides functions to read, write, manipulate, estimate,
  and summarize phylogenetic trees including species trees which
  contain not only the topology and branch lengths but also population
  sizes. The input/output functions can read tree files in which trees
  are presented in parenthetic format. The trees are read in as a
  string and then transformed to a matrix which describes the
  relationship of nodes and branch lengths. The nodes matrix provides
  an easy access for developers to further manipulate the tree, while
  the tree string provides interface with other phylogenetic R
  packages such as "ape". The input/output functions can also be used
  to change the format of tree files between NEXUS and PHYLIP. Some
  basic functions have already been established in the package for
  manipulating trees such as deleting and swapping nodes, rooting and
  unrooting trees, changing the root of the tree. The package also
  includes functions such as "consensus", "coaltime, "popsize",
  "treedist" for summarizing phylogenetic trees, calculating the
  coalescence time, population size, and tree distance. The function
  maxtree is built in the package to esimtate the species tree from
  multiple gene trees.

* pooh (0.2)
  Charles J. Geyer
  http://crantastic.org/packages/pooh

  functions for computing closures of relations

* potts (0.3-4)
  Charles J. Geyer
  http://crantastic.org/packages/potts

  the title says it all

* RcmdrPlugin.DoE (0.5-2)
  Ulrike Groemping
  http://crantastic.org/packages/RcmdrPlugin-DoE

  WARNING: This package is currently in beta status! The package
  provides a platform-independent GUI for design of experiments. It is
  implemented as a plugin to the R-Commander, which is a more general
  graphical user interface for statistics in R based on tcl/tk. DoE
  functionality can be accessed through the menu Design that is added
  to the R-Commander menus.

* RInside (0.1.0)
  Dirk Eddelbuettel
  http://crantastic.org/packages/RInside

  C++ classes to embed R in C++ applications The RInside packages makes
  it easier to have 'R inside' your C++ application by providing a few
  wrapper classes. . As R itself is embedded, a shared library build
  of R is required. This works on Linux and OS X, but not necessarily
  on Windows due to the way R is built on Windows.

* rWMBAT (1.0)
  Algorithm problem, email to
  http://crantastic.org/packages/rWMBAT

  The package contain all the functions to get a resulting Bayesian
  network.

Updated packages
----------------

AER (1.1-4), akima (0.5-3), ape (2.3-3), ash (1.0-12), BAYSTAR
(0.2-2), BiplotGUI (0.0-5), condGEE (0.1-1), denstrip (1.4), digest
(0.4.0), digest (0.4.1), dirmult (0.1.2), DoE.base (0.9-4), earth
(2.3-4), epicalc (2.9.2.2), fields (6.01), fishmethods (1.0-1),
Formula (0.2-0), frontier (0.995-2), frontier (0.995-6), GWAF (1.1),
HyperbolicDist (0.6-2), impute (1.18.0), integrOmics (2.4), klaR
(0.6-0), languageR (0.955), mboost (1.1-3), mcmc (0.7-2), mefa
(3.1-2), mhsmm (0.3.1), MLCM (0.0-3), MNP (2.6-1), modTempEff (1.1),
mstate (0.2.2), NeatMap (0.3.1), nFactors (2.3), nplplot (4.4),
OAIHarvester (0.0-6), OjaNP (0.9-3), party (0.9-999), pcalg (0.1-9),
phmm (0.6.1), plm (1.2-0), pomp (0.25-4), QCA (0.6-2), qpcR (1.2-2),
R.huge (0.1.9), RcmdrPlugin.DoE (0.5-2), RQDA (0.1-8), sdtoolkit
(2.31), sgeostat (1.0-23), sqldf (0-1.7), stringkernels (0.8.7),
survey (3.18), tripack (1.3-4), YourCast (1.1-3)

New reviews
-----------

* yaml, by bjorn.maeland
  http://crantastic.org/reviews/33

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