[R] CRAN (and crantastic) updates this week
Crantastic
cranatic at gmail.com
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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