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 This email provided as a service for the R community by http://crantastic.org. 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