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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CRAN (and crantastic) updates this week New packages ------------ * AGSDest (1.0) Niklas Hack http://crantastic.org/packages/AGSDest Estimation in adaptive group sequential trials * atmi (1.0) Waldemar Kemler, Peter Schaffner, http://crantastic.org/packages/atmi Analysis and usage of the trading rules, which are based on technical market indicators as well as on the time series analysis. * gamesNws (0.5) Markus Schmidberger http://crantastic.org/packages/gamesNws This is a package with different card games (e.g. uno, poker, ...) and using a NWS Server as card table. You can play the games with your friends in the whole world. Just install a NWS Server at one machine, send the login data to your friends and start the game. * geneListPie (1.0) Xutao Deng http://crantastic.org/packages/geneListPie "geneListPie" package is for mapping a gene list to function categories defined in GOSlim or Kegg. The results can be plotted as a pie chart to provide a quick view of the genes distribution of the gene list among the function categories. The gene list must contain a list of gene symbols. The package contains a set of pre-processed gene sets obtained from Gene Ontology and MSigDB including human, mouse, rat and yeast. To provide a high level concise view, only GO slim and kegg are provided. The gene sets are regulared updated. User can also use customized gene sets. User can use the R Pie() or Pie3D() function for plotting the pie chart. Users can also choose to output the gene function mapping results and use external software such as Excel(R) for ploting. * sBF (1.0) Unknown http://crantastic.org/packages/sBF Smooth Backfitting for additive models using Nadaraya-Watson estimator * speedglm (0.1) Marco ENEA http://crantastic.org/packages/speedglm Fitting LMs and GLMs to large data sets by updating algorithms. * VIF (0.5) Dongyu Lin http://crantastic.org/packages/VIF This package implements a fast regression algorithm for building linear model for large data as defined in the paper "VIF-Regression: A Fast Regression Algorithm for Large Data (2009)" by Dongyu Lin, Dean P. Foster and Lyle H. Ungar. * WMCapacity (0.9) Richard D. Morey http://crantastic.org/packages/WMCapacity A GUI R implementation of hierarchical Bayesian models of working memory, used for analyzing change detection data. Updated packages ---------------- ape (2.4), BAYSTAR (0.2-3), bdoc (1.1), bindata (0.9-16), bio.infer (1.2-5), boot (1.2-40), CADFtest (0.3-0), caret (4.25), cluster (1.12.1), cond (1.2-0), copula (0.8-12), corcounts (1.3), csampling (1.2-0), DEoptim (2.0-1), diseasemapping (0.5.3), doMC (1.2.0), dplR (1.1.9.3), earth (2.3-5), effects (2.0-8), ez (1.4.2), fds (1.1), FieldSim (2.1), FinTS (0.4-3), foreach (1.3.0), foreign (0.8-38), FrF2 (1.0), ftsa (1.1), gstat (0.9-63), IDPmisc (1.1.05), intamapInteractive (1.0-7), isa2 (0.2), iterators (1.0.3), ks (1.6.7), lattice (0.17-26), LogConcDEAD (1.4-0), marg (1.2-0), Matrix (0.999375-31), mcmc (0.7-3), MCPMod (1.0-5), metafor (0.5-5), MLCM (0.0-6), nlme (3.1-95), nlreg (1.2-0), operators (0.1-5), pegas (0.2), penalized (0.9-27), PKtools (1.5-0), psych (1.0-81), PTAk (1.2-0), rainbow (1.5), Rcmdr (1.5-3), RcmdrPlugin.DoE (0.5-4), RcmdrPlugin.DoE (0.5-5), rgcvpack (0.1-3), rgdal (0.6-19), RLadyBug (0.6-0), rmetasim (1.1.09), rms (2.1-0), RSiteSearch (1.0-6), seacarb (2.2), spdep (0.4-46), tmvtnorm (0.8-3), YourCast (1.1-5) New reviews ----------- * faraway, by aaronchall http://crantastic.org/reviews/37 * perm, by izahn http://crantastic.org/reviews/36 * ggplot2, by this.is.mvw http://crantastic.org/reviews/35 This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: cranatic at gmail.com.
CRAN (and crantastic) updates this week New packages ------------ * adaptTest (1.0) Marc Vandemeulebroecke http://crantastic.org/packages/adaptTest The functions defined in this program serve for implementing adaptive two-stage tests. Currently, four tests are included: Bauer and Koehne (1994), Lehmacher and Wassmer (1999), Vandemeulebroecke (2006), and the horizontal conditional error function. User-defined tests can also be implemented. Reference: Vandemeulebroecke, An investigation of two-stage tests, Statistica Sinica 2006. * bcv (1.0) Patrick O. Perry http://crantastic.org/packages/bcv This package implements methods for choosing the rank of an SVD approximation via cross validation. It provides both Gabriel-style "block" holdouts and Wold-style "speckled" holdouts. Also included is an implementation of the SVDImpute algorithm. For more information about Bi-cross-validation, see Owen & Perry's 2009 AOAS article (at http://arxiv.org/abs/0908.2062) and Perry's 2009 PhD thesis (at http://arxiv.org/abs/0909.3052). * dse1 (2009.10-1) Paul Gilbert http://crantastic.org/packages/dse1 This package is only to aid transition to the unbundled dse package. It has no functions, but simply requires package EvalEst. * dse2 (2009.10-1) Paul Gilbert http://crantastic.org/packages/dse2 This package is only to aid transition to the unbundled dse package. It has no functions, but simply requires package EvalEst. * EvalEst (2009.10-2) Paul Gilbert http://crantastic.org/packages/EvalEst Multivariate Time Series - extensions.See ?00dse-Intro for more details. * glmdm (0.51) Jeff Gill http://crantastic.org/packages/glmdm R CODE FOR SIMULATION OF GLMDM * integrativeME (1.1) Kim-Anh Le Cao http://crantastic.org/packages/integrativeME Mixture of experts models (Jacobs et al., 1991) were introduced to account for nonlinearities and other complexities in the data. It is based on a divide-and-conquer strategy. Mixture of experts are of interest due to their wide applicability and the advantages of fast learning via the expectation-maximization (EM) algorithm. We have extended and implemented mixture of experts to combine categorical clinical factors and continuous microarray data in a binary classification framework to analyze cancer studies. To provide a hybrid signature of clinical factors and gene markers, we propose to apply different gene selection procedures as a first step. * integrativeMEdata (1.0) Kim-Anh Le Cao http://crantastic.org/packages/integrativeMEdata This package contains data sets with matched categorical clinical factors and microarray data for three cancer studies. This is part of the integrativeME package that combines these two types of variables in a binary classification framework by selecting a hybrid signature of clinical factors and gene markers. * latticedl (1.0) Toby Dylan Hocking http://crantastic.org/packages/latticedl Direct labeling functions that use the lattice package. * nodeHarvest (0.1) Nicolai Meinshausen http://crantastic.org/packages/nodeHarvest Node harvest is a simple interpretable tree-like estimator for high-dimensional regression and classification. A few nodes are selected from an initially large ensemble of nodes, each associated with a positive weight. New observations can fall into one or several nodes and predictions are the weighted average response across all these groups. The package offers visualization of the estimator. Predictions can return the nodes a new observation fell into, along with the mean response of training observations in each node, offering a simple explanation of the prediction. * sublogo (1.0) Toby Dylan Hocking http://crantastic.org/packages/sublogo Visualize correlation in biological sequence data using sublogo dendrogram plots. Updated packages ---------------- adimpro (0.7.3), aplpack (1.2.2), approximator (1.1-6), aws (1.6-1), aylmer (1.0-4), BACCO (2.0-4), BB (2009.9-1), binMto (0.0-4), boot (1.2-41), bootspecdens (3.0), bqtl (1.0-25), CalciOMatic (1.1-3), calibrator (1.1-7), ccgarch (0.1.7), choplump (1.0), CircStats (0.2-4), clv (0.3-2), compare (0.2-3), condGEE (0.1-3), contfrac (1.1-8), Davies (1.1-5), deSolve (1.5), Devore7 (0.7.2), dlnm (1.0.2), dplR (1.1.9.4), drfit (0.05-95), dse (2009.10-1), dti (0.8-2), EDR (0.6-3), effects (2.0-9), effects (2.0-10), eha (1.2-12), eiPack (0.1-6), emulator (1.1-7), epicalc (2.9.2.8), FGN (1.2), FitAR (1.79), forward (1.0.3), fts (0.7.6), gamlss (3.0-1), gamlss.cens (3.0.1), gamlss.data (3.0-1), gamlss.dist (3.0-1), gamlss.mx (3.0-1), gamlss.nl (3.0-1), gamlss.tr (3.0-1), geoR (1.6-27), geoRglm (0.8-26), gld (1.8.4), glmmML (0.81-6), gplots (2.7.2), grouped (0.6-0), HAPim (1.3), hash (1.0.2), hdrcde (2.12), heplots (0.8-10), intervals (0.13.1), irtoys (0.1.2), isotone (0.8-7), ivivc (0.1.5), Kendall (2.1), kernlab (0.9-9), ks (1.6.8), lcda (0.2), LearnEDA (1.01), LoopAnalyst (1.2-2), lordif (0.1-2), ltm (0.9-2), magic (1.4-6), matlab (0.8-3), maxLik (0.6-0), MChtest (1.0-1), mclust (3.3.2), MCPAN (1.1-9), mefa (3.1-3), memisc (0.95-22), Metabonomic (3.3.1), mixstock (0.9.2), MLDA (2.0), mratios (1.3.11), multipol (1.0-4), mvna (1.1-10), NestedCohort (1.1-2), nFactors (2.3.1), nlme (3.1-96), nparLD (1.1), onion (1.2-3), pairwiseCI (0.1-17), paran (1.4.2), pheno (1.5), pmg (0.9-40), POT (1.1-0), proxy (0.4-4), pwt (6.3-0), QCA3 (0.0-2), QCAGUI (1.3-7), R2jags (0.01-26), randomForest (4.5-31), randomForest (4.5-32), rateratio.test (1.0-1), RBerkeley (0.7-1), RcmdrPlugin.Export (0.2-2), relax (1.3.1), RFOC (1.0-6), RgoogleMaps (1.1.6), RMTstat (0.2), RODBC (1.3-1), RPostgreSQL (0.1-5), rrcov (1.0-00), RSEIS (2.2-0), rsm (1.13), runjags (0.9.5-1), sampleSelection (0.6-8), scatterplot3d (0.3-29), scout (1.0.1), scrime (1.1.7), scuba (1.2-3), SimComp (1.4.1), smoothtail (1.1.4), SMPracticals (1.3-1), SpatialExtremes (1.4-0), SpatialNP (1.0-1), spatstat (1.16-3), spdep (0.4-49), spdep (0.4-47), ssanv (1.0-1), surveillance (1.1-2), TRAMPR (1.0-6), trip (1.1-3), tripEstimation (0.0-29), tuneR (0.2-11), untb (1.6-1), vcd (1.2-6), vrmlgen (1.1), WriteXLS (1.8.2), xts (0.6-8) New reviews ----------- * odfWeave, by eRic http://crantastic.org/reviews/40 * RODBC, by eRic http://crantastic.org/reviews/39 * reshape, by eRic http://crantastic.org/reviews/38 This email provided as a service for the R community by http://crantastic.org. 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CRAN (and crantastic) updates this week New packages ------------ * cudaBayesreg (0.1-1) Adelino Ferreira da Silva http://crantastic.org/packages/cudaBayesreg Compute Unified Device Architecture (CUDA) is a software platform for massively parallel high-performance computing on NVIDIA GPUs. This package provides a CUDA implementation of a Bayesian multilevel model for the analysis of brain fMRI data. A fMRI data set consists of time series of volume data in 4D space. Typically, volumes are collected as slices of 64 x 64 "voxels". Analysis of fMRI data often relies on fitting linear regression models at each voxel of the brain. The volume of the data to be processed, and the type of statistical analysis to perform in fMRI analysis, call for high-performance computing strategies. In this package, the CUDA programming model uses a separate thread for fitting a linear regression model at each voxel in parallel. The global statistical model implements a Gibbs Sampler for hierarchical linear models with a normal prior. This model has been proposed by Rossi, Allenby and McCulloch in "Bayesian Statistics and Marketing", Chapter 3, and is referred to as "rhierLinearModel" in the R-package "bayesm". A notebook equipped with a NVIDIA "GeForce 8400M GS" card having Compute Capability 1.1 has been used in the tests. * DesignPatterns (0.1.0) Jitao David Zhang http://crantastic.org/packages/DesignPatterns Design patterns are building blocks of reusable object-oriented software projects. This package provides data structures and tools to implement, study and reuse design patterns, especially the ones introduced in the book 'Gang of Four'. * geneARMA (1.0) Timothy McMurry http://crantastic.org/packages/geneARMA Fit models for periodic gene expression to time-course microarray data in a normal mixture model framework with mean approximated by a truncated Fourier series and covariance structure modeled by an ARMA(p,q) process. Estimation is performed with the EM algorithm. * SAFD (0.02) Wolfgang Trutschnig http://crantastic.org/packages/SAFD The aim of the package is to provide some basic functions for doing statistics with one dimensional Fuzzy Data (in the form of polygonal fuzzy numbers). In particular, the package contains functions for the basic operations on the class of fuzzy numbers (sum, scalar product, mean, Hukuhara difference) as well as for calculating (Bertoluzza) distance, sample variance, sample covariance, sample correlation, and the Dempster-Shafer (levelwise) histogram. Moreover a function to simulate fuzzy random variables, bootstrap tests for the equality of means, and a function to do linear regression given trapezoidal fuzzy data is included. * season (0.2-2) Adrian Barnett http://crantastic.org/packages/season Routines for the seasonal analysis of health data, including regression models, time-stratified case-crossover, plotting functions and residual checks. * skellam (0.0-8-7) Jerry W. Lewis http://crantastic.org/packages/skellam Functions for the Skellam distribution, including: density (pmf), cdf, quantiles and random variates. * textcat (0.0-1) Kurt Hornik http://crantastic.org/packages/textcat Text categorization based on n-grams Updated packages ---------------- AICcmodavg (1.03), amap (0.8-4), AnalyzeFMRI (1.1-11), aroma.apd (0.1.7), BayesDA (1.0-1), bestglm (0.14), BiodiversityR (1.4), cem (1.0.116), cem (1.0.120), cem (1.0.117), classInt (0.1-13), clim.pact (2.2-39), clusterSim (0.36-6), contrast (0.12), date (1.2-29), diveMove (0.9.6), dlnm (1.1.0), doBy (4.0.5), doBy (4.0.4), DPpackage (1.0-8), e1071 (1.5-20), ElemStatLearn (0.1-7), FITSio (1.1-0), FKF (0.1.0), frailtypack (2.2-9.5), gam (1.01), geiger (1.3-1), glmulti (0.5-3), gplots (2.7.3), httpRequest (0.0.8), introgress (1.2.1), irr (0.80), isotone (1.0-0), KFAS (0.4.5), KFAS (0.4.6), lme4 (0.999375-32), Mcomp (2.01), mixtools (0.4.3), multmod (0.6), multtest (2.1.3), pastecs (1.3-10), PBSmodelling (2.50.162), plink (1.2-2), PMA (1.0.4), qcc (2.0), quantreg (4.43), R.oo (1.6.2), R2wd (1.1), rbounds (0.4), RcmdrPlugin.DoE (0.6), relaimpo (2.1-4), RelativeRisk (1.1-1), ringscale (0.1.2), RPostgreSQL (0.1-6), rsm (1.20), sdcMicro (2.6.2), SimComp (1.4.2), skmeans (0.1-2), slam (0.1-6), snp.plotter (0.3), spatstat (1.17-0), spdep (0.4-50), svmpath (0.93), tau (0.0-4), twitteR (0.1.2) This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: cranatic at gmail.com.