CRAN (and crantastic) updates this week New packages ------------
* alabama (2010.7-1) Ravi Varadhan http://crantastic.org/packages/alabama Augmented Lagrangian Adaptive Barrier Minimization Algorithm for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed. * BMS (0.2.5) Stefan Zeugner http://crantastic.org/packages/BMS Bayesian Model Averaging for univariate linear models under Zellner's g prior. Options include: fixed (BRIC, UIP, ...) and flexible g priors (Empirical Bayes, hyper-g), 5 kinds of model prior concepts, and model sampling via model enumeration or MCMC samplers (Metropolis-Hastings plain or reversible jump). Post-processing allows for inference according to different concepts (likelihood vs MCMC-based) and for plotting (posterior model size and coefficient densities, best models, model convergence, BMA comparison). * compareGroups (0.1-3) Isaac Subirana http://crantastic.org/packages/compareGroups This package is meant to facilitate the construction of bivariate table (descriptives of several variables between groups) and generate reports in LaTeX or (CSV) plain text. Also, it includes a graphical interface to build these tables more easily. * constrainedKriging (0.1.0) Christoph Hofer http://crantastic.org/packages/constrainedKriging The constrainedKriging package provides functions for efficient computations of nonlinear spatial predictions with local change of support. The package supplies functions for tow-dimensional spatial interpolation by constrained, covariance-matching constrained and universal (external drift) kriging for points or block of any shape for data with a nonstationary mean function and an isotropic weakly stationary variogram. The linear spatial interpolation methods, constrained and covariance-matching constrained kriging, provide approximately unbiased prediction for nonlinear target values under change of support. The constrainedKriging package extends the range of geostatistical tools available in R and provides a veritable alternative to conditional simulation for nonlinear spatial prediction problems with local change of support. * dafs (1.0-34) James M. Curran http://crantastic.org/packages/dafs Data and miscellanea to support the book "Introduction to Data analysis with R for Forensic Scientists", Curran, J.M. 2010 CRC Press ISBN: 978-1-4200-8826-7 * dismo (0.5-1) Unknown http://crantastic.org/packages/dismo Functions for species distribution modeling, that is, predicting entire distributions form occurences at specific sites. * gaussDiff (1.0) Henning Rust http://crantastic.org/packages/gaussDiff A collection difference measures for multivariate Gaussian probability density functions, such as the Euclidian mean, the Mahalanobis distance, the Kullback-Leibler divergence, the J-Coefficient, the Minkowski L2-distance, the Chi-square divergence and the Hellinger Coefficient. * grt (0.1-1) Kazunaga Matsuki http://crantastic.org/packages/grt Functions to generate and analyze data for psychology experiments based on the General Recognition Theory. * HDclassif (1.0) L.Berge http://crantastic.org/packages/HDclassif New disciminant analysis and data clustering methods for high dimensional data, based on the asumption that high-dimensional data live in different subspaces with low dimensionality proposing a new parametrization of the Gaussian mixture model which combines the ideas of dimension reduction and constraints on the model. * pvclass (1.0) Niki Zumbrunnen http://crantastic.org/packages/pvclass Computes nonparametric p-values for the potential class memberships of new observations as well as cross-validated p-values for the training data. The p-values are based on permutation tests applied to an estimated Bayesian likelihood ratio, using a plug-in statistic for the Gaussian model, 'k nearest neighbors' or 'weighted nearest neighbors'. Additionally, it provides graphical displays and quantitative analyses of the p-values. * rAverage (0.3-2) Stefano Noventa http://crantastic.org/packages/rAverage Parameter estimation for the Averaging model of Anderson's Information Integration Theory * RGtk2Extras (0.0.1) Tom Taverner http://crantastic.org/packages/RGtk2Extras Useful add-ons for RGtk2 * rJython (0.0-2) Carlos J. Gil Bellosta http://crantastic.org/packages/rJython R interface to Python via Jython allowing R to call python code. * rTOFsPRO (1.1) Dariya Malyarenko http://crantastic.org/packages/rTOFsPRO rTOFsPRO provides functions for signal processing of the linear TOF spectra to produce aligned peak intensity matrix (and peak positions) * Runiversal (1.0) Mehmet Hakan Satman http://crantastic.org/packages/Runiversal This package contains some functions for converting R objects to Java style variables and XML. Generated Java code is interpretable by dynamic Java libraries such as Beanshell. Calling R externally and handling the Java or XML output is an other way to call R from other languages without native interfaces. * splinesurv (0.6-14) Emmanuel Sharef http://crantastic.org/packages/splinesurv Utilities for nonparametric Bayesian analysis of clustered survival data. The baseline hazard function and frailty density are modeled using penalized B-splines. Options include adaptive knot selection and the inclusion of a parametric component. * sprint (0.2.0) University of Edinburgh SPRINT Team http://crantastic.org/packages/sprint A simple framework for performing computation in parallel of R scripts and a library of parallelized R functions. * VecStatGraphs3D (1.0) Juan Carlos Ruiz Cuetos http://crantastic.org/packages/VecStatGraphs3D This package performs a 3D statistical analysis, both numerical and graphic, of a set of vectors. Since a vector has three components (a module and two angles) vector analysis is performed in two stages: modules are analyzed by means of linear statistics and orientations are analyzed by spherical statistics. Tests and spherical statistic parameters have associated a full range of graphing: vector maps, density maps, distribution modules and angles. The tests, spherical statistic parameters and graphs allow us detecting another distribution properties (I.e. anisotropy) and outliers. * WGCNA (0.92-3) Peter Langfelder http://crantastic.org/packages/WGCNA Functions necessary to perform Weighted Gene Co-Expression Network Analysis Updated packages ---------------- ada (2.0-2), adegenet (1.2-5), AER (1.1-6), allan (1.01), amei (1.0-4), aroma.affymetrix (1.7.0), aroma.core (1.7.0), aroma.light (1.16.1), BaM (0.98), Bergm (1.3), BioPhysConnectoR (1.6-5), BioStatR (1.0.1), BMS (0.2.5), candisc (0.5-18), car (2.0-0), car (2.0-1), caret (4.45), caroline (0.2-0), CAVIAR (1.1-0), choplump (1.0-0.1), DAAGxtras (0.7-9), DAAGxtras (0.7-8), ddst (1.02), DPpackage (1.1-1), EnQuireR (0.10), exact2x2 (1.0-1.1), exactci (1.1-0.1), expm (0.98-2), FactoClass (1.0.4), FieldSim (3.1.3), forecast (2.06), formula.tools (1.0.1), fxregime (1.0-1), gee (4.13-15), genefu (1.0.8), geosphere (1.2-7), geozoo (0.4.2), GEVcdn (1.0.1), GGally (0.2.1), granova (1.4), grt (0.1-1), gWidgetsRGtk2 (0.0-68), gWidgetstcltk (0.0-39), hda (0.1-10), heplots (0.9-3), hergm (1.2-7), HiddenMarkov (1.3-2), HistData (0.6-9), inline (0.3.6), interval (1.0-0.0), IPSUR (1.0), lmtest (0.9-27), MChtest (1.0-2), metafor (1.4-0), mixAK (1.1), mixsmsn (0.2-6), mra (2.7), multtest (2.5.14), mvgraph (1.2), MVpower (2.0), ncdf (1.6.2), ncdf (1.6.3), optmatch (0.7-0), ouch (2.7-1), outliers (0.13-3), perm (1.0-0.0), perturb (2.04), phylobase (0.6.1), plink (1.2-4), plspm (0.1-10), proftools (0.0-3), qpcR (1.2-9), qtl (1.17-39), R.utils (1.4.4), raster (1.3-4), rattle (2.5.37), rAverage (0.3-2), Rcmdr (1.6-0), RcmdrPlugin.SensoMineR (1.11-01), rconifers (1.0.1), Rcpp (0.8.5), RcppArmadillo (0.2.4), RcppExamples (0.1.1), relations (0.5-8), RHRV (2.5), rjags (2.1.0-6), rjson (0.2.0), RODBC (1.3-2), rsm (1.40), rwm (1.51), scrime (1.2.1), season (0.2-5), spatstat (1.20-1), spcosa (0.2-2), spdep (0.5-17), splinesurv (0.6-14), strucchange (1.4-1), termstrc (1.3.2), textcat (0.0-4), timeDate (2120.90), timeSeries (2120.89), tolerance (0.2.2), TSAgg (0.1-9), TSP (1.0-1), ttime (1.2.2) New reviews ----------- * data.table, by branson.owen http://crantastic.org/reviews/82 * psych, by ch.lalanne http://crantastic.org/reviews/81 * DEoptim, by mhsatman http://crantastic.org/reviews/80 This email provided as a service for the R community by http://crantastic.org. 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