CRAN (and crantastic) updates this week New packages ------------
* apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code published by Frey and Dueck. * BioPhysConnectoR (1.6-1) Franziska Hoffgaard http://crantastic.org/packages/BioPhysConnectoR Utilities and functions to investigate the relation between biomolecular structures, their interactions, and the evolutionary information revealed in sequence alignments of these molecules. * BradleyTerry2 (0.9-1) Heather Turner http://crantastic.org/packages/BradleyTerry2 Specify and fit the Bradley-Terry model and structured versions * catnet (1.00.0) Nikolay Balov http://crantastic.org/packages/catnet A package that handles discrete Bayesian network models and provides inference using the frequentist approach * CAVIAR (0.1-0) Cyrille Rathgeber http://crantastic.org/packages/CAVIAR Allows processing, visualisation and analysis of data coming from cambial activity and wood formation monitoring studies. * CCMtools (1.0) Mathieu Vrac http://crantastic.org/packages/CCMtools This package proposes a clustering method called "Correlation Clustering Model" (CCM) based on mixture of canonical correlation analysis (CCA). It also provides some tools for cluster analysis. * clusterCons (0.4) Dr. T. Ian Simpson http://crantastic.org/packages/clusterCons clusterCons is a package containing functions that generate robustness measures for clusters and cluster membership based on generating consensus matrices from bootstrapped clustering experiments in which a random proportion of rows of the data set are used in each individual clustering. This allows the user to prioritise clusters and the members of clusters based on their consistency in this regime. The functions allow the user to select several algorithms to use in the re-sampling scheme and with any of the parameters that the algorithm would normally take. * dagR (1.0.1) Lutz P Breitling http://crantastic.org/packages/dagR Functions to draw, manipulate and evaluate directed acyclic graphs. * DatABEL (0.0-6) Yurii Aulchenko http://crantastic.org/packages/DatABEL a package providing interface to C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyzes e.g. using GenABEL and ProbABEL * DeducerPlugInExample (0.1) Ian Fellows http://crantastic.org/packages/DeducerPlugInExample A example GUI plug-in package to serve as a template. * DiceDesign (1.0) D. Dupuy http://crantastic.org/packages/DiceDesign Space-Filling Designs and Uniformity Criteria. * DiceEval (1.0) D. Dupuy http://crantastic.org/packages/DiceEval Estimation, validation and prediction of metamodels (linear models, additive models, MARS and PolyMARS) * DiceKriging (1.0) O. Roustant http://crantastic.org/packages/DiceKriging Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km. * DiceOptim (1.0) D. Ginsbourger http://crantastic.org/packages/DiceOptim Expected Improvement. EGO algorithm. Parallelized versions of EGO: Constant Liars. * digitize (0.0.1-07) Timothee Poisot http://crantastic.org/packages/digitize Allows to get the data from a graph by providing calibration points * DistributionUtils (0.1-0) David Scott http://crantastic.org/packages/DistributionUtils This package contains utilities which are of use in the packages I have developed for dealing with distributions. Currently these packages are GeneralizedHyperbolic, VarianceGamma, and SkewHyperbolic. Additional packages are under development. Each of these packages requires DistributionUtils. Functionality includes sample skewness and kurtosis, log-histogram, moments by integration, changing the pint about which a moment is calculated, functions for testing distributions using inversion tests and the Massart inequality. * DoseFinding (0.1) Bjoern Bornkamp http://crantastic.org/packages/DoseFinding The DoseFinding package provides functions for the design and analysis of dose-finding experiments (for example pharmaceutical Phase II clinical trials). It provides functions for: multiple contrast tests, fitting non-linear dose-response models, calculating optimal designs and an implementation of the MCPMod methodology. Currently only normally distributed homoscedastic endpoints are supported. * GeneralizedHyperbolic (0.2-0) David Scott http://crantastic.org/packages/GeneralizedHyperbolic This package provides functions for the hyperbolic and related distributions. Density, distribution and quantile functions and random number generation are provided for the hyperbolic distribution, the generalized hyperbolic distribution, the generalized inverse Gaussian distribution and the skew-Laplace distribution. Additional functionality is provided for the hyperbolic distribution, including fitting of the hyperbolic to data. * hergm (1.1-1) Michael Schweinberger http://crantastic.org/packages/hergm * hglm (1.0) Lars Ronnegard http://crantastic.org/packages/hglm The hglm package is used to fit hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model. * HGLMMM (0.1) Marek Molas http://crantastic.org/packages/HGLMMM Hierarchical Generalized Linear Models * isopam (0.9-6) Sebastian Schmidtlein http://crantastic.org/packages/isopam Isopam clustering algorithm and utilities. Isopam optimizes clusters and optionally cluster numbers in a brute force style and aims at an optimum separation by a limited number of indicative descriptors (typically species). * MAd (0.2) AC Del Re http://crantastic.org/packages/MAd This is an integrated meta-analysis package for conducting a research synthesis with mean differences data. One of the unique features of this package is in its integration of user-friendly functions to complete most of the statistical steps involved in a meta-analysis with mean differences. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009). * mbmdr (2.0) Victor Urrea http://crantastic.org/packages/mbmdr Model Based Multifactor Dimension Reduction proposed by Calle et al. (2008) as a dimension reduction method for exploring gene-gene interactions. * minqa (1.1) Katharine Mullen http://crantastic.org/packages/minqa Derivative-free optimization by quadratic approximation based on an interface to Fortran implementations by M. J. D. Powell * mixOmics (2.6) Kim-Anh Le Cao http://crantastic.org/packages/mixOmics The package supplies two efficients methodologies: regularized CCA and sparse PLS to unravel relationships between two heterogeneous data sets of size (nxp) and (nxq) where the p and q variables are measured on the same samples or individuals n. These data may come from high throughput technologies, such as omics data (e.g. transcriptomics, metabolomics or proteomics data) that require an integrative or joint analysis. However, mixOmics can also be applied to any other large data sets where p+q>>n. rCCA is a regularized version of CCA to deal with the large number of variables. sPLS allows variable selection in a one step procedure and two frameworks are proposed: regression and canonical analysis. Numerous graphical outputs are provided to help interpreting the results. * MplusAutomation (0.2-3) Michael Hallquist http://crantastic.org/packages/MplusAutomation The MplusAutomation package leverages the flexibility of the R language to automate latent variable model estimation and interpretation using Mplus, a powerful latent variable modeling program developed by Muthen and Muthen (www.statmodel.com). Specifically, MplusAutomation provides routines for creating related groups of models, running batches of models, and extracting and tabulating model parameters and fit statistics. * mtsc (0.0.1) Charlotte Maia http://crantastic.org/packages/mtsc Place-holder package (roughly speaking an empty package) for finding clusters in multivariate timeseries. Full implementation pending. * ncdf4 (1.0) David Pierce http://crantastic.org/packages/ncdf4 This package provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files. * ordinal (2010.03-04) Rune Haubo B Christensen http://crantastic.org/packages/ordinal This package implements likelihood based models for ordinal (ordered categorical) data based on cumulative probabilities in the framework of cumulative link models. This includes the important proportional odds model but also allows for general regression structures for location as well as scale of the latent distribution, i.e. additive as well as multiplicative structures, structured thresholds (cut-points), nominal effects and flexible link functions. Further, a range of estimation procedures and a range of auxiliary functions are implemented. * oro.dicom (0.2.4) Brandon Whitcher http://crantastic.org/packages/oro-dicom Data input/output functions for data that conform to the Digital Imaging and Communications in Medicine (DICOM) standard, part of the Rigorous Analytics bundle. * oro.nifti (0.1.3) Brandon Whitcher http://crantastic.org/packages/oro-nifti Data input/output functions for data that follow either Analyze or NIfTI standards, part of the Rigorous Analytics bundle. * r2lh (0.6) Christophe M. Genolini http://crantastic.org/packages/r2lh generate univariate and bivariate analyses in LaTeX or HTML formats * random.polychor.pa (1.0) Fabio Presaghi http://crantastic.org/packages/random-polychor-pa The Function perform a parallel analysis using simulated polychoric correlation matrices. The nth-percentile of the eigenvalues distribution obtained from the randomly generated polychoric correlation matrices is returned. A plot comparing the two types of eigenvalues (real and simulated) will help determine the number of real eigenvalues that outperform random data. The function is based on the idea that if real data are non-normal and the polychoric correlation matrix is needed to perform a Factor Analysis, then the Parallel Analysis method used to choose a non-random number of factors should also be based on randomly generated polychoric correlation matrices and not on Pearson correlation matrices. * RcmdrPlugin.MAd (0.2) AC Del Re http://crantastic.org/packages/RcmdrPlugin-MAd This is an R-Commander plug-in for the MAd package (Meta-Analysis with Mean Differences). This package enables the user to conduct a meta-analysis in a menu-driven, graphical user interface environment (e.g., SPSS), while having the full statistical capabilities of R and the MAd package. The MAd package itself contains a variety of useful functions for conducting a research synthesis with mean differences data. One of the unique features of the MAd package is in its integration of user-friendly functions to complete many of the statistical steps involved in a meta-analysis with mean differences. It uses recommended procedures as described in The Handbook of Research Synthesis and Meta-Analysis (Cooper, Hedges, & Valentine, 2009). * RcppArmadillo (0.1.0) Dirk Eddelbuettel and Romain Francois http://crantastic.org/packages/RcppArmadillo R and Armadillo integration using Rcpp Armadillo is a C++ linear algebra library aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. Various matrix decompositions are provided through optional integration with LAPACK and ATLAS libraries. . A delayed evaluation approach is employed (during compile time) to combine several operations into one and reduce (or eliminate) the need for temporaries. This is accomplished through recursive templates and template meta-programming. . This library is useful if C++ has been decided as the language of choice (due to speed and/or integration capabilities), rather than another language. . This Armadillo / C integration provides a nice illustration of the capabilities of the Rcpp package for seamless R and C++ integration/ * RcppExamples (0.1.0) Dirk Eddelbuettel and Romain Francois http://crantastic.org/packages/RcppExamples Examples for Seamless R and C++ integration The Rcpp package contains a C++ library that facilitates the integration of R and C++ in various ways. This package provides examples. * Rdsm (1.0.0) Norm Matloff http://crantastic.org/packages/Rdsm Provides a threads-like programming environment for R, usable both on a multicore machine and across a network of multiple machines. The package gives the illusion of shared memory, again even across multiple machines on a network. * ris (1.0) Stephanie Kovalchik http://crantastic.org/packages/ris Importing RIS-formatted file into a list of Bibtex-like references; checking for duplications; converting references to citEntry objects * Rsolnp (1.0-2) Alexios Ghalanos http://crantastic.org/packages/Rsolnp General Non-linear Optimization Using Augmented Lagrange Multiplier Method * saws (0.9-3.1) M.P. Fay http://crantastic.org/packages/saws Tests coefficients with sandwich estimator of variance and with small samples. Regression types supported are gee, cox regression, and conditional logistic regression. * TreeRank (1.0-0) Nicolas Baskiotis http://crantastic.org/packages/TreeRank Implementation of the TreeRank methodology for building tree-based ranking rules for bipartite ranking through ROC curve optimization. * TreeSim (1.0) Tanja Stadler http://crantastic.org/packages/TreeSim The package simulates phylogenetic trees under a constant-rate birth-death process, conditioned on having a fixed number of final tips, or a fixed age, or a fixed age and number of tips. When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process. TreeSim further samples appropriately trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of leaves is first reached. This latter method is appropriate for m-tip trees generated under a big class of models (details in the bd.gsa.taxa man page). * tsne (0.1-1) Unknown http://crantastic.org/packages/tsne A "pure R" implementation of the t-SNE algorithm. * ttime (1.0) Radhakrishnan Nagarajan http://crantastic.org/packages/ttime Translate neurodevelopmental event timing across species. Predict unknown event timings and investigate phylogenetic proximity by hiearchical clustering of the known and predicted event timings. * UScensus2000blkgrp (0.03) Zack W. Almquist http://crantastic.org/packages/UScensus2000blkgrp US Census 2000 Block Group shapefiles and additional demographic data from the SF1 100 percent files. This data set contains polygon files in lat/lon coordinates and the corresponding demographic data for a number of different variables. * vcdExtra (0.4-1) Michael Friendly http://crantastic.org/packages/vcdExtra Provides additional data sets, methods and documentation to complement the vcd package for Visualizing Categorical Data. * VizCompX (0.1) Neil Diamond http://crantastic.org/packages/VizCompX Nimrod generates a Latin Hypercube Design using the emulator package. Based on this design, any function can be evaluated on the design points. A generalisation of the Nimrod/O test case is included. A Gaussian model can be fit to the data using the mlegp package. The resulting surface can be viewed using a wireframe plot with choice of viewing and conditioning variables and levels. * vmv (1.0) Waqas Ahmed Malik http://crantastic.org/packages/vmv Visualization of Missing Values * wq (0.2-2) Alan Jassby http://crantastic.org/packages/wq Functions to assist in the processing and exploration of data from monitoring programs for aquatic ecosystems. The focus is on time series data for physical and chemical properties of water, as well as the plankton. The package is intended for programs that sample approximately monthly at discrete stations. Updated packages ---------------- actuar (1.1-0), agricolae (1.0-9), AlgDesign (1.1-2), analogue (0.6-23), animation (1.1-0), aroma.affymetrix (1.5.0), aroma.core (1.5.0), arulesSequences (0.1-9), backtest (0.3-1), bayesclust (3.0), bcp (2.1.3), betareg (2.2-0), bio.infer (1.2-8), bipartite (1.07), BoolNet (1.4), BradleyTerry (0.8-8), CADStat (2.2-2), caGUI (0.1-4), caret (4.33), chemometrics (0.8), cocorresp (0.1-9), compHclust (1.0-1), conf.design (1.01), corpcor (1.5.6), countrycode (0.4), cshapes (0.2-3), Deducer (0.2-3), DEoptim (2.0-4), DescribeDisplay (0.2.2), deSolve (1.7), DiagnosisMed (0.2.3), diffractometry (0.1-02), DoE.base (0.9-17), dplR (1.2.9), dti (0.9-0), dynGraph (0.99100403), e1071 (1.5-23), eha (1.2-18), epitools (0.5-5), estout (1.0.1-1), extracat (1.0-1), extremevalues (2.0), far (0.6-3), farmR (1.1), FD (1.0-7), flashClust (1.00), flexmix (2.2-5), fmri (1.4-0), forensim (1.1-4), FrF2 (1.1), ftsa (1.5), fxregime (1.0-0), GAMens (1.1.1), gcExplorer (0.9-3), GEOmap (1.5-4), GeoXp (1.4.2), GeoXp (1.4.3), ggplot2 (0.8.7), gmt (1.1-4), gRapHD (0.1.6), gRbase (1.3.4), gsDesign (2.2-11), gstat (0.9-69), gWidgetsRGtk2 (0.0-62), gWidgetstcltk (0.0-31), helloJavaWorld (0.0-7), hergm (1.1-1), HiddenMarkov (1.3-1), hyperdirichlet (1.4-2), ibr (1.2.1), ic.infer (1.1-3), Imap (1.32), integrativeME (1.2), integrOmics (2.55), interval (0.9-9.6), ipw (1.0-4), kml (1.1.1), ks (1.6.11), latticeExtra (0.6-9), lda (1.2), lokern (1.0-9), longitudinalData (0.6.3), MAc (1.0.5), MAc (1.0.6), MAd (0.2), mboost (2.0-3), mc2d (0.1-7), mclust (3.4.3), MCMCglmm (2.03), mhsmm (0.3.2), mixAK (0.8), MKmisc (0.6.1), monomvn (1.8-1), MplusAutomation (0.2-2), MplusAutomation (0.2-3), multcomp (1.1-6), mvpart (1.3-1), ncvreg (2.0), neuralnet (1.3), nlstools (0.0-10), noia (0.94), nor1mix (1.1-2), party (0.9-9993), pcaPP (1.8), penalized (0.9-30), pgirmess (1.4.4), phyclust (0.1-5), picante (1.0-1), plotrix (2.8-3), plsdof (0.2-0), pmg (0.9-42), portfolio (0.4-5), portfolioSim (0.2-6), prefmod (0.8-19), PropCIs (0.1-5), PwrGSD (1.16), pyramid (1.2), qpcR (1.2-6), QRMlib (1.4.5), qvcalc (0.8-5), R.filesets (0.8.0), R2HTML (2.0.0), R2jags (0.02-02), randomSurvivalForest (3.6.2), rattle (2.5.24), rbenchmark (0.3), RcmdrPlugin.MAc (1.0.6), RcmdrPlugin.MAc (1.0.5), Rcpp (0.7.8), Rcpp (0.7.9), relations (0.5-7), reporttools (1.0.5), REQS (0.8-6), RFLPtools (1.1), RFOC (1.0-9), RGtk2DfEdit (0.5.4), rimage (0.5-8.1), rms (2.2-0), RQDA (0.1-9), Rsolnp (1.0-2), rsprng (1.0), RSQLite (0.8-4), RTOMO (1.0-7), runjags (0.9.6-3), s20x (3.1-7), sandwich (2.2-6), sbgcop (0.975), sdef (1.5), seacarb (2.3.2), season (0.2-4), seqinr (2.0-8), sfsmisc (1.0-11), SGP (0.0-5), signal (0.6-1), simecol (0.6-10), simPopulation (0.1.1), SkewHyperbolic (0.2-0), sm (2.2-4), snowfall (1.83), sp (0.9-61), spatstat (1.18-0), spBayes (0.1-6), spdep (0.4-59), stab (0.0.7), statmod (1.4.3), stoichcalc (1.1-1), strucchange (1.4-0), survey (3.21), SweaveListingUtils (0.4.3), tau (0.0-7), TeachingDemos (2.6), TeachingSampling (1.4.9), textcat (0.0-2), TGUITeaching (0.9.6), TGUITeaching (0.9.5), tm (0.5-3), tm.plugin.mail (0.0-2), tmvtnorm (1.0-2), tnet (2.5), topicmodels (0.0-4), topmodel (0.7.2), tradeCosts (0.3-1), trio (1.0.14), tsDyn (0.7-22), tseriesChaos (0.1-10), ttrTests (1.5), unmarked (0.8-3), UScensus2000 (0.07), UScensus2000add (0.04), UScensus2000cdp (0.03), UScensus2000tract (0.03), VarianceGamma (0.3-0), vars (1.4-7), vegan (1.17-2), WMBrukerParser (1.2) This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: crana...@gmail.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
