CRAN (and crantastic) updates this week New packages ------------
* bisectr (0.0.2) Maintainer: Winston Chang Author(s): Winston Chang <wins...@stdout.org> License: GPL-2 http://crantastic.org/packages/bisectr Tools to find bad commits with git bisect * CUMP (1.0) Maintainer: Xuan Liu Author(s): Xuan Liu <liux...@bu.edu> and Qiong Yang <qy...@bu.edu> License: GPL (>= 2) http://crantastic.org/packages/CUMP Combining Univariate Association Test Results of Multiple Phenotypes for Detecting Pleiotropy * cumplyr (0.1-1) Maintainer: John Myles White Author(s): John Myles White License: MIT http://crantastic.org/packages/cumplyr Extends ddply to allow calculation of cumulative quantities. * dma (1.1) Maintainer: Tyler H. McCormick Author(s): Tyler H. McCormick, Adrian Raftery, David Madigan License: GPL-2 http://crantastic.org/packages/dma Dynamic model averaging for binary and continuous outcomes. * fanc (0.18) Maintainer: Kei Hirose Author(s): Kei Hirose, Michio Yamamoto License: GPL (>= 2) http://crantastic.org/packages/fanc This package computes the penalized maximum likelihood estimates of factor loadings and unique variances for various tuning parameters. The pathwise coordinate descent along with EM algorithm is used. * fishmove (0.0-1) Maintainer: Johannes Radinger Author(s): Johannes Radinger License: GPL (>= 2) http://crantastic.org/packages/fishmove Functions to predict fish movement parameters based on multiple regression and plotting leptokurtic fish dispersal kernels * googlePublicData (0.12.05) Maintainer: George Vega Yon Author(s): George Vega Yon License: GPL (>= 3) http://crantastic.org/packages/googlePublicData package provides a collection of functions to set up Google Public Data Explorer data visualization tool with your own data, building automaticaly the corresponding DSPL (XML) metadata file jointly with the CSV files. All zipped up and ready to be published at Public Data Explorer. * gsmaRt (1.0) Maintainer: Stephan Artmann Author(s): Stephan Artmann, Mathias Fuchs License: GPL http://crantastic.org/packages/gsmaRt combined miRNA- and mRNA-testing * HIest (1.0) Maintainer: Unknown Author(s): Ben Fitzpatrick License: GPL (>= 3) http://crantastic.org/packages/HIest Uses likelihood to estimate ancestry and heterozygosity. Evaluates simple hybrid classifications (parentals, F1, F2, backcrosses). Estimates genomic clines. * igraphdata (0.1) Maintainer: Gabor Csardi Author(s): Gabor Csardi <csardi.ga...@gmail.com> License: GPL (>= 2) + file LICENSE http://crantastic.org/packages/igraphdata A small collection of various network data sets, to use with the igraph package. They also work with the igraph0 package. * irtrees (0.1.0) Maintainer: Ivailo Partchev Author(s): Ivailo Partchev and Paul De Boeck License: GPL (>= 2) http://crantastic.org/packages/irtrees Helper functions and example data sets accompanying De Boeck, P. and Partchev, I. (2012) IRTrees: Tree-Based Item Response Models of the GLMM Family, Journal of Statistical Software - Code Snippets, 48(1), 1-28. * lava (1.0-5) Maintainer: Klaus. K. Holst Author(s): Klaus K. Holst License: GPL-3 http://crantastic.org/packages/lava Estimation and simulation of latent variable models * lava.tobit (0.4-6) Maintainer: Klaus. K. Holst Author(s): Klaus K. Holst License: GPL-3 http://crantastic.org/packages/lava-tobit lava plugin allowing combinations of left and right censored and binary outcomes * LeafAngle (1.1) Maintainer: Unknown Author(s): Remko Duursma License: GPL http://crantastic.org/packages/LeafAngle A leaf angle distribution is a special distribution that is defined between 0 and 90 degrees, and a number of distributions are used to characterize the leaf angle distribution in real plant canopies. This package includes methods to fit distributions to data, visualize the fit, and compare fits of nine different distributions. * makeProject (1.0) Maintainer: Noah Silverman Author(s): Noah Silverman License: GPL-3 http://crantastic.org/packages/makeProject This package creates an empty framework of files and directories for the "Load, Clean, Func, Do" structure described by Josh Reich. * mcmcse (0.1) Maintainer: James M. Flegal Author(s): James M. Flegal <jfle...@ucr.edu> License: GPL http://crantastic.org/packages/mcmcse Tools for calculating Monte Carlo standard errors (MCSE) in Markov chain Monte Carlo (MCMC) settings. This package considers standard errors for expectation and quantile estimators. * MetaDE (1.0) Maintainer: Jia Li Author(s): Jia Li and Xingbin Wang License: GPL-2 http://crantastic.org/packages/MetaDE A collection of functions for conducting genomic meta-analysis in R. * mets (0.1-8) Maintainer: Klaus. K. Holst Author(s): Klaus K. Holst and Thomas Scheike License: GPL (>= 2) http://crantastic.org/packages/mets Implementation of various statistical models for multivariate event history data. Including multivariate cumulative incidence models, and bivariate random effects probit models (Liability models) * MultiOrd (1.0) Maintainer: Anup Amatya Author(s): Anup Amatya and Hakan Demirtas License: GPL-2 http://crantastic.org/packages/MultiOrd A method for multivariate ordinal data generation given marginal distributions and correlation based on the methodology proposed by Demirtas (2006). * PEIP (1.2) Maintainer: Jonathan M. Lees Author(s): Jonathan M. Lees License: GPL http://crantastic.org/packages/PEIP Several Functions for Aster Book on Inverse Theory. These functiuons are translations of MATLAB code developed by the authors to illustrate the concepts of Inverse theory as applied to geophysics. * pgnorm (1.1) Maintainer: Unknown Author(s): Steve Kalke License: GPL (>= 2) http://crantastic.org/packages/pgnorm Evaluation of the pdf and the cdf of the univariate p-generalized normal distribution. Sampling from the p-generalized normal distribution using either the p-generalized polar method, the p-generalized rejecting polar method, the Monty Python method, the Ziggurat method or the method of Nardon and Pianca. The package also includes routines for the simulation of the bivariate, p-generalized uniform distribution on the p-generalized unit circle and the simulation of the corresponding angular distribution. * RcmdrPlugin.SCDA (0.0) Maintainer: Isis Bulte Author(s): Isis Bulte and Patrick Onghena License: GPL (>= 2) http://crantastic.org/packages/RcmdrPlugin-SCDA This package provides a GUI for the SCVA, SCRT and SCMA packages. It is written as an Rcmdr plugin. * ri (0.9) Maintainer: Cyrus Samii Author(s): Peter M. Aronow <peter.aro...@yale.edu> and Cyrus Samii <cds2...@nyu.edu> License: GPL (>= 2) http://crantastic.org/packages/ri This package provides a set of tools for conducting exact or approximate randomization-based inference for experiments of arbitrary design. The primary functionality of the package is in the generation, manipulation and use of permutation matrices implied by given experimental designs. Among other features, the package facilitates estimation of average treatment effects, constant effects variance estimation, randomization inference for significance testing against sharp null hypotheses and visualization of data and results. * semTools (0.1-0) Maintainer: Sunthud Pornprasertmanit Author(s): Sunthud Pornprasertmanit <psunt...@ku.edu>, Patrick Miller <patr1...@ku.edu>, Alex Schoemann <schoem...@ku.edu>, Yves Rosseel <yves.ross...@ugent.be> License: GPL (>= 2) http://crantastic.org/packages/semTools This package provide useful tools for structural equation modeling analysis. * simsem (0.2-0) Maintainer: Sunthud Pornprasertmanit Author(s): Sunthud Pornprasertmanit <psunt...@ku.edu>, Patrick Miller <patr1...@ku.edu>, Alexander Schoemann <schoem...@ku.edu> License: GPL (>= 2) http://crantastic.org/packages/simsem This package can be used to generate data using the structural equation modeling framework. This package is tailored to use those simulated data for various purposes, such as model fit evaluation, power analysis, or missing data handling and planning. * simSummary (0.1.0) Maintainer: Gregor Gorjanc Author(s): Gregor Gorjanc License: GPL (>= 2) http://crantastic.org/packages/simSummary simSummary is a small utility package which eases the process of summarizing simulation results. Simulations often produce intermediate results - some focal statistics that need to be summarized over several scenarios and many replications. This step is in principle easy, but tedious. The package simSummary fills this niche by providing a generic way of summarizing the focal statistics of simulations. The useR must provide properly structured input, holding focal statistics, and then the summary step can be performed with one line of code, calling the simSummary function. * spartan (1.0) Maintainer: Kieran Alden Author(s): Kieran Alden, Mark Read, Paul Andrews, Jon Timmis, Henrique Veiga-Fernandes, Mark Coles License: GPL-2 http://crantastic.org/packages/spartan Computer simulations are becoming a popular technique to use in attempts to further our understanding of complex systems. This package provides code for four techniques described in available literature which aid the analysis of simulation results, at both single and multiple timepoints in the simulation run. The first technique addresses aleatory uncertainty in the system caused through inherent stochasticity, and determines the number of replicate runs necessary to generate a representative result. The second examines how robust asimulation is to parameter perturbation, through the use of a one-at-a-time parameter analysis technique. Thirdly, a latin hypercube based sensitivity analysis technique is included which can elucidate non-linear effects between parameters and indicate implications of epistemic uncertainty with reference to the system being modelled. Finally, a further sensitivity analysis technique, the extended Fourier Amplitude Sampling Test (eFAST) has been included to partition the variance in simulation results between input parameters, to determine the parameters which have a significant effect on simulation behaviour. * SPSL (0.1-5) Maintainer: Pavel V. Moskalev Author(s): Pavel V. Moskalev <moskale...@gmail.com> License: GPL-3 http://crantastic.org/packages/SPSL SPSL package provides functionality for labeling of percolation cluster on 2D & 3D square lattice with various lattice size, relative fraction of accessible sites (occupation probability), iso- & anisotropy, von Neumann & Moore d-neighborhood * tm.plugin.factiva (1.0) Maintainer: Milan Bouchet-Valat Author(s): Milan Bouchet-Valat <nalimi...@club.fr> License: GPL (>= 2) http://crantastic.org/packages/tm-plugin-factiva This package provides a tm Source to create corpora from articles exported from the Dow Jones Factiva content provider as XML files. Updated packages ---------------- adaptMCMC (1.0.3), bayesclust (3.1), bayesm (2.2-5), biwavelet (0.11), blm (2012.2.1), boss (1.1), BradleyTerry2 (1.0-0), CDVine (1.1-6), cloudRmpi (1.2), coxme (2.2-3), cvTools (0.3.2), dbstats (1.0.2), dcmle (0.2-1), DescribeDisplay (0.2.3), doBy (4.5-3), extracat (1.5-0), fanc (0.18), fanovaGraph (1.2), fastICA (1.1-15), fda (2.2.8), FrF2 (1.4-1), gdsfmt (0.9.9), gmp (0.5-2), HAC (0.2-2), heplots (0.9-12), HTMLUtils (0.1.5), ImageMetrics (0.5), IPMpack (1.1), IsotopeR (0.4.2), lifecontingencies (0.9.3), M3 (0.3), maps (2.2-6), MatrixEQTL (1.6.0), mefa4 (0.2-7), meta (2.1-0), MissingDataGUI (0.1-3), msgps (1.3), multitaper (1.0-1), muma (1.1), OrgMassSpecR (0.3-12), pcaPP (1.9-47), phenology (3.31), planar (1.2.1), plotrix (3.4-1), pomp (0.42-4), prefmod (0.8-31), primer (1.0), psychomix (1.0-0), psychotools (0.1-3), QUIC (1.0), QUIC (1.1), RcmdrPlugin.KMggplot2 (0.1-0), RcmdrPlugin.survival (1.0-1), RcppSMC (0.1.1), relsurv (2.0-2), rfishbase (0.0-9), Rmpfr (0.4-7), robCompositions (1.6.0), robustbase (0.9-1), rpartOrdinal (2.0.4), RProtoBuf (0.2.4), rrBLUP (3.8), rredis (1.6.6), RSEIS (3.0-6), sampSurf (0.6-4), SDMTools (1.1-12), secr (2.3.2), SemiParBIVProbit (3.2-1), semPLS (1.0-8), spatstat (1.27-0), tclust (1.1-02), timsac (1.2.7), tm.plugin.mail (0.0-5), WMTregions (3.2.5) 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.
