[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * anim.plots (0.1) Maintainer: David Hugh-Jones Author(s): David Hugh-Jones davidhughjo...@gmail.com License: GPL-2 http://crantastic.org/packages/anim-plots Simple animated versions of basic R plots, using the #39;animation#39; package. Includes animated versions of plot, barplot, persp, contour, filled.contour, hist, curve, points, lines, text, symbols, segments, and arrows. * aoos (0.0.1) Maintainer: Sebastian Warnholz Author(s): Sebastian Warnholz License: GPL-3 | file LICENSE http://crantastic.org/packages/aoos Another implementation of object-orientation in R. Private and public methods are part of the class-definition. Allows to write a lot of small methods as part of the class definition without cluttering the object. * CpGFilter (1.0) Maintainer: Jun Chen Author(s): Jun Chen License: GPL-2 http://crantastic.org/packages/CpGFilter Filter CpGs based on Intra-class Correlation Coefficients (ICCs) when replicates are available. ICCs are calculated by fitting linear mixed effects models to all samples including the un-replicated samples. Including the large number of un-replicated samples improves ICC estimates dramatically. The method accommodates any replicate design. * dfcomb (1.0-1) Maintainer: Marie-Karelle Riviere Author(s): Marie-Karelle Riviere and Jacques-Henri Jourdan License: GPL-3 http://crantastic.org/packages/dfcomb Phase I/II adaptive dose-finding design for combination studies. Several methods are proposed depending on the type of combinations: (1) the combination of two cytotoxic agents, and (2) combination of a molecularly targeted agent with a cytotoxic agent. * dfmta (1.0-1) Maintainer: Marie-Karelle Riviere Author(s): Marie-Karelle Riviere and Jacques-Henri Jourdan License: GPL-3 http://crantastic.org/packages/dfmta Phase I/II adaptive dose-finding design for single-agent Molecularly Targeted Agent (MTA), according to the paper quot;Phase I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau Determination using Adaptive Randomizationquot;, Statistics in Medicine, 2014. * dummy (0.1.0) Maintainer: Michel Ballings Author(s): Michel Ballings and Dirk Van den Poel License: GPL (= 2) http://crantastic.org/packages/dummy Efficiently create dummies of all factors and character vectors in a data frame. Support is included for learning the categories on one data set (e.g., a training set) and deploying them on another (e.g., a test set). * FAMILY (0.1.18) Maintainer: Asad Haris Author(s): Asad Haris License: GPL (= 2) http://crantastic.org/packages/FAMILY Fits penalized linear and logistic regression models with pairwise interaction terms. * geesmv (1.0) Maintainer: Zheng Li Author(s): Ming Wang mw...@phs.psu.edu License: GPL (= 3) http://crantastic.org/packages/geesmv Generalized estimating equations with the original sandwich variance estimator proposed by Liang and Zeger (1986), and eight types of more recent modified variance estimators for improving the finite small-sample performance. * geocodeHERE (0.1) Maintainer: Cory Nissen Author(s): Cory Nissen corynis...@gmail.com [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/geocodeHERE Wrapper for Nokia#39;s HERE geocoding API. See http://here.com/ for more information on HERE and https://developer.here.com/geocoder for more information on the HERE geocoding API. * ggswissmaps (0.0.2) Maintainer: Sandro Petrillo Burri Author(s): Sandro Petrillo Burri gibo@gmail.com License: GPL-2 http://crantastic.org/packages/ggswissmaps Offers various swiss maps as ggplot2 objects and gives the possibility to add layers of data on the maps. Data are publicly available from the swiss federal statistical office. * hcp (0.1) Maintainer: Yulei Wang Author(s): Stephen J.Ganocy, Jiayang Sun, and Yulei Wang License: GPL-2 | GPL-3 http://crantastic.org/packages/hcp Estimation of parameters in 3-segment (i.e. 2 change-point) regression models with heteroscedastic variances is provided based on both likelihood and hybrid Bayesian approaches, with and without continuity constraints at the change points. * heritability (1.0) Maintainer: Willem Kruijer Author(s): Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke. License: GPL-3 http://crantastic.org/packages/heritability implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * addreg (1.2) Maintainer: Mark Donoghoe Author(s): Mark Donoghoe mark.donog...@mq.edu.au License: GPL (= 2) http://crantastic.org/packages/addreg Methods for fitting identity-link GLMs and GAMs to discrete data. The package uses EM-type algorithms with more stable convergence properties than standard methods. * CateSelection (1.0) Maintainer: Yi Xu Author(s): Yi Xu and Jixiang Wu License: GPL (= 2) http://crantastic.org/packages/CateSelection A multi-factor dimensionality reduction based forward selection method for genetic association mapping. * DAMOCLES (1.0) Maintainer: Rampal S. Etienne Author(s): Rampal S. Etienne Alex L. Pigot License: GPL-2 http://crantastic.org/packages/DAMOCLES Simulates and computes (maximum) likelihood of a dynamical model of community assembly that takes into account the phylogenetic history * exCon (0.1-0) Maintainer: Bryan A. Hanson Author(s): Bryan Hanson [aut, cre], Kristina Mulry [ctb] License: GPL-3 http://crantastic.org/packages/exCon exCon is an interactive tool to explore topographic-like data sets. Such data sets take the form of a matrix in which the rows and columns provide location/frequency information, and the matrix elements contain altitude/response information. Such data is found in cartography, 2D spectroscopy and chemometrics. exCon creates an interactive web page showing the contoured data set along with slices from the original matrix parallel to each dimension. The page is written in d3/javascript. * genpathmox (0.1) Maintainer: quot;Giuseppe Lambertiquot; Author(s): Giuseppe Lamberti [aut, cre] License: GPL-3 http://crantastic.org/packages/genpathmox genpathmox provides a very interesting solution for handling segmentation variables in complex statistical methodology. It contains en extended version of the PATHMOX algorithm in the context of partial least square path modeling (Sanchez, 2009) including the F-block test (to detect the responsible latent endogenous equations of the difference), the F-coefficient (to detect the path coefficients responsible of the difference) and the invariance test (to realize a comparison between the sub-models#39; latent variables). Furthermore, the package contains a generalized version of the PATHMOX algorithm to approach different methodologies: linear regression and least absolute regression models. * hermite (1.0) Maintainer: David Moriña Soler Author(s): David Moriña (Centre for Research in Environmental Epidemiology, CREAL), Manuel Higueras (Universitat Autònoma de Barcelona and Public Health England) and Pedro Puig (Universitat Autònoma de Barcelona) License: GPL (= 2) http://crantastic.org/packages/hermite Probability functions for the generalized Hermite distribution * MfUSampler (0.9) Maintainer: Alireza S. Mahani Author(s): Alireza S. Mahani, Mansour T.A. Sharabiani License: GPL (= 2) http://crantastic.org/packages/MfUSampler Convenience Functions for Multivariate MCMC Using Univariate Samplers, including Slice Sampler with Stepout and Shrinkage (Neal, 2003), and Adaptive Rejection Sampler (Gilks and Wild, 1992). * myTAI (0.0.1) Maintainer: Hajk-Georg Drost Author(s): Hajk-Georg Drost License: GPL-3 http://crantastic.org/packages/myTAI The present collection of functions can be used to perform phylotranscriptomics analyses to investigate phenomena within the field of Evolutionary Developmental Biology * PrevMap (1.0) Maintainer: Emanuele Giorgi Author(s): Emanuele Giorgi, Peter J. Diggle License: GPL (= 2) http://crantastic.org/packages/PrevMap The PrevMap package provides functions for both likelihood-based and Bayesian analysis of spatially referenced prevalence data. #39;PrevMap#39; is also an extension of the #39;geoR#39; package which should be installed first together with the #39;maxLik#39;, #39;raster#39; and #39;pdist#39; packages. * qdm (0.1-0) Maintainer: Nora Umbach Author(s): Nora Umbach [aut, cre], Florian Wickelmaier [aut] License: GPL (= 2) http://crantastic.org/packages/qdm This package provides different specifications of a Quadrilateral Dissimilarity Model which can be used to fit same-different judgments in order to get a predicted matrix that satisfies regular minimality [Colonius amp; Dzhafarov, 2006, Measurement and representations of sensations, Erlbaum]. From such a matrix, Fechnerian distances can be computed. * RealVAMS (0.3-1) Maintainer: Andrew Karl Author(s): Andrew Karl, Jennifer Broatch, and Jennifer Green License: GPL-2 http://crantastic.org/packages/RealVAMS The RealVAMs package fits a multivariate value-added model (VAM) (see Broatch and Lohr 2012) with normally distributed test scores and a binary outcome indicator. This material is based upon work supported
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * BayesMixSurv (0.9) Maintainer: Alireza S. Mahani Author(s): Alireza S. Mahani, Mansour T.A. Sharabiani License: GPL (= 2) http://crantastic.org/packages/BayesMixSurv Bayesian Mixture Survival Models using Additive Mixture-of-Weibull Hazards, with Lasso Shrinkage and Stratification * cdcsis (1.0) Maintainer: Canhong Wen Author(s): Canhong Wen, Wenliang Pan, Mian Huang, and Xueqin Wang License: GPL (= 2) http://crantastic.org/packages/cdcsis Gives conditional distance correlation and performs the conditional distance correlation sure independence screening procedure for ultrahigh dimensional data. The conditional distance correlation is a novel conditional dependence measurement of two random variables given a third variable. The conditional distance correlation sure independence screening is used for screening variables in ultrahigh dimensional setting. * choroplethrMaps (1.0) Maintainer: Ari Lamstein Author(s): Ari Lamstein arilamst...@gmail.com License: BSD_3_clause + file LICENSE http://crantastic.org/packages/choroplethrMaps Contains 3 maps. 1) US States 2) US Counties 3) Countries of the world. * commentr (0.1) Maintainer: Erik Bulow Author(s): Erik Bulow License: GPL-2 http://crantastic.org/packages/commentr Functions to produce nicely formatted comments to use in R-scripts (or Latex/HTML/markdown etc). A comment with formatting is printed to the console and can then be copied to a script. * DetMCD (0.0.1) Maintainer: Vakili Kaveh Author(s): Vakili Kaveh [aut, cre], Mia Hubert [ths] License: GPL (= 2) http://crantastic.org/packages/DetMCD DetMCD is a new algorithm for robust and deterministic estimation of location and scatter. The benefits of robust and deterministic estimation are explained in Hubert, M., Rousseeuw, P.J. and Verdonck, T. (2012),quot;A deterministic algorithm for robust location and scatterquot;, Journal of Computational and Graphical Statistics, Volume 21, Number 3, Pages 618--637. * FDGcopulas (1.0) Maintainer: Gildas Mazo Author(s): Gildas Mazo, Stephane Girard License: GPL (= 3) http://crantastic.org/packages/FDGcopulas FDG copulas are a class of copulas featuring an interesting balance between flexibility and tractability. This package provides tools to construct, calculate the pairwise dependence coefficients of, simulate from, and fit FDG copulas. The acronym FDG stands for #39;one-Factor with Durante Generators#39;, as an FDG copula is a one-factor copula -- that is, the variables are independent given a latent factor -- whose linking copulas belong to the Durante class of bivariate copulas (also referred to as exchangeable Marshall-Olkin or semilinear copulas). * glmvsd (1.0) Maintainer: Yi Yang Author(s): Ying Nan nanx0...@gmail.com, Yi Yang yiy...@umn.edu, Yuhong Yang yy...@stat.umn.edu License: GPL-2 http://crantastic.org/packages/glmvsd Variable selection deviation measures and instability tests for high-dimensional model selection methods such as LASSO, SCAD and MCP, etc., to decide whether the sparse patterns identified by those methods are reliable. * highD2pop (1.0) Maintainer: Karl Gregory Author(s): Karl Gregory License: GPL (= 2) http://crantastic.org/packages/highD2pop Performs the generalized component test from Gregory et al (2015), as well as the tests from Chen and Qin (2010), Srivastava and Kubokawa (2013), and Cai, Liu, and Xia (2014) for equality of two population mean vectors when the length of the vectors exceeds the sample size. * indicoio (0.3) Maintainer: Madison May Author(s): Alexander Gedranovich gedranov...@gmail.com License: MIT + file LICENSE http://crantastic.org/packages/indicoio R-based client for Machine Learning APIs at http://indico.io. Provides wrappers for following APIs: Positive/Negative Sentiment Analysis, Political Sentiment Analysis, Image Feature Extraction, Facial Emotion Recognition, Facial Feature Extraction, Language Detection * JMdesign (1.1) Maintainer: Shannon Holloway Author(s): Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim License: GPL-2 http://crantastic.org/packages/JMdesign Performs power calculations for joint modeling of longitudinal and survival data with k-th order trajectories when the variance-covariance matrix, Sigma_theta, is unknown. * lmenssp (1.0) Maintainer: Ozgur Asar Author(s): Ozgur Asar, Peter J. Diggle License: GPL (= 2) http://crantastic.org/packages/lmenssp Fit, filter and smooth mixed models with non-stationary processes * managelocalrepo (0.1.4) Maintainer: Imanuel Costigan Author(s): Imanuel Costigan i.costi...@me.com License: GPL-2 http://crantastic.org/packages/managelocalrepo This will allow easier management of a CRAN-style repository on local
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * bio3d (2.1-1) Maintainer: Barry Grant Author(s): Barry Grant, Xin-Qiu Yao, Lars Skjaerven, Julien Ide License: GPL (= 2) http://crantastic.org/packages/bio3d Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation networkanalysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information. * CLME (1.0-1) Maintainer: Casey M. Jelsema Author(s): Casey M. Jelsema License: GPL-2 | GPL-3 http://crantastic.org/packages/CLME Implements constrained inference for linear mixed effects models using residual bootstrap methodology. * CP (1.5) Maintainer: Andreas Kuehnapfel Author(s): Andreas Kuehnapfel License: GPL-3 http://crantastic.org/packages/CP Functions for calculating the conditional power for different models in survival time analysis within randomized clinical trials with two different treatments to be compared and survival as an endpoint. * dataRetrieval (1.4.0) Maintainer: Laura DeCicco Author(s): Robert Hirsch [aut], Laura DeCicco [aut, cre] License: Unlimited | file LICENSE http://crantastic.org/packages/dataRetrieval Collection of functions to help retrieve USGS data from either web services or user-provided data files. * ecoval (1.0) Maintainer: Nele Schuwirth Author(s): Nele Schuwirth nele.schuwi...@eawag.ch and Peter Reichert peter.reich...@eawag.ch with contributions by Simone Langhans License: GPL (= 2) http://crantastic.org/packages/ecoval Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions. * enigma (0.1.0) Maintainer: Scott Chamberlain Author(s): Scott Chamberlain [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/enigma Enigma (https://enigma.io) holds many public datasets from governments, companies, universities, and organizations. Enigma provides an API for data, metadata, and statistics on each of the datasets. enigma is an R client to interact with the Enigma API, including getting the data and metadata for datasets in Enigma, as well as collecting statistics on datasets. In addition, you can download a gzipped csv file of a dataset if you want the whole dataset. An API key from Enigma is required to use enigma. * flam (1.0) Maintainer: Ashley Petersen Author(s): Ashley Petersen License: GPL (= 2) http://crantastic.org/packages/flam Implements the fused lasso additive model as proposed in Petersen, A., Witten, D., and Simon, N. (2014). Fused Lasso Additive Model. arXiv preprint arXiv:1409.5391. * gets (0.1) Maintainer: Genaro Sucarrat Author(s): Genaro Sucarrat License: GPL-2 http://crantastic.org/packages/gets Automated multi-path General-to-Specific (GETS) model selection of either an AR-X model with log-ARCH-X errors, or a log-ARCH-X model of the log-variance. The three main functions of the package are arx, getsm and getsv. The first function estimates an AR-X model with log-ARCH-X errors. The second function undertakes GETS model selection of the mean specification of an arx object, whereas the third function undertakes GETS model selection of the log-variance specification of an arx object. * ggRandomForests (1.0.0) Maintainer: John Ehrlinger Author(s): John Ehrlinger john.ehrlin...@gmail.com License: GPL (= 3) http://crantastic.org/packages/ggRandomForests The ggRandomForests package contains tools for creating and plotting data structures to visually understand random forest models. The functions are designed for use with the randomForestSRC package. This package is structured to extract intermediate data objects from the random forest. S3 Plot functions, which use the ggplot2 package, are included for each data object. * highTtest (1.0) Maintainer: Shannon Holloway Author(s): Hongyuan Cao [aut], Michael Kosorok [aut], Shannon Holloway [aut, cre] License: GPL-2 http://crantastic.org/packages/highTtest Implements the method developed by Cao and Kosorok (2011) for the significance analysis of thousands of features in high-dimensional biological studies. It is an
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * adwave (1.0) Maintainer: Murray Cox Author(s): Jean Sanderson License: GPL (= 2) http://crantastic.org/packages/adwave Implements wavelet-based approaches for describing population admixture. Principal Components Analysis (PCA) is used to define the population structure and produce a localized admixture signal for each individual. Wavelet summaries of the PCA output describe variation present in the data and can be related to population-level demographic processes. For more details, see accompanying paper. * bdscale (1.0) Maintainer: Dave Mills Author(s): Dave Mills dave.a.mi...@gmail.com License: GPL-2 http://crantastic.org/packages/bdscale Provides a continuous date scale, omitting weekends and holidays * BNSP (1.0.0) Maintainer: Georgios Papageorgiou Author(s): Georgios Papageorgiou License: GPL (= 2) http://crantastic.org/packages/BNSP Markov chain Monte Carlo algorithms for non- and semi-parametric models * CEC (0.9.1) Maintainer: Konrad Kamieniecki Author(s): Konrad Kamieniecki License: GPL-3 http://crantastic.org/packages/CEC Cross-Entropy Clustering (CEC) divides the data into Gaussian type clusters. It performs the automatic reduction of unnecessary clusters, while at the same time allows the simultaneous use of various type Gaussian mixture models. * ENiRG (0.1) Maintainer: Fernando Garcia Canovas Author(s): Fernando Canovas, Chiara Magliozzi, Jose Antonio Palazon-Ferrando, Frederico Mestre, Mercedes Gonzalez-Wanguemert License: GPL (= 2) http://crantastic.org/packages/ENiRG The package allows to perform the Ecological Niche Factor Analysis, calculate habitat suitability maps and classify the habitat in suitability classes. Computations are executed in a throw-away GRASS environment from R in order to be able to perform analysis with large data sets. * HiDimMaxStable (0.1) Maintainer: Alexis Bienvenue Author(s): Alexis Bienvenüe [aut, cre], Christian Robert [aut] License: GPL (= 2) http://crantastic.org/packages/HiDimMaxStable Inference of high dimensional max-stable distributions, from the paper quot;Likelihood based inference for high-dimensional extreme value distributionsquot;, by A. Bienvenüe and C. Robert, arXiv:1403.0065 [stat.AP]. * HierO (0.1) Maintainer: Kari Tokola Author(s): Kari Tokola License: GPL-2 http://crantastic.org/packages/HierO HierO is a graphical user interface (GUI) tool for calculating optimal statistical power and sample size for hierarchical data structure. HierO constructs a user defined sample size optimization problem to GAMS (General Algebraic Modeling System)form and uses Rneos package to send the problem to NEOS server for solving. * ibelief (1.0) Maintainer: Kuang Zhou Author(s): Kuang Zhou kzhoum...@163.com; Arnaud Martin arnaud.mar...@univ-rennes1.fr License: GPL (= 2) http://crantastic.org/packages/ibelief This package contains several basic functions to implement belief functions. * MareyMap (1.2) Maintainer: Aurelie Siberchicot Author(s): Aurelie Siberchicot, Clement Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais License: GPL (= 2) http://crantastic.org/packages/MareyMap A package to graphically estimate local recombination rates across a genome using marey maps. * mfblock (1.0) Maintainer: Marc Fortier Author(s): Marc Fortier License: GPL-3 http://crantastic.org/packages/mfblock Implementation of the simulated method of moments (smm) of Oh and Patton for copula-based multivariate models * msBP (1.0) Maintainer: Antonio Canale Author(s): Antonio Canale License: GPL-2 http://crantastic.org/packages/msBP Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2014). * mvprpb (1.0.4) Maintainer: Noboru Nomura Author(s): Noboru Nomura License: BSD_3_clause + file LICENSE http://crantastic.org/packages/mvprpb Computes orthant probabilities multivariate normal distribution. * NB (0.9) Maintainer: Tin-Yu Hui Author(s): Tin-Yu Hui @ Imperial College London License: GPL (= 2) http://crantastic.org/packages/NB Estimate the effective population size of a closed population using genetic data collected from two or more data points. * PerFit (1.2) Maintainer: Jorge N. Tendeiro Author(s): Jorge N. Tendeiro License: GPL (= 2) http://crantastic.org/packages/PerFit PerFit contains several person fit indices that allow assessing whether individual response patterns to tests or questionnaires are (im)plausible given the other respondents in the sample or a specified Item Response Theory model. * PLordprob (1.0) Maintainer: Euloge Clovis Kenne Pagui Author(s): Euloge Clovis Kenne Pagui [aut,cre],
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * activity (1.0) Maintainer: Marcus Rowcliffe Author(s): Marcus Rowcliffe marcus.rowcli...@ioz.ac.uk License: GPL-3 http://crantastic.org/packages/activity Provides functions to fit kernel density functions to animal activity time data; plot activity distributions; quantify overall levels of activity; statistically compare activity metrics through bootstrapping; and evaluate variation in linear variables with time (or other circular variables). * atmcmc (1.0) Maintainer: Jinyoung Yang Author(s): Jinyoung Yang License: GPL (= 2) http://crantastic.org/packages/atmcmc Uses adaptive diagnostics to tune and run a random walk Metropolis MCMC algorithm, to converge to a specified target distribution and estimate means of functionals. * blocksdesign (1.1) Maintainer: Rodney Edmondson Author(s): R. N. Edmondson License: GPL (= 2) http://crantastic.org/packages/blocksdesign Nested block designs for unstructured treatment sets where blocks can be repeatedly nested and treatments can have different levels of replication. Blocks strata are optimized hierarchically with each set of nested blocks optimized within the levels of the preceding set. Block sizes are equal if the number of blocks exactly divides the number of plots, otherwise they differ by at most one plot. The design output is a data table giving a randomised allocation of treatments to blocks together with a plan table showing treatments in blocks and a set of blocks-by-treatments incidence matrices, one for each blocks stratum. * checkpoint (0.3.2) Maintainer: Andrie de Vries Author(s): Revolution Analytics License: GPL-2 http://crantastic.org/packages/checkpoint The goal of checkpoint is to solve the problem of package reproducibility in R. Specifically, checkpoint allows you to install packages as they existed on CRAN on a specific snapshot date as if you had a CRAN time machine. To achieve reproducibility, the checkpoint() function installs the packages required or called by your project and scripts to a local library exactly as they existed at the specified point in time. Only those packages are available to your project, thereby avoiding any package updates that came later and may have altered your results. In this way, anyone using checkpoint#39;s checkpoint() can ensure the reproducibility of your scripts or projects at any time. To create the snapshot archives, once a day (at midnight UTC) we refresh the Austria CRAN mirror, on the quot;Managed R Archived Networkquot; server (http://mran.revolutionanalytics.com/). Immediately after completion of the rsync mirror process, we take a snapshot, thus creating the archive. Snapshot archives exist starting from 2014-09-17. * DynNom (1.0) Maintainer: Amirhossein Jalali Author(s): Amirhossein Jalali, Alberto Alvarez-Iglesias, John Newell License: GPL-2 http://crantastic.org/packages/DynNom The DynNom function makes it possible to present the results of an lm or glm model object as a dynamic nomogram that can be displayed in an R Studio panel or web browser. * enpls (1.0) Maintainer: Xiao Nan Author(s): Nan Xiao road2s...@gmail.com, Dong-Sheng Cao oriental-...@163.com, Qing-Song Xu dason...@gmail.com License: GPL (= 2) http://crantastic.org/packages/enpls R package for ensemble partial least squares regression, a unified framework for feature selection, outlier detection, and ensemble learning. * gender (0.4.1) Maintainer: Lincoln Mullen Author(s): Lincoln Mullen [aut, cre], Cameron Blevins [ctb], Ben Schmidt [ctb] License: MIT + file LICENSE http://crantastic.org/packages/gender Encodes gender based on names and dates of birth, using either the Social Security Administration#39;s data set of first names by year of birth or Census Bureau data from 1789 to 1940, both from the United States of America. By using these data sets instead of lists of male and female names, this package is able to more accurately guess the gender of a name, and it is able to report the probability that a name was male or female. * lazyeval (0.1.9) Maintainer: Hadley Wickham Author(s): Hadley Wickham [aut, cre], RStudio [cph] License: GPL-3 http://crantastic.org/packages/lazyeval A disciplined approach to non-standard evaluation. * mdsdt (1.0) Maintainer: Robert X.D. Hawkins Author(s): Robert X.D. Hawkins r...@stanford.edu, Joe Houpt joseph.ho...@wright.edu, Noah Silbert noahp...@gmail.com, Leslie Blaha leslie.bl...@wpafb.af.mil, Thomas D. Wickens twick...@socrates.berkeley.edu License: GPL (= 2) http://crantastic.org/packages/mdsdt This package contains a series of tools associated with General Recognition Theory (Townsend amp; Ashby, 1986), including Gaussian model fitting of 4x4 and more general confusion
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * ADDT (1.0) Maintainer: Yili Hong Author(s): Yili Hong, Yimeng Xie, and Caleb King License: GPL-2 http://crantastic.org/packages/ADDT Accelerated destructive degradation tests (ADDT) are often used to collect necessary data for assessing the long-term properties of polymeric materials. Based on the collected data, a thermal index (TI) is estimated. The TI can be useful for material rating and comparison. This package performs the least squares (LS) and maximum likelihood (ML) procedures for estimating TI for polymeric materials. The LS approach is a two-step approach that is currently used in industrial standards, while the ML procedure is widely used in the statistical literature. The ML approach allows one to do statistical inference such as quantifying uncertainties in estimation, hypothesis testing, and predictions. Two publicly available datasets are provided to allow users to experiment and practice with the functions. * ASMap (0.3) Maintainer: Julian Taylor Author(s): Julian Taylor julian.tay...@adelaide.edu.au, David Butler david.but...@daff.qld.gov.au. License: GPL (= 2) http://crantastic.org/packages/ASMap Functions for (A)ccurate and (S)peedy linkage map construction, manipulation and diagnosis of double haploid, backcross and and RIL R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008). * causaleffect (1.0) Maintainer: Santtu Tikka Author(s): Santtu Tikka License: GPL-2 http://crantastic.org/packages/causaleffect An implementation of the complete identification algorithm constructed by Ilya Shpitser and Judea Pearl (2006) for deriving expressions of joint interventional distributions in causal models, which contain unobserved variables and induce directed acyclic graphs. * Compind (1.0) Maintainer: Francesco Vidoli Author(s): Francesco Vidoli, Elisa Fusco License: GPL-3 http://crantastic.org/packages/Compind Compind package contains several functions to enhance approaches to the Composite Indicators (http://stats.oecd.org/glossary/detail.asp?ID=6278}, https://composite-indicators.jrc.ec.europa.eu/) methods, focusing, in particular, on the normalisation and weighting-aggregation steps. * crayon (1.0.0) Maintainer: quot;Gabor Csardiquot; Author(s): Gabor Csardi [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/crayon Crayon adds support for colored terminal output on terminals that support ANSI color and highlight codes. ANSI color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the chalk JavaScript project. * deming (1.0-1) Maintainer: Terry Therneau Author(s): Terry Therneau License: LGPL (= 2) http://crantastic.org/packages/deming Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions. * documair (0.6-0) Maintainer: Jean-Baptiste Denis Author(s): Jean-Baptiste Denis jean-baptiste.de...@jouy.inra.fr, Regis Pouillot rpouil...@yahoo.fr, Kien Kieu kien.k...@jouy.inra.fr License: GPL (= 2.15) http://crantastic.org/packages/documair Production of R packages from tagged comments introduced within the code and a minimum of additional documentation files. * GenWin (0.1) Maintainer: Timothy M. Beissinger Author(s): Timothy M. Beissinger beissin...@ucdavis.edu License: MIT + file LICENSE http://crantastic.org/packages/GenWin Defines window or bin boundaries for the analysis of genomic data. Boundaries are based on the inflection points of a cubic smoothing spline fitted to the raw data. Along with defining boundaries, a technique to evaluate results obtained from unequally-sized windows is provided. Applications are particularly pertinent for, though not limited to, genome scans for selection based on variability between populations (e.g. using Wright#39;s fixations index, Fst, which measures variability in subpopulations relative to the total population). * ivprobit (1.0) Maintainer: Zaghdoudi Taha Author(s): Zaghdoudi Taha License: Artistic-2.0 http://crantastic.org/packages/ivprobit ivprobit fit an Instrumental variables probit model using the generalized least squares estimator * kofnGA (1.0) Maintainer: Mark A. Wolters Author(s): Mark A. Wolters License: GPL-2 http://crantastic.org/packages/kofnGA Function kofnGA uses a genetic algorithm to choose a subset of a fixed size k from the integers 1:n, such that a user-supplied objective function is minimized at that subset. The selection step is done by tournament selection based on ranks, and elitism may be used to retain a portion of the best solutions from one generation to the next. * MetFns (1.0) Maintainer:
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * adaptDA (1.0) Maintainer: Charles Bouveyron Author(s): Charles Bouveyron License: GPL-2 http://crantastic.org/packages/adaptDA The adaptive mixture discriminant analysis (AMDA) allows to adapt a model-based classifier to the situation where a class represented in the test set may have not been encountered earlier in the learning phase. * aRxiv (0.5.2) Maintainer: Karl W Broman Author(s): Karthik Ram [aut], Karl Broman [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/aRxiv An interface to the API for arXiv, a repository of electronic preprints for computer science, mathematics, physics, quantitative biology, quantitative finance, and statistics. * audited (1.9) Maintainer: Tim Bergsma Author(s): Tim Bergsma License: GPL http://crantastic.org/packages/audited Classifies a data.frame such that row deletions and additions are tracked. A mechanism exists to give formal names to the row subsets that are coming or going. These names are used to populate a directed graph giving an account of all the transactions contributing to the state of the data.frame. The generic as.audited() has a method for keyed data.frames that creates an audited data.frame. Methods exist that track row count changes for the generics: Ops, !, ^, |, [, subset, head, tail, unique, cast, melt, aggregate, and merge. audit() extracts the transaction table from the audited object, while write.audit() and read.audit() control exchange with the file system. An audit method for as.igraph() creates a graph object that can be displayed with the corresponding plot method. Use options(audit= ) to provide an extra level of classification. Use options(artifact=TRUE) and as.xlsx() to save dropped records to file. * BEANSP (1.0) Maintainer: Yiqun Yang Author(s): Chong He, Yiqun Yang, Jing Cao License: GPL-2 http://crantastic.org/packages/BEANSP Computing age specific nest survival rates based on a Bayesian hierarchical model. This package can handle unknown nest age, irregular visiting schedule and nest-specific covariates. * binequality (0.6.1) Maintainer: Samuel V. Scarpino Author(s): Samuel V. Scarpino, Paul von Hippel, and Igor Holas License: GPL (= 3.0) http://crantastic.org/packages/binequality Methods for model selection, model averaging, and calculating metrics, such as the Gini, Theil, Mean Log Deviation, etc, on binned income data where the topmost bin is right-censored. We provide both a non-parametric method, termed the bounded midpoint estimator (BME), which assigns cases to their bin midpoints; except for the censored bins, where cases are assigned to an income estimated by fitting a Pareto distribution. Because the usual Pareto estimate can be inaccurate or undefined, especially in small samples, we implement a bounded Pareto estimate that yields much better results. We also provide a parametric approach, which fits distributions from the generalized beta (GB) family. Because some GB distributions can have poor fit or undefined estimates, we fit 10 GB-family distributions and use multimodel inference to obtain definite estimates from the best-fitting distributions. We also provide binned income data from all United States of America school districts, counties, and states. * BOIN (1.0) Maintainer: Ying Yuan Author(s): Ying Yuan and Suyu Liu License: GPL-2 http://crantastic.org/packages/BOIN The Bayesian optimal interval (BOIN) design is a novel phase I clinical trial design for finding the maximum tolerated dose (MTD). The BOIN design is motivated by the top priority and concern of clinicians when testing a new drug, which is to effectively treat patients and minimize the chance of exposing them to subtherapeutic or overly toxic doses. The prominent advantage of the BOIN design is that it achieves simplicity and superior performance at the same time. The BOIN design is algorithm-based and can be implemented in a simple way similar to the traditional 3+3 design. The BOIN design yields average performance comparable to the continual reassessment method (CRM, one of the best model-based design) in terms of selecting the MTD, but has a substantially lower risk of assigning patients to subtherapeutic or overly toxic doses. * confidence (1.0-0) Maintainer: Dennis Walvoort Author(s): Willem M. G. M. van Loon [aut, cph], Dennis J. J. Walvoort [aut, cre] License: GPL (= 3) http://crantastic.org/packages/confidence Functions for estimating and reporting multiyear averages and corresponding confidence intervals and distributions. A potential use case is reporting the chemical and ecological status of surface waters according to the European Water Framework Directive. * GlobalOptions (0.0.1) Maintainer: Zuguang Gu Author(s): Zuguang Gu License: GPL (= 2)
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * cmvnorm (1.0) Maintainer: Robin Hankin Author(s): Robin K. S. Hankin License: GPL-2 http://crantastic.org/packages/cmvnorm various utilities for the complex multivariate Gaussian distribution * couchDB (1.3.0) Maintainer: Aleksander Dietrichson Author(s): Aleksander Dietrichson License: AGPL-3 http://crantastic.org/packages/couchDB Interface to couchDB * eegkit (1.0-0) Maintainer: Nathaniel E. Helwig Author(s): Nathaniel E. Helwig hel...@umn.edu License: GPL (= 2) http://crantastic.org/packages/eegkit Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for plotting (a) EEG caps, (b) single- and multi-channel EEG time courses, and (c) EEG spatial maps. Also includes smoothing and Independent Component Analysis functions for EEG data analysis. * eegkitdata (1.0) Maintainer: Nathaniel E. Helwig Author(s): Nathaniel E. Helwig hel...@umn.edu License: GPL (= 2) http://crantastic.org/packages/eegkitdata Contains the example EEG data used in the package eegkit. Also contains code for easily creating larger EEG datasets from the EEG Database on the UCI Machine Learning Repository. * ForwardSearch (1.0) Maintainer: Bent Nielsen Author(s): Bent Nielsen License: GPL-3 http://crantastic.org/packages/ForwardSearch Forward Search analysis of time series regressions. Implements the asymptotic theory developed in Johansen and Nielsen (2013, 2014). * FRESA.CAD (1.0) Maintainer: Jose Gerardo Tamez-Pena Author(s): Jose Gerardo Tamez-Pena License: LGPL (= 2) http://crantastic.org/packages/FRESA-CAD FRESA.CAD provides a set of functions and feature selection algorithms for building Computer Aided Diagnosis Models * funFEM (1.0) Maintainer: Charles Bouveyron Author(s): Charles Bouveyron License: GPL-2 http://crantastic.org/packages/funFEM The funFEM algorithm (Bouveyron et al., 2014) allows to cluster functional data by modeling the curves within a common and discriminative functional subspace. * funHDDC (1.0) Maintainer: Charles Bouveyron Author(s): C. Bouveyron J. Jacques License: GPL-2 http://crantastic.org/packages/funHDDC The package provides the funHDDC algorithm (Bouveyron amp; Jacques, 2011) which allows to cluster functional data by modeling each group within a specific functional subspace. * gapmap (0.0.1) Maintainer: Ryo Sakai Author(s): Ryo Sakai License: GPL-2 | GPL-3 http://crantastic.org/packages/gapmap The gap encodes the distance between clusters and improves interpretation of cluster heatmaps. The gaps can be of the same distance based on a height threshold to cut the dendrogram. Another option is to vary the size of gaps based on the distance between clusters. * GENLIB (1.0) Maintainer: Marie-Helene Roy-Gagnon Author(s): Louis Houde, Jean-Francois Lefebvre, Valery Roy-Lagace, Sebastien Lemieux License: GPL (= 2) http://crantastic.org/packages/GENLIB Takes genealogical data frames and calculates different demographic variables such as genetic contribution, kinship, etc... * lefse (0.1) Maintainer: Nathan G. Swenson Author(s): Nathan G. Swenson License: GPL-2 | GPL-3 http://crantastic.org/packages/lefse Utilizing phylogenetic and functional information for the analyses of ecological datasets. The analyses include methods for quantifying the phylogenetic and functional diversity of assemblages. * lunar (0.1-04) Maintainer: Emmanuel Lazaridis Author(s): Emmanuel Lazaridis [aut, cre] License: MIT + file LICENSE http://crantastic.org/packages/lunar Provides functions to calculate lunar and other environmental covariates. * micropan (1.0) Maintainer: Lars Snipen Author(s): Lars Snipen and Kristian Hovde Liland License: GPL-2 http://crantastic.org/packages/micropan A collection of functions for computations and visualizations of microbial pan-genomes. * nettools (1.0.1) Maintainer: Michele Filosi Author(s): Michele Filosi [aut, cre], Roberto Visintainer [aut], Samantha Riccadonna [aut], Giuseppe Jurman [ctb], Cesare Furlanello [ctb] License: CC BY-NC-SA 4.0 http://crantastic.org/packages/nettools A collection of network inference methods for co-expression networks, quantitative network distances and a novel framework for network stability analysis. * RDML (0.4-2) Maintainer: Konstantin A. Blagodatskikh Author(s): Konstantin A. Blagodatskikh [cre, aut], Stefan Roediger [aut], Michal Burdukiewicz [aut] License: GPL (= 2) http://crantastic.org/packages/RDML Imports real-time thermo cycler (qPCR) data from RDML format files and transforms to the appropriate formats of the #39;qpcR#39; and #39;chipPCR#39; packages. * saery (1.0) Maintainer: Agustin Perez Martin Author(s): Maria Dolores Esteban Lefler, Domingo Morales Gonzalez,
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * classyfire (0.1-0) Maintainer: Eleni Chatzimichali Author(s): Eleni Chatzimichali ea.chatzimich...@gmail.com and Conrad Bessant c.bess...@qmul.ac.uk License: GPL (= 2) http://crantastic.org/packages/classyfire A collection of functions for the creation and application of highly optimised, robustly evaluated ensembles of support vector machines (SVMs). The package takes care of training individual SVM classifiers using a fast parallel heuristic algorithm, and combines individual classifiers into ensembles. Robust metrics of classification performance are offered by bootstrap resampling and permutation testing. * cooptrees (1.0) Maintainer: Manuel Fontenla Author(s): Manuel Fontenla License: GPL-3 http://crantastic.org/packages/cooptrees Computes several cooperative games and allocation rules associated with minimum cost spanning tree problems and minimum cost arborescence problems. * coreTDT (1.0) Maintainer: Yu Jiang Author(s): Yu Jiang, Andrew S Allen License: GPL-3 http://crantastic.org/packages/coreTDT Use to analysis case-parent trio sequencing studies. Test the compound heterozygous and recessive disease models * descomponer (1.0) Maintainer: Francisco Parra Author(s): Francisco Parra parra...@cantabria.es License: GPL (= 2) http://crantastic.org/packages/descomponer Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain. * Frames2 (0.0.3) Maintainer: David Molina Author(s): Antonio Arcos ar...@ugr.es, Maria del Mar Rueda mru...@ugr.es, Maria Giovanna Ranalli giovanna.rana...@stat.unipg.it and David Molina dmoli...@ugr.es License: GPL (= 2) http://crantastic.org/packages/Frames2 Point and interval estimation in dual frame surveys. In contrast to classic sampling theory, where only one sampling frame is considered, dual frame methodology assumes that there are two frames available for sampling and that, overall, they cover the entire target population. Then, two probability samples (one from each frame) are drawn and information collected is suitably combined to get estimators of the parameter of interest. * GUILDS (1.2) Maintainer: Thijs Janzen Author(s): Thijs Janzen License: GPL-2 http://crantastic.org/packages/GUILDS The GUILDS package combines a range of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen 2014), and the guilds sampling formula conditioned on guild size (Janzen 2014). * iBATCGH (1.0) Maintainer: Alberto Cassese Author(s): Alberto Cassese License: GPL-2 http://crantastic.org/packages/iBATCGH Bayesian integrative models of gene expression and comparative genomic hybridization data. The package provides inference on copy number variations and their association with gene expression * ica (1.0-0) Maintainer: Nathaniel E. Helwig Author(s): Nathaniel E. Helwig hel...@umn.edu License: GPL (= 2) http://crantastic.org/packages/ica Independent Component Analysis (ICA) using various algorithms: FastICA, Information-Maximization (Infomax), and Joint Approximate Diagonalization of Eigenmatrices (JADE). * insuranceData (1.0) Maintainer: Alicja Wolny--Dominiak Author(s): Alicja Wolny--Dominiak and Michal Trzesiok License: GPL-2 http://crantastic.org/packages/insuranceData Insurance datasets, which are often used in claims severity and claims frequency modelling. It helps testing new regression models in those problems, such as GLM, GLMM, HGLM, non-linear mixed models etc. Most of the data sets are applied in the project quot;Mixed models in ratemakingquot; supported by grant NN 111461540 from Polish National Science Center. * JAGUAR (1.1) Maintainer: Chaitanya Acharya Author(s): Chaitanya R. Acharya and Andrew S. Allen License: GPL-2 http://crantastic.org/packages/JAGUAR Implements a 2 degree-of-freedom score test that measures 1) the overall shift in the gene expression due to genotype, and 2) group-specific changes in gene expression due to genotype (interaction term) in a mixed-effects model framework. * mpcv (1.0) Maintainer: Krzysztof Ciupke Author(s): Krzysztof Ciupke krzysztof.ciu...@polsl.pl License: GPL (= 2.0) http://crantastic.org/packages/mpcv Multivariate process capability analysis using the multivariate process capability vector. Allows to analyze a
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * complex.surv.dat.sim (1.0) Maintainer: David Moriña Author(s): David Moriña, Centre Tecnològic de Nutrició i Salut and Albert Navarro, Universitat Autònoma de Barcelona License: GPL (= 2) http://crantastic.org/packages/complex-surv-dat-sim Simulation of complex survival data * EpiEstim (1.0-0) Maintainer: Anne Cori Author(s): Anne Cori a.c...@imperial.ac.uk License: GPL (= 2) http://crantastic.org/packages/EpiEstim This package provides tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence. * JMLSD (1.0) Maintainer: Emil A. Cornea Author(s): Emil A. Cornea, Liddy M. Chen, Bahjat F. Qaqish, Haitao Chu, and Joseph G. Ibrahim License: GPL-2 http://crantastic.org/packages/JMLSD The package contains a R-function to perform power calculation for joint modeling of longitudinal and survival data, with k-th order trajectories, when the variance-covariance matrix Sigma_theta is unknown. * mpMap (1.14) Maintainer: Emma Huang Author(s): Emma Huang License: GPL-2 http://crantastic.org/packages/mpMap Tools for constructing linkage maps, reconstructing haplotypes, estimating linkage disequilibrium and QTL mapping in multi-parent RIL designs (e.g. MAGIC) * phcfM (1.0) Maintainer: Ghislain Vieilledent Author(s): Ghislain Vieilledent ghislain.vieilled...@cirad.fr License: GPL (= 2) http://crantastic.org/packages/phcfM A package for modelling anthropogenic deforestation * qtlnet (1.2.4) Maintainer: Brian S. Yandell Author(s): Elias Chaibub Neto echai...@hotmail.com and Brian S. yandell yand...@stat.wisc.edu License: GPL (= 2) http://crantastic.org/packages/qtlnet Functions to Simultaneously Infer Causal Graphs and Genetic Architecture * R330 (1.0) Maintainer: Alan Lee Author(s): Alan Lee, Blair Robertson License: GPL-2 http://crantastic.org/packages/R330 This is a collection of useful functions and data for Stats 330 * RIFS (0.1-5) Maintainer: Pavel V. Moskalev Author(s): Pavel V. Moskalev, Alexey G. Bukhovets and Tatyana Ya. Biruchinskay License: GPL-3 http://crantastic.org/packages/RIFS RIFS package provides functionality for generating amp; plotting prefractals in R^n with various protofractal sets and partition coefficient for iterative segments * rriskDistributions (1.7) Maintainer: Federal Institute for Risk Assessment, Matthias Greiner Author(s): Natalia Belgorodski (STAT-UP Statistical Consulting, Germany), Matthias Greiner (Federal Institute for Risk Assessment, Germany), Kristin Tolksdorf (Federal Institute for Risk Assessment, Germany), Katharina Schueller (STAT-UP Statistical Consulting, Germany) License: GPL (= 3) http://crantastic.org/packages/rriskDistributions Collection of functions for fitting distributions to given data or by known quantiles. Two main functions fit.perc() and fit.cont() provide users a GUI that allows to choose a most appropriate distribution without any knowledge of the R syntax. * spclust (1.0) Maintainer: Emma Huang Author(s): Emma Huang License: GPL-2 http://crantastic.org/packages/spclust Selection of subsets of experimental crosses in order to maximize genetic diversity * SteinerNet (1.0) Maintainer: Afshin Sadeghi Author(s): Afshin Sadeghi, Holger Froehlich License: GPL-3 http://crantastic.org/packages/SteinerNet A set of graph functions writen in R to perform steiner tree network data analysis on biological pathway data * Voss (0.1-4) Maintainer: Pavel V. Moskalev Author(s): Pavel V. Moskalev License: GPL-3 http://crantastic.org/packages/Voss Voss package provides functionality for generating realizations of a fractal Brownian function on uniform 1D amp; 2D grid with classic and generic versions of the Voss algorithm (random sequential additions) Updated packages AICcmodavg (1.25), anametrix (0.2), arm (1.5-05), bayesDem (1.7-0), bayesPop (2.0-2), betategarch (1.2), Biograph (2.0.1), bios2mds (1.2.2), CHCN (1.5), countrycode (0.7), crs (0.15-17), cvplogistic (2.1-0), deducorrect (1.2-0), DiceOptim (1.3.1), DiceView (1.2-1), directlabels (2.6), DSL (0.1-2), editrules (2.5-0), faoutlier (0.2.3), fda.usc (0.9.8), ffbase (0.5), fGarch (2110.80.1), forecast (3.22), forensim (3.1), gdata (2.10.0), gdata (2.10.5), gplots (2.11.0), gRim (0.1-9), gWidgetstcltk (0.0-51), gWidgetsWWW (0.0-23), harvestr (0.4), HMPTrees (1.1), iDEMO (0.2-01), IPMpack (1.2), joineR (1.0-2), LaplacesDemon (12.06.04), lazyWeave (2.1.4), leiv (2.0-5), markdown (0.5.1), mc2d (0.1-13), minPtest (1.3), mirt (0.2.5), modelcf (2.1.1), ModelMap (2.3.2), movMF (0.0-1), MultiPhen (0.6), pacose (1.1), partykit (0.1-4), pdfCluster (1.0-0), phyclust (0.1-12), pracma (1.1.0), qvcalc (0.8-8), R2Cuba (1.0-7), rainbow (2.9),
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * anametrix (0.1) Maintainer: Roman Jugai Author(s): Roman Jugai License: LGPL http://crantastic.org/packages/anametrix Connects to Anametrix API and extracts data into R data structure * assertive (0.1-4) Maintainer: Richard Cotton Author(s): Richard Cotton [aut, cre] License: Unlimited http://crantastic.org/packages/assertive assertive contains lots of is_* functions to check the state of your variables, and assert_* functions to throw errors if they aren't in the right form. * crblocks (0.5-0) Maintainer: David Allingham Author(s): David Allingham, D.J. Best License: GPL (= 2) http://crantastic.org/packages/crblocks Implements a statistical test for comparing bar plots or histograms of categorical data derived from a randomized block repeated measures layout. * deltaPlotR (1.0) Maintainer: David Magis Author(s): David Magis (U Liege), Bruno Facon (Univ Lille-Nord de France) License: GPL (= 2) http://crantastic.org/packages/deltaPlotR The deltaPlot package proposes an implementation of Angoff's elta Plot method to detect dichotomous DIF. Several detection thresholds are included, either from multivariate normality asumption, random simulation, or by prior determination. Item purification is supported. * disp2D (1.0) Maintainer: Guillermo Ayala Author(s): Guillermo Ayala License: GPL-2 http://crantastic.org/packages/disp2D An implementation of two exact algorithms for testing the Hausdorff and simplex dispersion orderings * foodweb (1-0) Maintainer: Giselle Perdomo Author(s): Giselle Perdomo License: GPL (= 2) http://crantastic.org/packages/foodweb Calculates twelve commonly-used, basic measures of food web network structure from binary, predator-prey matrices: species richness, connectance, total number of links, link density, number of trophic positions, predator:prey ratio, and fraction of carnivores, herbivores, top species and intermediate species. Employs food web language in the code and output, translates between a couple of common food web formats, can handle food webs consisting of multiple levels, and can automate the analysis for a large number of webs. The program produces 3-dimensional graphs of high quality that can be customized by the user. * genomicper (1.3) Maintainer: Claudia Cabrera Author(s): Claudia P.Cabrera-Cardenas,Pau Navarro,Chris S.Haley License: GPL-2 http://crantastic.org/packages/genomicper Circular genomic permutation approach uses GWAS results to establish the significance of pathway/gene-set associations whilst accounting for genomic structure. All SNPs in the GWAS are placed in a 'circular genome' according to their location. Then the complete set of SNP association p-values are permuted by rotation with respect to the SNPs' genomic locations * hiPOD (1.0) Maintainer: Wei E. Liang Author(s): Wei E. Liang License: GPL-3 http://crantastic.org/packages/hiPOD Based on hierarchical modeling, this package provides a few practical functions to find and present the optimal designs for a pooled NGS design. * intpoint (1.0) Maintainer: Alejandro Quintela del Rio Author(s): Alejandro Quintela del Rio License: GPL-2 http://crantastic.org/packages/intpoint Solves linear programming problems by the interior point method, and plots the graphical solution of a linear programming problem of two dimensions. * jmec (1.0-3) Maintainer: Willem M. van der Wal Author(s): Willem M. van der Wal w.m.vd@umcutrecht.nl License: GPL (= 2) http://crantastic.org/packages/jmec Fit joint model for event and censoring, with cluster-level frailties, according to Huang amp; Wolfe (2002). * knnGarden (1.0) Maintainer: Boxian Wei Author(s): Boxian Wei Fan Yang Xinmiao Wang Yanni Ge License: GPL (= 2) http://crantastic.org/packages/knnGarden Muti-distance based k-Nearest Neighbors Classification with K Threshold Value Check and Same K_i Problem Dealing, Missing Observations Filling * longclust (1.1) Maintainer: K. Raju Jampani Author(s): P. D. McNicholas, K. Raju Jampani and Sanjeena Subedi License: GPL-2 http://crantastic.org/packages/longclust Clustering or classification of longitudinal data based on a mixture of multivariate t or Gaussian distributions with a Cholesky-decomposed covariance structure. * OIdata (1.0) Maintainer: Andrew P Bray Author(s): Andrew P Bray and David M Diez License: GPL-2 | GPL-3 http://crantastic.org/packages/OIdata A collection of data sets from several sources that may be useful for teaching, practice, or other purposes. Functions have also been included to assist in the retrieval of table data from websites or in visualizing sample data. * ParamHelpers (1.0-55) Maintainer: Bernd Bischl Author(s): Bernd Bischl bernd_bis...@gmx.net, Patrick Koch
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * awsMethods (1.0-0) Maintainer: Joerg Polzehl Author(s): Joerg Polzehl polz...@wias-berlin.de License: GPL (= 2) http://crantastic.org/packages/awsMethods The package defines method extract that in needed in several packages * BatchExperiments (1.0-486) Maintainer: Michel Lang Author(s): Bernd Bischl bernd_bis...@gmx.net, Michel Lang michell...@gmail.com, Olaf Mersmann ol...@p-value.net License: BSD http://crantastic.org/packages/BatchExperiments Extends the BatchJobs package to run statistical experiments on batch computing clusters. For further details see the project web page. * BatchJobs (1.0-485) Maintainer: Bernd Bischl Author(s): Bernd Bischl bernd_bis...@gmx.net, Michel Lang michell...@gmail.com, Olaf Mersmann ol...@p-value.net License: BSD http://crantastic.org/packages/BatchJobs Provides Map, Reduce and Filter variants to generate jobs on batch computing systems like PBS/Torque, LSF and Sun Grid Engine. Multicore and SSH systems are also supported. For further details see the project web page. * CpGassoc (1.1) Maintainer: R Barfield Author(s): Barfield, R., Conneely, K., Kilaru,V License: GPL (= 2) http://crantastic.org/packages/CpGassoc CpGassoc is designed to test for association between methylation at CpG sites across the genome and a phenotype of interest, adjusting for any relevant covariates. The package can perform standard analyses of large datasets very quickly with no need to impute the data. It can also handle mixed effects models with chip or batch entering the model as a random intercept. CpGassoc also includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites. * dataframe (2.5) Maintainer: Tim Hesterberg Author(s): Tim Hesterberg License: GPL-2 http://crantastic.org/packages/dataframe This contains versions of standard data frame functions in R, modified to avoid making extra copies of inputs. This is faster, particularly for large data. * fgof (0.2-1) Maintainer: Jun Yan Author(s): Ivan Kojadinovic and Jun Yan License: GPL (= 3) http://crantastic.org/packages/fgof Goodness-of-fit test with multiplier or parametric bootstrap. * ForeCA (0.0.1) Maintainer: Georg M. Goerg Author(s): Georg M. Goerg g...@stat.cmu.edu License: GPL (= 2) http://crantastic.org/packages/ForeCA ForeCA is a new blind source separation (BSS) technique for temporally dependent signals. Contrary to PCA or ICA it explicitly searches for the best linear transformation that makes the obtained sources as ''forecastable'' as possible. The measure of forecastability Omega(x_t) is the entropy of the spectral density of the signal. * Luminescence (0.1.7) Maintainer: Sebastian Kreutzer Author(s): Sebastian Kreutzer [aut, cre], Christoph Schmidt [aut, ctb], Margret C. Fuchs [aut, ctb], Michael Dietze [aut, ctb], Manfred Fischer [aut, ctb], Markus Fuchs [ths] License: GPL-3 http://crantastic.org/packages/Luminescence Package provides a collection of various R functions for Luminescence Dating data analysis. * mada (0.4) Maintainer: Philipp Doebler Author(s): Philipp Doebler License: GPL-2 http://crantastic.org/packages/mada This package provides functions for diagnostic meta-analysis. Next to basic analysis and visualization the bivariate Model of Reitsma et al. (2005) that is equivalent to the HSROC of Rutteramp;Gatsonis (2001) can be fitted. A new approach based to diagnostic meta-analysis of Boehning et al. is also available. Standard methods like summary, plot and so on are provided. * MetaPath (0.9) Maintainer: Kui Shen Author(s): Kui Shen and Geroge Tseng License: GPL (= 2.0) http://crantastic.org/packages/MetaPath This R package was implemented to perform the Meta-analysis for Pathway Enrichment (MAPE) methods introduced by Shen and Tseng (2010). It includes functions to automatically perform MAPE_G (integrating multiple studies at gene level), MAPE_P (integrating multiple studies at pathway level) and MAPE_I (a hybrid method integrating MAEP_G and MAPE_P methods). In the simulation and real data analyses in the paper, MAPE_G and MAPE_P have complementary advantages and detection power depending on the data structure. In general, the integrative form of MAPE_I is recommended to use. In the case that MAPE_G (or MAPE_P) detects almost none pathway, the integrative MAPE_I does not improve performance and MAPE_P (or MAPE_G) should be used. Reference: Shen, Kui, and George C Tseng. Meta-analysis for pathway enrichment analysis when combining multiple microarray studies.Bioinformatics (Oxford, England) 26, no. 10 (April 2010): 1316-1323. doi:10.1093/bioinformatics/btq148.
[R] CRAN (and crantastic) updates this week
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 quot;Load, Clean, Func, Doquot; 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)
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * AGD (0.30) Maintainer: Stef van Buuren Author(s): Stef van Buuren stef.vanbuu...@tno.nl License: GPL-2 | GPL-3 http://crantastic.org/packages/AGD Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23 2012, Rotterdam. * bigml (0.1-1) Maintainer: Justin Donaldson Author(s): Justin Donaldson [aut, cre] License: LGPL-3 http://crantastic.org/packages/bigml The bigml package contains bindings for the BigML API. The package includes methods that provide straightforward access to basic API functionality, as well as methods that accommodate idiomatic R datatypes and concepts. * BVS (4.12.0) Maintainer: Melanie Quintana Author(s): Melanie Quintana maw27.wil...@gmail.com License: Unlimited http://crantastic.org/packages/BVS The functions in this package focus on analyzing case-control association studies involving a group of genetic variants. In particular, we are interested in modeling the outcome variable as a function of a multivariate genetic profile using Bayesian model uncertainty and variable selection techniques. The package incorporates functions to analyze data sets involving common variants as well as extensions to model rare variants via the Bayesian Risk Index (BRI) as well as haplotypes. Finally, the package also allows the incorporation of external biological information to inform the marginal inclusion probabilities via the iBMU. * gsbDesign (0.95) Maintainer: Unknown Author(s): Florian Gerber, Thomas Gsponer License: GPL-3 http://crantastic.org/packages/gsbDesign Group Sequential Operating Characteristics for Clinical, Bayesian two-arm Trials with known Sigma and Normal Endpoints. * marqLevAlg (1.0) Maintainer: Melanie Prague Author(s): D. Commenges daniel.commen...@isped.u-bordeaux2.fr, M. Prague melanie.pra...@isped.u-bordeaux2.fr and Amadou Diakite License: GPL (= 2.0) http://crantastic.org/packages/marqLevAlg This algorithm provides a numerical solution to the problem of minimizing a function. This is more efficient than the Gauss-Newton-like algorithm when starting from points vey far from the final minimum. A new convergence test is implemented (RDM) in addition to the usual stopping criterion : stopping rule is when the gradients are small enough in the parameters metric (GH-1G). * p2distance (1.0.1) Maintainer: A.J. Perez-Luque Author(s): A.J. Perez-Luque; R. Moreno; R. Perez-Perez and F.J. Bonet License: GPL http://crantastic.org/packages/p2distance The welfare's synthetic indicator provides an ideal tool for measuring multi-dimensional concepts such as welfare, development, living standards, etc. It enables information from the various indicators to be aggregated into a single synthetic measure. * pcaPA (1.0) Maintainer: Carlos A. Arias Author(s): Carlos A. Arias car...@icfes.gov.co and Víctor H. Cervantes vcervan...@icfes.gov.co. License: GPL (= 2) http://crantastic.org/packages/pcaPA A set of functions to perform parallel analysis for principal components analysis intended mainly for large data sets. It performs a parallel analysis of continuous, ordered (including dichotomous/binary as a special case) or mixed type of data associated with a principal components analysis. Polychoric correlations among ordered variables, Pearson correlations among continuous variables and polyserial correlation between mixed type variables (one ordered and one continuous) are used. Whenever the use of polyserial or polychoric correlations yields a non positive definite correlation matrix, the resulting matrix is transformed into the nearest positive definite matrix. For details on the GSL installation in windows please visit the following link: http://wiki.rglab.org/index.php?title=Public:Installation_of_GSL_from Windows_binary * phia (0.0-2) Maintainer: Helios De Rosario-Martinez Author(s): Helios De Rosario-Martinez License: GPL (= 3) http://crantastic.org/packages/phia Analysis of terms in linear and generalized linear models, on the basis of multiple comparisons of factor contrasts. Specially suited for the analysis of interaction terms. * plmDE (1.0) Maintainer: Jonas Author(s): Jonas Mueller License: GPL (= 2) http://crantastic.org/packages/plmDE A set of tools for identifying genes whose differential expression is associated with measurements of other covariates on a continuous scale. These methods rely on generalized additive partially linear models which can be fitted efficiently using a B-spline basis approximation. Still under development: methods for interfacing with objects extending the eSet class and a function to pass linear models in edgeR and DEseq format. * polywog (0.1-0) Maintainer: Brenton Kenkel Author(s): Brenton Kenkel and Curtis S. Signorino License: GPL (= 2)
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * condmixt (1.0) Maintainer: Julie Carreau Author(s): Julie Carreau License: GPL-2 http://crantastic.org/packages/condmixt Conditional density estimation with mixtures for heavy-tailed distributions * crrstep (2012-5.3) Maintainer: Ravi Varadhan Author(s): Ravi Varadhan Deborah Kuk License: GPL (= 2) http://crantastic.org/packages/crrstep Performs forward and backwards stepwise regression for the Proportional subdistribution hazards model in competing risks (Fine amp; Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k = log(n*), where n* is the number of primary events. * discreteMTP (0.1-2) Maintainer: Shay Yaacoby Author(s): Ruth Heller [aut], Hadas Gur [aut], Shay Yaacoby [aut, cre] License: GPL (= 2) http://crantastic.org/packages/discreteMTP Multiple testing procedures for discrete test statistics, that use the known discrete null distribution of the p-values for simultaneous inference. * gglasso (1.0) Maintainer: Yi Yang Author(s): Yi Yang yiy...@umn.edu, Hui Zou h...@stat.umn.edu License: GPL-2 http://crantastic.org/packages/gglasso This package implements a unified algorithm, blockwise-majorization-decent (BMD), for efficiently computing the solution paths of the group-lasso penalized least squares, logistic regression, Huberized SVM and squared SVM. * ISBF (0.1) Maintainer: Pierre Alquier Author(s): Pierre Alquier License: GPL http://crantastic.org/packages/ISBF Selection of features for sparse regression estimation (like the LASSO). Selection of blocks of features when the regression parameter is sparse and constant by blocks (like the Fused-LASSO). Application to cgh arrays. TEST VERSION, USE AT YOUR OWN RISK! * mmm2 (1.0) Maintainer: Ozgur Asar Author(s): Ozgur Asar, Ozlem Ilk License: GPL (= 2) http://crantastic.org/packages/mmm2 Fits multivariate marginal models with shared regression parameters for discrete and continuous responses * Momocs (0.1-01) Maintainer: Vincent Bonhomme Author(s): Vincent Bonhomme, Sandrine Picq, Julien Claude License: GPL (= 2) http://crantastic.org/packages/Momocs Momocs is intended to ease and popularize shape analysis of outlines (especially using elliptical Fourier analysis). It mostly hinges on the functions developped in Morphometrics with R (Claude, 2008). From outline extraction of images and elliptical Fourier calculation to multivariate analysis and the visualization of transformations within the morphological space, Momocs provides a complete and convenient toolkit to specialists within every field that are, or may be, interested in morphological comparisons of outlines. * mpoly (0.0.1) Maintainer: David Kahle Author(s): David Kahle david.ka...@gmail.com License: MIT http://crantastic.org/packages/mpoly mpoly allows for the symbolic manipulation of multivariate polynomials in a general and consistent way designed especially for sparse and super sparse polynomials. It also allows for basic differential calculus with multivariate polynomials and Grobner basis calculations from computational algebraic geometry. * R.devices (2.1.1) Maintainer: Henrik Bengtsson Author(s): Henrik Bengtsson License: LGPL (= 2.1) http://crantastic.org/packages/R-devices This package provides utility methods that enhance the existing graphical device functions already available in R for the purpose of simplify the creation of figure files of various image formats and much more. * RcmdrPlugin.EBM (1.0-1) Maintainer: Daniel Leucuta Author(s): Daniel-Corneliu Leucuta danny@gmail.com License: GPL (= 2) http://crantastic.org/packages/RcmdrPlugin-EBM This package provides an Rcmdr plug-in for Evidence Based Medicine medical indicators calculations (Sensitivity, specificity, absolute risk reduction, relative risk, ...). * RSeed (0.1.31) Maintainer: Claus Jonathan Fritzemeier Author(s): Claus Jonathan Fritzemeier License: GNU General Public License http://crantastic.org/packages/RSeed an implementation of the analysis about seed components from borenstein 2008 * SemiParSampleSel (0.1) Maintainer: Giampiero Marra Author(s): Giampiero Marra giampi...@stats.ucl.ac.uk and Rosalba Radice rosalba.rad...@lshtm.ac.uk License: GPL (= 2) http://crantastic.org/packages/SemiParSampleSel Routine for fitting continuous response sample selection models with semiparametric predictors, including linear and nonlinear effects. * stellaR (0.2-0) Maintainer: Matteo Dell'Omodarme Author(s): Matteo Dell'Omodarme [aut, cre], Giada Valle [aut] License: GPL (= 2) http://crantastic.org/packages/stellaR A package to manage and display stellar tracks and isochrones from Pisa low-mass database. Includes tools for isochrones construction and tracks interpolation.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * anoint (1.0) Maintainer: S. A. Kovalchik Author(s): Ravi Varadhan rvarad...@jhmi.edu and Stephanie Kovalchik License: GPL (= 2) http://crantastic.org/packages/anoint Tools for assessing multiple treatment-covariate interactions with data from a parallel-group randomized controlled clinical trial * BINCO (0.1-1) Maintainer: Shuang Li Author(s): Shuang Li shuan...@fhcrc.org,Li Hsu l...@fhcrc.org, Jie Peng jiep...@ucdavis.edu, Pei Wang pw...@fhcrc.org, License: GPL (= 2) http://crantastic.org/packages/BINCO Network construction based on inference on edge selection frequencies generated from bootstrap resamples * binomlogit (1.0) Maintainer: Agnes Fussl Author(s): Agnes Fussl License: GPL-3 http://crantastic.org/packages/binomlogit The R package contains different MCMC schemes to estimate the regression coefficients of a binomial (or binary) logit model within a Bayesian framework: a data-augmented independence MH-sampler, an auxiliary mixture sampler and a hybrid auxiliary mixture (HAM) sampler. All sampling procedures are based on algorithms using data augmentation, where the regression coefficients are estimated by rewriting the logit model as a latent variable model called difference random utility model (dRUM). * biwavelet (0.1) Maintainer: Tarik C. Gouhier Author(s): Tarik C. Gouhier, Aslak Grinsted License: GPL (= 2) http://crantastic.org/packages/biwavelet This is a port of the WTC MATLAB package written by Aslak Grinsted and the wavelet program written by Christopher Torrence and Gibert P. Compo. This package can be used to perform univariate and bivariate (cross-wavelet, wavelet coherence) wavelet analyses. * CePa (0.1) Maintainer: Zuguang Gu Author(s): Zuguang Gu License: GPL (= 2) http://crantastic.org/packages/CePa Use pathway topology information to assign weight to pathway nodes. * fracprolif (1.0.2) Maintainer: Shawn Garbett Author(s): Shawn Garbett, Darren Tyson License: GPL-2 http://crantastic.org/packages/fracprolif Functions for fitting data to a quiescent growth model, i.e. a growth process that involves members of the population who stop dividing or propagating. * GUniFrac (1.0) Maintainer: Jun Chen Author(s): Jun Chen License: GPL-2 http://crantastic.org/packages/GUniFrac Generalized UniFrac distance for comparing microbial communities. Permutational multivariate analysis of variance using multiple distance matrices. * MAMS (0.1) Maintainer: Thomas Jaki Author(s): Thomas Jaki jaki.tho...@gmail.com and Dominic Magirr d.mag...@lancaster.ac.uk License: GPL-2 http://crantastic.org/packages/MAMS Designing multi-arm multi-stage studies with normal endpoints and known variance * mmand (0.1.0) Maintainer: Jon Clayden Author(s): Jon Clayden License: GPL-2 http://crantastic.org/packages/mmand This package provides tools for performing mathematical morphology operations, such as erosion and dilation, on data of arbitrary dimensionality. It can also be used for smoothing and other image processing-style operations. * muma (1.0) Maintainer: Edoardo Gaude Author(s): Edoardo Gaude, Dimitrios Spiliotopoulos, Silvia Mari, Andrea Spitaleri and Michela Ghitti License: GPL-2 http://crantastic.org/packages/muma Preprocessing of metabolomic data (normalization and scalings); Principal Component Analysis with help tool for choosing best-separating principal components and automatic outlier testing; automatic univariate analysis for parametric and non-parametric data, with report generation (volcano and box plots); partial least sqaure discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); Ratio Analysis NMR SpectroscopY (RANSY). * okmesonet (0.1.1) Maintainer: Brady Allred Author(s): Brady Allred, Torre Hovick, Samuel Fuhlendorf License: GPL (= 2) http://crantastic.org/packages/okmesonet okmesonet retrieves and summarizes Oklahoma (USA) Mesonet climatological data provided by the Oklahoma Climatological Survey. Measurements are recorded every five minutes at approximately 120 stations throughout Oklahoma and are available in near real-time. * QRM (0.4-7) Maintainer: Bernhard Pfaff Author(s): Bernhard Pfaff License: GPL (= 2) http://crantastic.org/packages/QRM This package is designed to accompany the book Quantitative Risk Management: Concepts, Techniques and Tools by Alexander J. McNeil, Rudiger Frey and Paul Embrechts. * rcppbugs (0.0.8) Maintainer: Whit Armstrong Author(s): Whit Armstrong armstrong.w...@gmail.com License: GPL-3 http://crantastic.org/packages/rcppbugs R binding for cppbugs * RfmriVC (1.0) Maintainer: Stefanie Kalus Author(s): Ludwig Bothmann, Stefanie Kalus
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * appell (0.0-3) Maintainer: Daniel Sabanes Bove Author(s): Daniel Sabanes Bove daniel.sabanesb...@ifspm.uzh.ch with contributions by F. D. Colavecchia, R. C. Forrey, G. Gasaneo, N. L. J. Michel, L. F. Shampine, M. V. Stoitsov and H. A. Watts. License: GPL (= 3) http://crantastic.org/packages/appell This package wraps Fortran code by F. D. Colavecchia and G. Gasaneo for computing the Appell's F1 hypergeometric function. Their program uses Fortran code by L. F. Shampine and H. A. Watts. Moreover, the hypergeometric function with complex arguments is computed with Fortran code by N. L. J. Michel and M. V. Stoitsov or with Fortran code by R. C. Forrey. See the function documentations for the references and please cite them accordingly. * bayesPop (0.2-2) Maintainer: Hana Sevcikova Author(s): Hana Sevcikova, Adrian Raftery License: GPL (= 2) http://crantastic.org/packages/bayesPop The package allows to generate population projections for all countries of the world using several probabilistic components, such as total fertility rate (TFR) and life expectancy. * cec2005benchmark (1.0.0) Maintainer: Yasser González-Fernández Author(s): Yasser González-Fernández ygonzalezfernan...@gmail.com and Marta Soto mr...@icimaf.cu License: GPL (= 3) http://crantastic.org/packages/cec2005benchmark This package is a wrapper for the C implementation of the 25 benchmark functions for the CEC 2005 Special Session on Real-Parameter Optimization. The original C code by Santosh Tiwari and related documentation are available at http://www.ntu.edu.sg/home/EPNSugan/. * compound.Cox (1.0) Maintainer: Takeshi Emura, Graduate Institute of Statistics, National Central University, Taiwan Author(s): Takeshi Emura Yi-Hau Chen License: GPL-2 http://crantastic.org/packages/compound-Cox Calculate regression coefficients and their standard errors under the Cox proportional hazard model with the large number of covariates. * dgmb (1.0) Maintainer: Alba Martinez-Ruiz Author(s): Alba Martinez-Ruiz amart...@ucsc.cl and Claudia Martinez-Araneda cmarti...@ucsc.cl License: GPL (= 2) http://crantastic.org/packages/dgmb Random data generation for PLS structural models. * diffEq (1.0) Maintainer: Karline Soetaert Author(s): Karline Soetaert karline.soeta...@nioz.nl License: GPL http://crantastic.org/packages/diffEq Functions and examples from the book Solving Differential Equations in R by Karline Soetaert, Jeff R Cash and Francesca Mazzia. Springer, 2012. * dkDNA (0.1.0) Maintainer: Gota Morota Author(s): Gota Morota and Masanori Koyama License: GPL-2 http://crantastic.org/packages/dkDNA Compute diffusion kernels on DNA polymorphisms, including SNP and bi-allelic genotypes. * frmqa (0.1-0) Maintainer: Thanh T. Tran Author(s): Thanh T. Tran License: GPL (= 2) http://crantastic.org/packages/frmqa R and C++ functions for financial risk management and quantative analysis, using the generalized perbolic and its related distributions. * geospt (0.4-9) Maintainer: Alí Santacruz Author(s): Carlos Melo cm...@udistrital.edu.co, Alí Santacruz, Oscar Melo oome...@unal.edu.co and others License: GPL (= 2) http://crantastic.org/packages/geospt This package contains functions for: estimation of the variogram through trimmed mean, radial basis functions (optimization, prediction and cross-validation), summary statistics from cross-validation, pocket plot, and design of optimal sampling networks through sequential and simultaneous points methods * JohnsonDistribution (0.24) Maintainer: A.I. McLeod Author(s): A.I. McLeod and Leanna King License: GPL (= 2) http://crantastic.org/packages/JohnsonDistribution Johnson curve distributions. Implementation of AS100 and AS99. * labeledLoop (0.1) Maintainer: Kohske Takahashi Author(s): Kohske Takahashi License: MIT http://crantastic.org/packages/labeledLoop Support labeled loop and escape from nested loop * logitnorm (0.8.26) Maintainer: Thomas Wutzler Author(s): Thomas Wutzler License: GPL-2 http://crantastic.org/packages/logitnorm Density, distribution, quantile and random generation function for the logitnormal distribution. Estimation of the mode and the first two moments. Estimation of distribution parameters. * LOST (1.0) Maintainer: Jessica Arbour Author(s): J. Arbour and C. Brown License: GPL (= 2) http://crantastic.org/packages/LOST LOST includes functions for simulating missing morphometric data randomly, with taxonomic bias and with anatomical bias. This package also includes functions for estimating missing morphometric data based on regression. * NHPoisson (1.0) Maintainer: Ana C. Cebrian Author(s): Ana C. Cebrian License: GPL (= 2)
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week
New packages
* disclapmix (0.1)
Maintainer: Mikkel Meyer Andersen
Author(s): Mikkel Meyer Andersen and Poul Svante Eriksen
License: GPL-2
http://crantastic.org/packages/disclapmix
disclapmix makes inference in a mixture of Discrete Laplace
distributions using the EM algorithm.
* EstSimPDMP (1.1)
Maintainer: Unknown
Author(s): Romain Azais
License: GPL (= 2)
http://crantastic.org/packages/EstSimPDMP
This package deals with the estimation of the jump rate for
piecewise-deterministic Markov processes (PDMPs), from only one
observation of the process within a long time. The main functions
provide an estimate of this function. The state space may be
discrete or continuous. The associated paper is given in References.
Other functions provide a method to simulate random variables from
their (conditional) hazard rate, and then to simulate PDMPs.
* faoutlier (0.2.2)
Maintainer: Phil Chalmers
Author(s): Phil Chalmers rphilip.chalm...@gmail.com
License: GPL (= 2)
http://crantastic.org/packages/faoutlier
Tools for detecting and summarize influential cases that can affect
exploratory and confirmatory factor analysis models as well as
structural equation models more generally.
* FastImputation (1.0)
Maintainer: Stephen R. Haptonstahl
Author(s): Stephen R. Haptonstahl
License: GPL (= 2)
http://crantastic.org/packages/FastImputation
TrainFastImputation uses training data to describe a multivariate
normal distribution that the data approximates or can be transformed
into approximating and stores this information as an object of class
FastImputationPatterns. The FastImputation function uses this
FastImputationPatterns object to impute (make a good guess at)
missing data in a single line or a whole dataframe of data. This
approximates the process used by Amelia
(\url{http://gking.harvard.edu/amelia/}) but is much faster when
filling in values for a single line of data.
* hydroPSO (0.1-54-1)
Maintainer: Mauricio Zambrano-Bigiarini
Author(s): Mauricio Zambrano-Bigiarini [aut, cre] and Rodrigo Rojas [ctb]
License: GPL (= 2)
http://crantastic.org/packages/hydroPSO
This package implements a state-of-the-art version of the Particle
Swarm Optimisation (PSO) algorithm, with a special focus on the
calibration of environmental models. hydroPSO is model-independent,
allowing the user to easily interface any model code with the
calibration engine (PSO). hydroPSO includes a series of controlling
options and PSO variants to fine-tune the performance of the
calibration engine. An advanced sensitivity analysis function
together with user-friendly plotting summaries facilitate the
interpretation and assessment of the calibration results. Bugs
reports/comments/questions are very welcomed.
* OOmisc (1.0)
Maintainer: Ozgur Asar
Author(s): Ozgur Asar, Ozlem Ilk
License: GPL (= 2)
http://crantastic.org/packages/OOmisc
Includes miscellaneous functions.
* robustHD (0.1.0)
Maintainer: Andreas Alfons
Author(s): Andreas Alfons
License: GPL (= 2)
http://crantastic.org/packages/robustHD
Robust methods for high-dimensional data, in particular linear model
selection techniques based on least angle regression and sparse
regression.
* sparseLTSEigen (0.1.0)
Maintainer: Andreas Alfons
Author(s): Andreas Alfons
License: GPL (= 2)
http://crantastic.org/packages/sparseLTSEigen
Use RcppEigen to fit least trimmed squares regression models with an
L1 penalty in order to obtain sparse models.
* sROC (0.1-2)
Maintainer: Xiao-Feng Wang
Author(s): Xiao-Feng Wang
License: GPL (= 3)
http://crantastic.org/packages/sROC
This package contains a collection of functions to perform
nonparametric estimation of receiver operating characteristic (ROC)
curves for continuous data.
* sybilDynFBA (0.0.1)
Maintainer: Abdelmoneim Amer Desouki
Author(s): Abdelmoneim Amer Desouki
License: GPL-3
http://crantastic.org/packages/sybilDynFBA
In this package the dynamic FBA technique proposed by Varma was
implemented.
* tfplot (2012.4-1)
Maintainer: Paul Gilbert and Erik Meijer
Author(s): Paul Gilbert pgilbert.tt...@ncf.ca
License: GPL-2
http://crantastic.org/packages/tfplot
Utilities in this package are for simple manipulation and quick
plotting of time series data. These utilities use the tframe package
which provides a programming kernel for time series. Extension to
tframe provided in tframePlus can also be used. See the Guide
vignette for examples.
* varbvs (1.0)
Maintainer: Peter Carbonetto
Author(s): Peter Carbonetto
License: GPL (= 3)
http://crantastic.org/packages/varbvs
Implements the variational inference procedure for Bayesian variable
selection, as described in the quot;Scalable variational inference for
Bayesian variable selection in regression, and its accuracy in
genetic association studiesquot;
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * bigdata (0.1) Maintainer: Han Liu Author(s): Han Liu, Tuo Zhao License: GPL-2 http://crantastic.org/packages/bigdata The big data package is a collection of scalable methods for large-scale data analysis. * boss (1.0) Maintainer: Arend Voorman Author(s): Arend Voorman License: GPL (= 2) http://crantastic.org/packages/boss BOSS uses parameter estimates obtained without genotype to boost standard one-step approximations, and precomputes as much as possible without genotype (using boss.set) to minimize effort required. * Distance (0.6) Maintainer: David L Miller Author(s): David L. Miller License: GPL (= 2) http://crantastic.org/packages/Distance A library that provides a simple way of fitting detection functions to distance sampling data for both line and point transects. Adjustment term selection, left and right truncation as well as monotonicity constraints and binning are supported. Abundance and density estimates can also be calculated if survey area information is provided. * FinAsym (1.0) Maintainer: Paolo Zagaglia Author(s): Paolo Zagaglia License: GPL-3 http://crantastic.org/packages/FinAsym This package accomplishes two tasks: a) it classifies implicit trading activity from quotes in OTC markets using the algorithm of Lee and Ready (1991); b) based on information for trade initiation, the package computes the probability of informed trading of Easley and O'Hara (1987). * gammSlice (1.2-5) Maintainer: Tung Pham Author(s): Tung Pham and Matt Wand License: GPL (= 2) http://crantastic.org/packages/gammSlice Uses a slice sampling-based Markov chain Monte Carlo to conduct Bayesian fitting and inference for generalized additive mixed models (GAMM). Generalized linear mixed models and generalized additive models are also handled as special cases of GAMM. * GenOrd (1.0.1) Maintainer: Alessandro Barbiero Author(s): Alessandro Barbiero, Pier Alda Ferrari License: GPL http://crantastic.org/packages/GenOrd The package implements a procedure for generating samples from ordinal/discrete random variables with pre-specified correlation matrix and marginal distributions. * Lambda4 (1.0) Maintainer: Unknown Author(s): Tyler Hunt License: GPL (= 2) http://crantastic.org/packages/Lambda4 This code provides 4 different estimates of maximized lambda4 (A split half reliability estimate) * leapp (1.0) Maintainer: Yunting Sun Author(s): Yunting Sun yunti...@stanford.edu , Nancy R.Zhang nzh...@stanford.edu, Art B.Owen o...@stanford.edu License: GPL (= 2) http://crantastic.org/packages/leapp These functions take a gene expression value matrix, a primary covariate vector, an additional known covariates matrix. A two stage analysis is applied to counter the effects of latent variables on the rankings of hypotheses. The estimation and adjustment of latent effects are proposed by Sun, Zhang and Owen (2011). quot;leappquot; is developed in the context of microarray experiments, but may be used as a general tool for high throughput data sets where dependence may be involved. * lxb (1.1) Maintainer: Björn Winckler Author(s): Björn Winckler bjorn.winck...@gmail.com License: BSD http://crantastic.org/packages/lxb Functions to quickly read LXB parameter data. * markdown (0.3) Maintainer: JJ Allaire Author(s): JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte License: GPL-3 http://crantastic.org/packages/markdown Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats. This package provides R bindings to the Sundown markdown rendering library. * phenology (3.28) Maintainer: Marc Girondot Author(s): Marc Girondot License: GPL-2 http://crantastic.org/packages/phenology Functions to fit and test the phenology of species based on counts. * RAFM (1.0) Maintainer: Unknown Author(s): Markku Karhunen, Uni. Helsinki License: GPL-2 http://crantastic.org/packages/RAFM Fits AFM by Metropolis-Hastings, calculates theta and FST out of AFM parameters * SCMA (0.0) Maintainer: Isis Bulte Author(s): Isis Bulte and Patrick Onghena License: GPL (= 2) http://crantastic.org/packages/SCMA A package for probability combining (additive and multiplicative method) and for calculating some effect size measures on single-case data (SMD, PND and PEM). * skewtools (0.1.0) Maintainer: Javier E. Contreras-Reyes Author(s): Javier E. Contreras-Reyes License: GPL (= 2) http://crantastic.org/packages/skewtools This package include functions related to following topics: 1. Information Theory: Entropy and Mutual Informacion Index for Multivariate Skew-t and Skew-Normal distributions. 2. Estimation of Growth models parameters (Von Bertalanffy, Gompertz, Logistic and Richards) using the robust ECME method via
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * EffectStars (1.0) Maintainer: Unknown Author(s): Gunther Schauberger License: GPL-2 http://crantastic.org/packages/EffectStars The package provides functions to visualize regression models with categorical response. The effects of the covariates are plotted with star plots in order to allow for an optical impression of the fitted model. * extraBinomial (2.0) Maintainer: Xin Yang Author(s): Xin Yang License: GPL-3 http://crantastic.org/packages/extraBinomial This package tests for differences in minor allele frequency between groups and is based on an extra-binomial variation model for pooled sequencing data. A set of simulated pooled sequencing data can be generated using this package. * Familias (1.0) Maintainer: Petter Mostad Author(s): Petter Mostad mos...@chalmers.se License: GPL-2 http://crantastic.org/packages/Familias This package represents a bare-bones implementation of an interface to the core Familias functions (www.familias.name), which are programmed in C++. The package itself functions as a kind of database, where information about persons, pedigrees, allele systems and observations for persons are entered stepwise. In the end, probability calculations are made. * JPSurv (1.0.1) Maintainer: Yongwu Shao Author(s): Yongwu Shao yws...@gmail.com, License: GPL (= 2) http://crantastic.org/packages/JPSurv Functions, methods, and datasets for cancer survival analysis, including the proportional hazard relative survival model, the join point relative survival model. * kappaSize (1.0) Maintainer: Michael A Rotondi Author(s): Michael A Rotondi mroto...@yorku.ca License: GPL (= 2) http://crantastic.org/packages/kappaSize This package contains basic tools for the purpose of sample size estimation in studies of interobserver/interrater agreement (reliability). This package contains sample size estimation functions for both the power-based and confidence interval-based methods, with binary or multinomial outcomes and two through six raters. * koRpus (0.04-27) Maintainer: m.eik michalke Author(s): m.eik michalke meik.micha...@hhu.de, with contributions from Earl Brown eabr...@csumb.edu, Alberto Mirisola, and Laura Hauser License: GPL (= 3) http://crantastic.org/packages/koRpus A set of tools to analyze texts. Includes, amongst others, functions for automatic language detection, hyphenation, several indices of lexical diversity (e.g., type token ratio, HD-D/vocd-D, MTLD) and readability (e.g., Flesch, SMOG, LIX, Dale-Chall). Basic import functions for language corpora are also provided, to enable frequency analyses (supports Celex and Leipzig Corpora Collection file formats). #' Note: For full functionality a local installation of TreeTagger is recommended. Be encouraged to send feedback to the author(s)! * networkDynamic (0.2-2) Maintainer: Ayn Leslie-Cook Author(s): Ayn Leslie-Cook, Zack Almquist, Pavel N. Krivitsky, Skye Bender-deMoll, David R. Hunter, Martina Morris, Carter T. Butts License: GPL-3 http://crantastic.org/packages/networkDynamic Simple interface routines to facilitate the handling of network objects with complex intertemporal data. * qLearn (1.0) Maintainer: Bibhas Chakraborty Author(s): Jingyi Xin, Bibhas Chakraborty, and Eric B. Laber License: GPL-2 http://crantastic.org/packages/qLearn Functions to implement Q-learning for estimating optimal dynamic treatment regimes from two stage sequentially randomized trials, and to perform inference via m-out-of-n bootstrap for parameters indexing the optimal regime. * Rdistance (1.0) Maintainer: Trent McDonald Author(s): Trent McDonald License: GNU General Public License http://crantastic.org/packages/Rdistance Analysis of line transect surveys. Estimates distance-based sightability functions and abundances. * relSim (0.1-33) Maintainer: James M. Curran Author(s): James M. Curran License: GPL (= 2) http://crantastic.org/packages/relSim A set of tools to explore the behaviour statistics used for forensic DNA interpretation when close relatives are involved * RForcecom (0.1) Maintainer: Takekatsu Hiramura Author(s): Takekatsu Hiramura License: BSD http://crantastic.org/packages/RForcecom RForcecom provides the connection to Force.com (Salesforce.com) from R. * SAScii (0.1) Maintainer: Anthony Joseph Damico Author(s): Anthony Joseph Damico License: GPL (= 2) http://crantastic.org/packages/SAScii Using any importation code designed for SAS users to read ASCII files into sas7bdat files, the SAScii package parses through the INPUT block of a (.sas) syntax file to design the parameters needed for a read.fwf function call. This allows the user to specify the location of the ASCII (often a .dat) file and the location
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages BradleyTerry2 (0.9-3), COUNT (1.1.1), DeducerPlugInScaling (0.0-6) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages BARD (1.18), BAS (0.92), CollocInfer (0.1.2), CompQuadForm (1.1), CompRandFld (0.2), COUNT (1.1.0), DPpackage (1.1-2), FAiR (0.4-6) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages BioPhysConnectoR (1.6-6), Deducer (0.4-1) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages CORElearn (0.9.30) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * aratio (1.0) Maintainer: Daniel McMillen Author(s): Daniel McMillen http://crantastic.org/packages/aratio Tools for analyzing assessment ratios * DeducerPlugInScaling (0.0-5) Maintainer: Alberto Mirisola Author(s): Alberto Mirisola alberto.miris...@gmail.com http://crantastic.org/packages/DeducerPlugInScaling A Deducer plugin for factor analysis and reliability analysis, using psych, GPArotation and mvnormtest packages. * IMIS (0.0) Maintainer: Le Bao Author(s): Adrian Raftery, Le Bao http://crantastic.org/packages/IMIS IMIS algorithm draws samples from the posterior distribution. The user has to define the following R functions in advance: prior(x) calculates prior density of x, likelihood(x) calculates the likelihood of x, and sample.prior(n) draws n samples from the prior distribution. * OrgMassSpecR (0.2-2) Maintainer: Nathan Dodder Author(s): Nathan G. Dodder, Southern California Coastal Water Research Project (SCCWRP). Contributions from Katharine M. Mullen. http://crantastic.org/packages/OrgMassSpecR Functions related to instrument operation and data analysis. * RNiftyReg (0.2.0) Maintainer: Jon Clayden Author(s): Jon Clayden; based on original code by Marc Modat and Pankaj Daga http://crantastic.org/packages/RNiftyReg This package provides an R interface to the NiftyReg image registration tools lt;http://sourceforge.net/projects/niftyreg/gt;. * RWekajars (3.7.1-1) Maintainer: Kurt Hornik Author(s): Kurt Hornik http://crantastic.org/packages/RWekajars External jars required for package RWeka. * SE.IGE (1.0) Maintainer: Unknown Author(s): Piter Bijma http://crantastic.org/packages/SE-IGE Predicts standard errors of estimated genetic parameters for IGE Updated packages BAS (0.91), Bchron (3.1.1), Bergm (1.4), CORElearn (0.9.29), FitAR (1.86), FrF2 (1.1-5), GPseq (0.3), Hmisc (3.8-3), IBrokers (0.2-8), JM (0.7-0), JOP (1.0.5), MetabolAnalyze (1.2), Metabonomic (3.4), MuMIn (0.13.14), NCBI2R (1.3.2), NCBI2R (1.3.1), Rcpp (0.8.6), RNiftyReg (0.2.0), ROracleUI (1.2-0), RProtoBuf (0.2.0), Rsolnp (1.0-5), RWeka (0.4-2), SIS (0.6), TSAgg (0.2-1), WGCNA (0.94) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * CFL (0.1) Maintainer: Pablo Michel Marin Ortega Author(s): Pablo Michel Marin Ortega, Kornelius Rohmeyer http://crantastic.org/packages/CFL The main results on this project are: a package to analyze the data based on compensatory fuzzy logic algorithms and a reasoner for the compensatory fuzzy logic. * LVQTools (1.0) Maintainer: Sander Kelders Author(s): Sander Kelders sakeld...@gmail.com http://crantastic.org/packages/LVQTools This package provides several LVQ algorithms along with different usage methods and output visualization. Updated packages adimpro (0.7.5), Boruta (1.3), CORElearn (0.9.28), DoE.wrapper (0.8-1), Epi (1.1.17), FBN (1.5), GenABEL (1.6-4), GeneReg (1.1.2), Metabonomic (3.3.2), MIfuns (4.0.17), MIfuns (4.0.18), OrdFacReg (1.0.2), PairViz (1.1), R.matlab (1.3.2), R2Cuba (1.0-5), R2Cuba (1.0-6), RcmdrPlugin.qual (1.0.0), RExcelInstaller (3.1-8), Rserve (0.6-2), SMCP (1.1.2), SMCP (1.1.3), SPOT (0.1.1016), SubpathwayMiner (3.1) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * ProjectTemplate (0.1-2) Maintainer: John Myles White Author(s): John Myles White http://crantastic.org/packages/ProjectTemplate The ProjectTemplate package provides a function, create.project(), that automatically builds a directory for a new R project with a clean sub-directory structure and automatic data and library loading tools. The hope is that standardized data loading, automatic importing of best practice packages, integrated unit testing and useful nudges towards keeping a cleanly organized codebase will improve the quality of R coding. * QuACN (1.0) Maintainer: Laurin Mueller Author(s): Laurin Mueller http://crantastic.org/packages/QuACN Quantitative Analysis of Complex Networks. This package offers a set of topological network measures to analyze complex Networks structurally. * RandForestGUI (1.0) Maintainer: Rory Michelland Author(s): Rory Michelland rory.michell...@gmail.com, Genevieve Grundmann grund...@biomserv.univ-lyon1.fr http://crantastic.org/packages/RandForestGUI A graphical user interface program to analyze microbial profiles (taxonomic sequences, fingerprints and microarrays) based on conditional inference random forest * RcmdrPlugin.TextMining (0.1-0) Maintainer: Dzemil Lusija Author(s): Dzemil Lusija http://crantastic.org/packages/RcmdrPlugin-TextMining WARNING: This package is currently in beta status! This package provide GUI for demonstration of text mining concepts and quot;tmquot; package. It is implemented as a plugin to the R-Commander, which is based on tcl/tk. This set of dialogs can be accessed through the menu TextMining that is added to the R-Commander menus. * SMCP (1.1.1) Maintainer: Jin (Gordon) Liu Author(s): Jin (Gordon) Liu http://crantastic.org/packages/SMCP A package containing functions that generate microarray data, fit the marginalized linear model with MCP and QA penalties and conduct cross-validation to select the tuning parameter. Updated packages anapuce (2.2), archetypes (2.0-2), assist (3.0), BLR (1.2), CADStat (2.2-6), CHNOSZ (0.9-2), coin (1.0-16), demography (1.03), DEoptim (2.0-6), FEST (0.08), FitAR (1.85), FunNet (1.00-10), futile.paradigm (1.0.3), GGally (0.2.2), GGMselect (0.1-2), glmulti (0.6-3), JOP (1.0.4), MIfuns (4.0.16), mondate (0.9.08.23), multitaper (0.1-2), MuMIn (0.13.9), MuMIn (0.13.8), mutossGUI (0.1-4), nls2 (0.1-3), NMF (0.5.02), nnc (1.12), party (0.9-9998), PBSddesolve (1.08.11), penalizedSVM (1.1), PET (0.4.9), pomp (0.32-1), PowerTOST (0.7-2), pROC (1.3.2), ProjectTemplate (0.1-2), REQS (0.8-7), Rlabkey (2.1.114), ROracleUI (1.1-3), RPyGeo (0.9-2), RSAGA (0.91-1), RSiena (1.0.11.119), sifds (0.9-1), SPACECAP (1.0.1), spatstat (1.20-3), spBayes (0.2-0), stringr (0.4), TIMP (1.10), TRIANG (1.2), WGCNA (0.93), YieldCurve (3.1) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * DCGL (1.0) Bao-Hong Liu http://crantastic.org/packages/DCGL Functions for basic differential coexpression analyses: gene filtering, link filtering, DCG (Differentially-Coexpressed Gene) identification and DCL (Differentially-Coexpressed Links) identification.Two algorithms,named DCP and DCe, are provided for DCG-identification or DCG and DCL-identification. * fmsb (0.11) Minato Nakazawa http://crantastic.org/packages/fmsb Several utility functions for the book entitled quot;Practices of Medical and Health Data Analysis using Rquot; (Pearson Education Japan, 2007) * IniStatR (1.0.0) Frederic Bertrand http://crantastic.org/packages/IniStatR This packages provides datasets for the book quot;Initiation à la Statistique avec Rquot;, Dunod, 2010. * isva (1.0) Unknown http://crantastic.org/packages/isva Independent Surrogate Variable Analysis is a general algorithm for feature selection in the presence of potentially confounding factors. * mritc (0.3-1) Dai Feng http://crantastic.org/packages/mritc Various methods for MRI tissue classification. * mutoss (0.1-1) Kornelius Rohmeyer http://crantastic.org/packages/mutoss The Mutoss package and accompanying mutossGUI package are designed to ease the application and comparison of multiple hypothesis testing procedures. * mutossGUI (0.1-2) Kornelius Rohmeyer http://crantastic.org/packages/mutossGUI A graphical user interface for the MuToss Project * refund (0.1-0) Lei Huang http://crantastic.org/packages/refund Functions for regression with functional data. The principal methods currently implemented are (1) functional-response/scalar-predictor regression by penalized OLS or GLS; and (2) functional principal component regression for scalar responses and functional predictors. * soiltexture (1.0) Julien MOEYS http://crantastic.org/packages/soiltexture quot;The Soil Texture Wizardquot; is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle / classification into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Several texture triangles are predefined: USDA; FAO (which is also the triangle for the soil map of Europe); Aisne (France); GEPPA (France); German triangle (Bodenkundliche Kartieranleitung 1994); Soil Survey of England and Wales (UK); Australian triangle; Belgian triangle; Canadian triangle; ISSS triangle; Romanian traingle. The Soil Texture Wizard is initially develloped from the functions 'soil.texture()' from the package 'plotrix' by Jim Lemon et al. * TunePareto (1.0) Hans Kestler http://crantastic.org/packages/TunePareto Generic methods for parameter tuning of classification algorithms using multiple scoring functions Updated packages ade4 (1.4-16), adlift (1.2-3), AICcmodavg (1.08), aqp (0.94-1), aspace (2.5), aspace (2.4), BioStatR (1.0.2), bnlearn (2.2), caret (4.54), caret (4.53), clustTool (1.6.5), coarseDataTools (0.3), constrainedKriging (0.1.2), DEMEtics (0.8.1), emdbook (1.2.2.1), FitAR (1.80), fpc (2.0-2), futile.paradigm (1.0.1), futile.paradigm (1.0.2), gamlss (4.0-3), gamlss.add (4.0-1), gamlss.data (4.0-1), genoPlotR (0.5.1), GEOmap (1.5-9), GEVcdn (1.0.2), GillespieSSA (0.5-4), gllm (0.33), glmperm (1.0-3), gRapHD (0.1.7), HFWutils (0.9.4.2010.08.20), hts (1.3), HWEintrinsic (1.1.1), igraph (0.5.4-1), intervals (0.13.3), ipw (1.0-6), laeken (0.1.3), LDheatmap (0.2-9), lme4 (0.999375-35), lmPerm (1.1-2), lordif (0.1-6), lpSolveAPI (5.5.2.0), magma (0.2.1-3), MCMCglmm (2.06), mondate (0.9.08.15), mondate (0.9.08.19.02), mratios (1.3.13), nacopula (0.4-3), nleqslv (1.7), nlt (2.1-1), NMF (0.5), pROC (1.3.1), qpcR (1.3-1), qpcR (1.3-0), qtl (1.18-7), qualityTools (1.01), R.utils (1.5.0), r4ss (1.10), rAverage (0.3-3), rbounds (0.5), RcmdrPlugin.HH (1.1-26), robCompositions (1.4.3), RPMG (2.0-0), RSEIS (2.4-4), rTOFsPRO (1.2), Runiversal (1.0.1), rwm (1.52), sdcMicro (2.6.5), sem (0.9-21), simFrame (0.3.2), simFrame (0.3.3), simFrame (0.3.1), spdep (0.5-19), spikeslab (1.1.1), TGUICore (0.9.12), TGUITeaching (0.9.12), tm (0.5-4), traitr (0.10), TraMineR (1.6-1), TSAgg (0.2-0), vegan (1.17-4), VIM (1.4.1), wq (0.2-5) 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
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * ber (1.0) Unknown http://crantastic.org/packages/ber In this package there are functions for adjusting the data to remove batch effects * charlson (1.0) Vanessa Cox http://crantastic.org/packages/charlson Input patient id and icd9 codes and obtain summary index * DeducerExtras (1.1) Ian Fellows http://crantastic.org/packages/DeducerExtras Added functionality for Deducer. This package includes additional dialogs for calculating distribution function values, cluster analysis, factor analysis and more. * demography (1.02) Rob J Hyndman http://crantastic.org/packages/demography Functions for demographic analysis including lifetable calculations; Lee-Carter modelling; functional data analysis of mortality rates, fertility rates, net migration numbers; and stochastic population forecasting. * futile.paradigm (1.0.0) Brian Lee Yung Rowe http://crantastic.org/packages/futile-paradigm Provides dispatching implementations suitable for functional programming paradigms. The framework provides a mechanism for attaching guards to functions similar to Erlang, while also providing the safety of assertions reminiscent of Eiffel. * igraphtosonia (1.0) Sean J Westwood http://crantastic.org/packages/igraphtosonia This program facilitates exporting igraph graphs to the SoNIA file format * interactivity (0.1) Jeroen Ooms http://crantastic.org/packages/interactivity Toggle R interactive mode by setting C level global variable R_Interactive. * isdals (1.0-1) Claus Ekstrom http://crantastic.org/packages/isdals Provides data sets for Introduction to Statistical Data Analysis for the Life Sciences * magma (0.2.1-2) Brian J. Smith http://crantastic.org/packages/magma Magma matrix classes and methods for parallel processing of matrix algebra operations. Operations are performed with algorithms developed by the MAGMA research project. MAGMA aims to achieve the fastest possible linear algebra libraries on hybrid multicore CPU and GPU architectures by exploiting their massive parallelism and minimizing communication latencies. * normwhn.test (1.0) Peter Wickham http://crantastic.org/packages/normwhn-test Includes Omnibus Univariate and Multivariate Normality Tests (See Doornik and Hansen (1994)). One variation allows for the possibility of weak dependence rather than independence in the variable(s). Also included is an univariate white noise test where the null hypothesis is quot;white noisequot; rather than strict quot;white noisequot;. * pathmox (0.1) Gaston Sanchez http://crantastic.org/packages/pathmox companion package of plspm with approaches of segmentation trees in PLS Path Modeling. * phitest (1.0-0) Leah R. Jager http://crantastic.org/packages/phitest This package perform a generalized goodness-of-fit test based on phi-divergences. This test works by considering the maximum 'distance' between the hypothesized distribution function and the empirical distribution function, where the measure of 'distance' is based on a phi-divergence. This generalized family of tests is indexed by a real-valued parameter, s, wich can take values in [-1,2]. Special cases of this family include the Berk-Jones statistic (s=0), the supremum form of the Anderson-Darling statistic (s=2), and the statistic of Jaescke and Eicker (s=-1). See the references for the phi.test() function for references regarding these special cases. In addition to performing a statistical test, this package will also invert the test statistic to form and plot confidence bands for the true distribution function for sample sizes up to 10,000. Updated packages aqp (0.94), BaM (0.98.1), bayesm (2.2-3), BB (2010.7-1), blighty (3.1-2), brainwaver (1.5), caret (4.49), caret (4.51), caroline (0.3-0), catnet (1.08.2), catnet (1.08.1), classGraph (0.7-4), cobs (1.2-1), cobs99 (0.9-10), coin (1.0-14), constrainedKriging (0.1.1), countrycode (0.5), cyclones (1.2-9), DAAG (1.02), dafs (1.0-35), Deducer (0.4-0), DeducerExtras (1.1), delftfews (0.3-33), delftfews (0.3-30), delftfews (0.3-27), delftfews (0.3-19), demography (1.02), diptest (0.25-3), DoE.wrapper (0.8), doMPI (0.1-5), evir (1.7), expm (0.98-3), fgui (1.0-1), FNN (0.6-2), fpc (2.0-1), ftnonpar (0.1-84), gene2pathway (1.6.1), geofd (0.4.6), geoR (1.6-29), gridExtra (0.7), hergm (1.2-8), HiddenMarkov (1.4-0), HTMLUtils (0.1.4), interval (1.0-1.0), irr (0.83), ISOcodes (2010.08.12-1), laeken (0.1.2), lmomco (1.0.1), magma (0.2.1-2), maptools (0.7-36), Matching (4.7-10), MatchIt (2.4-14), maxLik (0.8-0), mcgibbsit (1.0.6), mclust (3.4.6), MCMCglmm (2.05), micEcon (0.6-6), micEconCES (0.6-8), miscTools (0.6-6), mixOmics (2.8-1), mugnet (0.13.2), mugnet (0.13.1), multcomp (1.2-0), pgfSweave (1.0.6), PHYLOGR (1.0.7), plink (1.2-5), plspm (0.1-11), PowerTOST (0.7-1), pROC (1.3),
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * cumSeg (1.0) Vito M.R. Muggeo http://crantastic.org/packages/cumSeg Estimation of number and location of change points in mean-shift (piecewise constant) models. Particularly useful to model genomic sequences of continuous measurements. * GWASExactHW (1.0) Ian Painter http://crantastic.org/packages/GWASExactHW This package contains a function to do exact Hardy-Weinburg testing (using Fisher's test) for SNP genotypes as typically obtained in a Genome Wide Association Study (GWAS). * HapEstXXR (0.1-3) Sven Knueppel http://crantastic.org/packages/HapEstXXR Haplotype-Based Analysis of Association for genetic traits * MatrixModels (0.1-1) Doug and Martin http://crantastic.org/packages/MatrixModels Modelling with sparse and dense 'Matrix' matrices, using modular prediction and response module classes. * mhurdle (0.1-0) Yves Croissant http://crantastic.org/packages/mhurdle * MSToolkit (2.0) MSToolkit http://crantastic.org/packages/MSToolkit MSToolkit library for evaluating clinical trial design and analysis operating characteristics through simulation. * nnc (1.10) Unknown http://crantastic.org/packages/nnc Computes nearest neighbour autocovariates * optimx (0.84) John C. Nash http://crantastic.org/packages/optimx Provides a replacement and extension of the optim() function to unify and streamline optimization capabilities in R for smooth, possibly box constrained functions of several or many parameters * SlimPLS (0.3) Ofer Lavi http://crantastic.org/packages/SlimPLS SlimPLS is an implementation of SlimPLS multivariate feature selection. Updated packages benchmark (0.3-1), Bolstad (0.2-18), bqtl (1.0-26), caret (4.47), cmprskContin (1.7), combinat (0.0-8), corpcor (1.5.7), DatABEL (0.9-0), depmixS4 (1.0-0), dismo (0.5-4), diveMove (1.1), DoE.base (0.12), DOSim (2.0), flexmix (2.2-8), Flury (0.1-3), FrF2 (1.1-4), Geneclust (1.0.1), GPseq (0.2), hexView (0.3-2), HMR (0.2.1), igraph (0.5.4), iid.test (1.6), IsoGene (1.0-17), kknn (1.0-8), lpSolve (5.6.5), Matrix (0.999375-43), MSBVAR (0.5.0), optparse (0.9.0), pamctdp (0.1.8), PerformanceAnalytics (1.0.3), pmml (1.2.23), rainbow (2.1), rattle (2.5.38), RcppArmadillo (0.2.5), realized (1.0), RExcelInstaller (3.1-6), RInside (0.2.3), RQuantLib (0.3.3), Runuran (0.15.0), siar (4.0.1), spBayes (0.1-9), svcR (1.6.5), tau (0.0-8), timereg (1.3-5), ttime (1.2.4), ttime (1.2.3), twang (1.0-2), UsingR (0.1-13), vegetarian (1.2), wgaim (0.99-2), WMCapacity (0.9.5.1), xts (0.7-4) 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.
[R] CRAN (and crantastic) updates this week
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 quot;Introduction to Data analysis with R for Forensic Scientistsquot;, 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
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * evaluate (0.1) Hadley Wickham http://crantastic.org/packages/evaluate Parsing and evaluation tools that make it easy to recreate the command line behaviour of R. * multitaper (0.1-1) Karim Rahim http://crantastic.org/packages/multitaper * operator.tools (1.0.0) Christopher Brown http://crantastic.org/packages/operator-tools Utilities for working with R's operators * pglm (0.1-0) Yves Croissant http://crantastic.org/packages/pglm Estimation of panel models for glm-like models: this includes binomial models (logit and probit) count models (poisson and negbin) and ordered models (logit and probit) * rvgtest (0.5.0) Josef Leydold http://crantastic.org/packages/rvgtest Test suite for non-uniform pseudo-random number generators. * sigclust (1.0.0) Hanwen Huang http://crantastic.org/packages/sigclust SigClust is a statistical method for testing the significance of clustering results. SigClust can be applied to assess the statistical significance of splitting a data set into two clusters. For more than two clusters, SigClust can be used iteratively. * SII (1.0.0) Gregory R. Warnes http://crantastic.org/packages/SII This package calculates ANSI S3.5-1997 Speech Intelligibility Index (SII), a standard method for computing the intelligibility of speech from acoustical measurements of speech, noise, and hearing thresholds. This package includes data frames corresponding to Tables 1 - 4 in the ANSI standard as well as a function utilizing these tables and user-provided hearing threshold and noise level measurements to compute the SII score. The methods implemented here extend the standard computations to allow calculation of SII when the measured frequencies do not match those required by the standard by applying interpolation to obtain values for the required frequencies -- Development of this package was funded by the Center for Bioscience Education and Technology (CBET) of the Rochester Institute of Technology (RIT). * someMTP (1.0) Unknown http://crantastic.org/packages/someMTP It is a collection of functions for Multiplicty Correction and Multiple Testing. Updated packages actuar (1.1-1), AnalyzeFMRI (1.1-12), aqp (0.90), asbio (0.3-12), BAS (0.90), bibtex (0.2-1), bigtabulate (1.0.13), binGroup (1.0-6), caret (4.44), CHNOSZ (0.9-1), cmaes (1.0-9), COZIGAM (2.0-3), cxxPack (7.0.6), dcemriS4 (0.32), distrMod (2.2.2), DoseFinding (0.2-2), DOSim (1.2), dplR (1.3.6), dti (0.9-2.1), dynaTree (1.0-1), epiR (0.9-26), ergm (2.2-5), eVenn (1.21), FAMT (2.1), flashClust (1.00-2), forensim (1.1-7), GEOmap (1.5-8), gridExtra (0.6.5), hergm (1.2-6), hmm.discnp (0.1-3), hts (1.2), HWEintrinsic (1.1), JM (0.6-2), lqa (1.0-3), mclust (3.4.5), MCPMod (1.0-7), memisc (0.95-31), miniGUI (0.7.0), minqa (1.1.9), mixsmsn (0.2-5), mlogit (0.1-8), mokken (2.4), mondate (0.9.6), MplusAutomation (0.3-3), mra (2.6), np (0.40-3), ordinal (2010.07-06), pamctdp (0.1.5), pcaPP (1.8-2), pgirmess (1.4.7), phylobase (0.6.0), picante (1.2-0), plm (1.2-5), plspm (0.1-7), plyr (1.1), PolynomF (0.94), PowerTOST (0.6-2), psych (1.0-90), PtProcess (3.2-5), R.filesets (0.8.3), r4ss (1.07), raster (1.3-1), rattle (2.5.36), rbugs (0.4-4), Rcgmin (0.8), RFLPtools (1.3), rgdal (0.6-28), RMySQL (0.7-5), RpgSQL (0.1-3.1), rredis (1.4), RSEIS (2.4-1), RSQLite (0.9-2), Rvmmin (0.95), rwm (1.49), saws (0.9-3.3), SensoMineR (1.11), simPopulation (0.1.3), soil.spec (1.4), sp (0.9-66), sparr (0.2-1), spdep (0.5-16), spgrass6 (0.6-19), stratigraph (0.62), SV (1.3.0), TeachingSampling (1.7.9), tgp (2.3-4), traitr (0.9), TripleR (0.4), vegdata (0.1.8), x12 (0.0-7), xlsx (0.2.2), YieldCurve (3.0) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages BSDA (1.0) New reviews --- * ggplot2, by elaliberte http://crantastic.org/reviews/69 * FD, by elaliberte http://crantastic.org/reviews/68 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * AIM (1.01) Rob Tibshirani http://crantastic.org/packages/AIM R functions for adaptively constructing index models for continuous, binary and survival outcomes. Implementation requires loading R-pacakge survival * BLR (1.1) Paulino Perez Rodriguez http://crantastic.org/packages/BLR Bayesian Linear Regression * CMC (1.0) Michela Cameletti http://crantastic.org/packages/CMC Calculation and plot of the stepwise Cronbach-Mesbah Curve Updated packages ADaCGH (1.5-3), AquaEnv (1.0-1), BAS (0.80), Bergm (1.1), BTSPAS (1.0.03), CADStat (2.2-5), CGIwithR (0.72-1), CPE (1.4.1) New reviews --- * data.table, by khoda http://crantastic.org/reviews/67 * data.table, by phubaba http://crantastic.org/reviews/66 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages Amelia (1.2-16), AMORE (0.2-12), Bolstad (0.2-17), CADStat (2.2-4) 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.
[R] CRAN (and crantastic) updates this week
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
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * dcemriS4 (0.20.1) Brandon Whitcher http://crantastic.org/packages/dcemriS4 A collection of routines and documentation that allows one to perform a quantitative analysis of dynamic contrast-enhanced or diffusion-weighted MRI data. Medical imaging data should be organized using either the Analyze or NIfTI data formats. * genefu (1.0.0) Benjamin Haibe-Kains http://crantastic.org/packages/genefu R package providing various functions relevant for gene expression analysis with emphasis on breast cancer. * micEconAids (0.6-0) Arne Henningsen http://crantastic.org/packages/micEconAids Demand analysis with the Almost Ideal Demand System (AIDS) suggested by Deaton and Muellbauer (1980) * miscTools (0.6-0) Arne Henningsen http://crantastic.org/packages/miscTools Miscellanneous small tools and utilities * nytR (0.1) Shane Conway http://crantastic.org/packages/nytR Provides access to various data sources (congressional vote data) through the NY Times API. * partitionMetric (1.0) Unknown http://crantastic.org/packages/partitionMetric partitionMetric computes a distance between two partitions of a set. Updated packages accuracy (1.35), arm (1.2-13), aspect (1.0-0), BAS (0.4), BAS (0.45), coin (1.0-9), fitdistrplus (0.1-2), frontier (0.996-4), gap (1.0-22), gRbase (1.3.0), gRbase (1.2.0), inline (0.3.4), KFAS (0.4.9), LambertW (0.1.8), mi (0.08-06), micEcon (0.6-0), nparLD (1.2), partDSA (0.6.0), pomp (0.26-3), RcmdrPlugin.IPSUR (0.1-6), rgl (0.89), sdcTable (0.0.8), SpatialExtremes (1.5-0), TShistQuote (2009.12-1) 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * batch (1.0-0) Thomas Hoffmann http://crantastic.org/packages/batch Functions to allow you to easily pass command-line arguments into R (primary use is linux), and functions to aid in submitting your R code in parallel on a cluster and joining the results afterward (e.g. multiple parameter values for simulations running in parallel, splitting up a permutation test in parallel, etc.). See `parseCommandArgs(...)' for the main example of how to use this package. * bfast (1.1) Jan Verbesselt http://crantastic.org/packages/bfast BFAST integrates the decomposition of time series into trend, seasonal, and remainder components with methods for detecting and characterizing abrupt changes within the trend and seasonal components. BFAST can be used to analyze different types of satellite image time series and can be applied to other disciplines dealing with seasonal or non-seasonal time series, such as hydrology, climatology, and econometrics. The algorithm can be extended to label detected changes with information on the parameters of the fitted piecewise linear models. * bibtex (0.1-3) Romain Francois http://crantastic.org/packages/bibtex Utility to parse a bibtex file * BioStatR (1.0.0) Frederic Bertrand http://crantastic.org/packages/BioStatR This packages provides datasets for the book Exercices et problèmes de statistique avec le logiciel R. * boolfun (0.2.1) Frederic Lafitte http://crantastic.org/packages/boolfun This package can be used to assess cryptographic properties of Boolean functions (such as nonlinearity, algebraic immunity, resiliency, ...). * BoSSA (1.1) Pierre Lefeuvre http://crantastic.org/packages/BoSSA Sort sequence from genbank. Retrieve sequence information from genbank (designed for viruses sequences and retrieve information such as isolation dates and host). Detect group of sequences presenting phylogeography signal. Read PDB file (protein 3D structure file). * CCP (0.1) Uwe Menzel to http://crantastic.org/packages/CCP Significance tests for canonical correlation analysis, including asymptotic tests and a Monte Carlo method * cubature (1.0) Balasubramanian Narasimhan http://crantastic.org/packages/cubature Adaptive multivariate integration over hypercubes * doMPI (0.1-3) Steve Weston http://crantastic.org/packages/doMPI Provides a parallel backend for the %dopar% function using the Rmpi package. * GrassmannOptim (1.0) Kofi Placid Adragni http://crantastic.org/packages/GrassmannOptim Optimizing a function F(U), where U is a semi-orthogonal matrix and F is invariant under an orthogonal transformation of U * heavy (0.1-1) Felipe Osorio http://crantastic.org/packages/heavy Estimation in linear mixed effects models using heavy-tailed distributions * Imap (1.01) John R. Wallace http://crantastic.org/packages/Imap Zoom in and out of maps or any supplied lines or points, with control for color, poly fill, and aspect. * openintro (1.0) David Diez http://crantastic.org/packages/openintro This package is intended to be a supplement to the Open Intro open source book project. This package contains data sets used in the book along with functions used to make the book's figures. * r2dRue (1.0) Unknown http://crantastic.org/packages/r2dRue 2dRUE is a methodology to make a diagnostic of land condition in a large territory during a given time period. Was developed under the DeSurvey IP. * RcmdrPlugin.sos (0.1-0) Liviu Andronic http://crantastic.org/packages/RcmdrPlugin-sos Rcmdr interface to sos. The plug-in renders the sos searching functionality easily accessible via the Rcmdr menus. It also simplifies the task of performing multiple searches and subsequently obtaining the union or the intersection of the search results. * rngWELL (0.9) Christophe Dutang http://crantastic.org/packages/rngWELL It is a dedicated package to WELL pseudo random generators. But it is not intended to use it directly, you are strongly __encouraged__ to directly use the 'randtoolbox' package, which depends on this package. * SampleSizeMeans (1.0) Lawrence Joseph http://crantastic.org/packages/SampleSizeMeans A set of R functions for calculating sample size requirements using three different Bayesian criteria in the context of designing an experiment to estimate a normal mean or the difference between two normal means. Functions for calculation of required sample sizes for the Average Length Criterion, the Average Coverage Criterion and the Worst Outcome Criterion in the context of normal means are provided. Functions for both the fully Bayesian and the mixed Bayesian/likelihood approaches are provided. * SampleSizeProportions (1.0) Lawrence Joseph http://crantastic.org/packages/SampleSizeProportions A set of R functions for calculating
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages New reviews --- * deal, by newfuntek http://crantastic.org/reviews/45 * bnlearn, by newfuntek http://crantastic.org/reviews/44 * gRain, by newfuntek http://crantastic.org/reviews/43 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * Bergm (1.0) Alberto Caimo http://crantastic.org/packages/Bergm Functions implementing Bayesian estimation for exponential random graph models via exchange algorithm Updated packages lmtest (0.9-26), logcondens (1.3.5), MTSKNN (0.0-4), pmml (1.2.21), r2lUniv (0.9.4), rattle (2.5.11), rgdal (0.6-23), robustX (1.1-2), sandwich (2.2-4), sp (0.9-51) 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.
[R] CRAN (and crantastic) updates this week
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: 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.
[R] CRAN (and crantastic) updates this week
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),
[R] CRAN (and crantastic) updates this week
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: 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * EQL (1.0-0) Thorn Thaler http://crantastic.org/packages/EQL Computation of the EQL for a given family of variance functions, Saddlepoint-approximations and related auxiliary functions (e.g. Hermite polynomials) * flsa (1.03) Holger Hoefling http://crantastic.org/packages/flsa This package implements a path algorithm for the Fused Lasso Signal Approximator. For more details see the help files * glmperm (1.0-1) Wiebke Werft http://crantastic.org/packages/glmperm A permutation test is used for inference in generalized linear models (glm). The procedure is useful when parameter estimates in ordinary glm fail to converge or are unreliable due to small sample size. * HMR (0.1.0) Asger R. Pedersen http://crantastic.org/packages/HMR Statistical analysis of static chamber concentration data for trace gas flux estimation * inlinedocs (1.0) Toby Dylan Hocking http://crantastic.org/packages/inlinedocs Generates Rd files from R source code with comments, providing for quick, sustainable package development. The syntax keeps code and documentation close together, and is inspired by the Don't Repeat Yourself principle. * intamap (1.2-18) Edzer J. Pebesma http://crantastic.org/packages/intamap A package that provides classes and methods for automated spatial interpolation. * intamapInteractive (1.0-6) Edzer J. Pebesma http://crantastic.org/packages/intamapInteractive A package that provides classes and methods for automated spatial interpolation. * lda (1.1) Jonathan Chang http://crantastic.org/packages/lda This package implements latent Dirichlet allocation (LDA) and related models. This includes (but is not limited to) sLDA, corrLDA, and the mixed-membership stochastic blockmodel. Inference for all of these models is implemented via a fast collapsed Gibbs sampler writtten in C. Utility functions for reading/writing data typically used in topic models, as well as tools for examining posterior distributions are also included. * phull (0.2-1) Marek Gagolewski http://crantastic.org/packages/phull The package computes the p-hull of a finite planar set, which is a generalization of the convex hull, X-Y hull and bounding rectangle. A fast, O(n log n) Graham-scan based routine is used. * psgp (0.2-7) Jon Skoien http://crantastic.org/packages/psgp implements projected sparse Gaussian process kriging for the intamap package * QCA3 (0.0-1) HUANG Ronggui http://crantastic.org/packages/QCA3 A set of functions is for Qulitative Comparative Analysis (QCA). It can be used for all three types of QCA. * RC (1.0.1.27) Send complaints to http://crantastic.org/packages/RC The RC package allows the user to create and use reproducible computations for the purpose of research and education. The meta data about the computations are stored in a remote repository which is hosted at www.freestatistics.org * RelativeRisk (1.0-1) Bob Wheeler http://crantastic.org/packages/RelativeRisk Relative risk estimation for prospective and retrospective data. * ttutils (1.0-0) Thorn Thaler http://crantastic.org/packages/ttutils Contains some auxiliary functions. Updated packages AICcmodavg (1.02), AlgDesign (1.0-12), alr3 (1.1.12), arm (1.2-9.01), benchden (1.0.2), BMN (1.01), caret (4.23), caret (4.24), clustTool (1.6.4), coin (1.0-7), ctv (0.5-4), DEoptim (2.0-0), dplR (1.1.9.2), eba (1.5-5), Epi (1.1.7), epicalc (2.9.2.3), epicalc (2.9.2.5), ez (1.4.1), fArma (2100.76), fAsianOptions (2100.76), fAssets (2100.78), fBasics (2100.78), fBonds (2100.75), fCopulae (2100.77), fExoticOptions (2100.76), fExtremes (2100.77), fGarch (2100.79), fImport (2100.77), flsa (1.03), fMultivar (2100.76), fNonlinear (2100.76), fOptions (2100.76), fPortfolio (2100.78), fRegression (2100.76), fTrading (2100.76), fUnitRoots (2100.76), fUtilities (2100.77), Geneland (3.1.5), glmulti (0.5-2), haplo.stats (1.4.4), hash (1.0), hmm.discnp (0.1-0), KFAS (0.4.2), KFAS (0.4.3), KFAS (0.4.4), locpol (0.4-0), lpSolveAPI (5.5.0.15), MCMCglmm (1.12), meboot (1.0-1), mi (0.08-04.02), MLCM (0.0-5), MLDS (0.2-3), npmlreg (0.44), oce (0.1-78), optmatch (0.6-0), OrdFacReg (1.0.1), PearsonDS (0.91), peperr (1.1-4), plink (1.2-1), plm (1.2-1), psych (1.0-80), psyphy (0.1-3), qtl (1.14-2), quantmod (0.3-12), RcmdrPlugin.DoE (0.5-3), RInside (0.1.1), rmeta (2.16), robust (0.3-9), SensoMineR (1.10), sos (1.1-5), spatialsegregation (2.11), STAR (0.3-4), statmod (1.4.1), SuppDists (1.1-6), tikzDevice (0.4.8), tileHMM (1.0-3), timeDate (2100.86), timeSeries (2100.84), tlnise (1.1), ttrTests (1.2), urca (1.2-3), VR (7.2-49), WINRPACK (1.0-9) New reviews --- * distrEx, by cranktastic http://crantastic.org/reviews/34 This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know:
[R] CRAN (and crantastic) updates this week
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
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * ant (0.0-6) Romain Francois http://crantastic.org/packages/ant Version of the ant apache build tool, with a few R specific tasks to ease use of ant within an R package * caroline (0.1-1) David M. Schruth http://crantastic.org/packages/caroline * CircNNTSR (0.1) Maria Mercedes Gregorio-Dominguez http://crantastic.org/packages/CircNNTSR Functions for the analysis of circular data using distributions based on Nonnegative Trigonometric Sums (NNTS). Functions for calculation of densities and distributions, the estimation of parameters, plotting and more * expsmooth (2.00) Rob J Hyndman http://crantastic.org/packages/expsmooth Data sets from the book Forecasting with exponential smoothing: the state space approach by Hyndman, Koehler, Ord and Snyder (Springer, 2008). * farmR (1.0) Ira R. Cooke http://crantastic.org/packages/farmR A mixed integer description of an arable farm. Finds optimal farming plans given economic and social preference information. * fds (1.0) Han Lin Shang http://crantastic.org/packages/fds Functional data sets * fma (2.00) Rob J Hyndman http://crantastic.org/packages/fma All data sets from Forecasting: methods and applications by Makridakis, Wheelwright Hyndman (Wiley, 3rd ed., 1998). * forecast (2.00) Rob J Hyndman http://crantastic.org/packages/forecast Methods and tools for displaying and analysing univariate time series forecasts including exponential smoothing via state space models and automatic ARIMA modelling. * ftsa (1.0) Han Lin Shang http://crantastic.org/packages/ftsa Functions for functional time series * gamm4 (0.0-1) Simon Wood http://crantastic.org/packages/gamm4 Fit generalized additive mixed models via a version of mgcv's gamm function, using lme4 for estimation via Fabian Scheipl's trick. * Geneclust (1.0.0) Sophie Ancelet http://crantastic.org/packages/Geneclust Simulation and analysis of spatial structure of population genetics data * marelacTeaching (1.0) Karline Soetaert http://crantastic.org/packages/marelacTeaching Datasets and tutorials for use in the MArine, Riverine, Estuarine, LAcustrine and Coastal sciences * maticce (0.9-2) Andrew Hipp http://crantastic.org/packages/maticce Tools for an information-theoretic approach to estimating the probability of continuous character transitions on phylogenetic trees * Mcomp (2.00) Rob J Hyndman http://crantastic.org/packages/Mcomp The 1001 time series from the M-competition (Makridakis et al. 1982) and the 3003 time series from the IJF-M3 competition (Makridakis and Hibon, 2000). * MLCM (0.0-1) Ken Knoblauch http://crantastic.org/packages/MLCM Conjoint measurement is a psychophysical procedure in which stimulus pairs are presented that vary along n 2 dimensions and the observer is required to compare the stimuli along one of them. This package contains functions to estimate the contribution of the n scales to the judgment by a maximum likelihood method under several hypotheses of how the perceptual dimensions interact. * rms (2.0-2) Frank E Harrell Jr http://crantastic.org/packages/rms Regression modeling, testing, estimation, validation, graphics, prediction, and typesetting by storing enhanced model design attributes in the fit. rms is a collection of about 180 functions that assist and streamline modeling, especially for biostatistical and epidemiologic applications. It also contains new functions for binary and ordinal logistic regression models and the Buckley-James multiple regression model for right-censored responses, and implements penalized maximum likelihood estimation for logistic and ordinary linear models. rms works with almost any regression model, but it was especially written to work with binary or ordinal logistic regression, Cox regression, accelerated failure time models, ordinary linear models, the Buckley-James model, generalized least squares for serially or spatially correlated observations, generalized linear models, and quantile regression. * RPMM (1.0) E. Andres Houseman http://crantastic.org/packages/RPMM Recursively Partitioned Mixture Model for Beta and Gaussian Mixtures. This is a model-based clustering algorithm that returns a hierarchy of classes, similar to hierarchical clustering, but also similar to finite mixture models. * sos (1.1-3) Spencer Graves http://crantastic.org/packages/sos R related Search Engines * tikzDevice (0.4.7) The tikzDevice team: http://crantastic.org/packages/tikzDevice The TikZ device enables LaTeX-ready output from R graphics functions. This is done by producing code that can be understood by the TikZ graphics language. All text in a graphic output with the tikz() function will can be typeset by LaTeX and therefore will match whatever fonts are currently
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * AICcmodavg (1.01) Marc J. Mazerolle http://crantastic.org/packages/AICcmodavg This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). Tables are printed with delta AIC and Akaike weights. The package also includes functions to conduct model averaging (multimodel inference) for a given parameter of interest or predicted values. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with lm, glm, and lme object classes. * amer (0.5) Fabian Scheipl http://crantastic.org/packages/amer Fitting generalized additive mixed models based on the mixed model algorithm of lme4 * frbf (0.9) Fernando Martins http://crantastic.org/packages/frbf Flexible kernerl for radial basis function network implementation. * GGMselect (0.1-0) Annie Bouvier http://crantastic.org/packages/GGMselect GGMselect is a package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix. * lemma (1.2-1) Haim Bar http://crantastic.org/packages/lemma LEMMA is used to detect nonnull genes - genes for which the average response in treatment group 1 is significantly different from the average response in group 2, in normalized microarray data. LEMMA is an implementation of an approximate EM algorithm to estimate the parameters in the assumed linear model in Bar, Booth, Schifano, Wells (2009). Updated packages AICcmodavg (1.01), betareg (2.0-0), BioIDMapper (1.2), boolean (2.0-1), boolean (2.0-0), boot (1.2-39), cem (1.0.111), clue (0.3-30), DAKS (2.0-0), dcemri (0.10.5), dplR (1.1.9.1), drc (1.7-7), epicalc (2.9.2.0), etm (0.4-6), exams (1.0-2), feature (1.2.4), GenABEL (1.4-4), gnumeric (0.5-2), gputools (0.1-3), hash (0.40), Hmisc (3.7-0), Iso (0.0-7), ISOcodes (0.2-5), KernSmooth (2.23-3), longitudinalData (0.6), mapReduce (1.02), MCMCglmm (1.11), meta (1.0-6), mhsmm (0.3.0), multmod (0.5), nleqslv (1.5), nlme (3.1-94), OAIHarvester (0.0-5), orientlib (0.9.3), phmm (0.6), R.matlab (1.2.5), rainbow (1.4), Rcplex (0.2-3), relations (0.5-4), rgdal (0.6-17), Rmpfr (0.1-6), RWeka (0.3-21), sdef (1.2), SigWinR (1.0.1), simecol (0.6-9), simFrame (0.1.1), skmeans (0.1-1), Snowball (0.0-7), spgrass6 (0.6-8), spgrass6 (0.6-9), SubpathwayMiner (2.0), tau (0.0-3), tau (0.0-2), TeachingSampling (1.0.2), tsDyn (0.7-1), tseries (0.10-19), ttrTests (1.1), YourCast (1.1-2) New reviews --- * wavethresh, by cranktastic http://crantastic.org/reviews/27 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages New reviews --- 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.
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages New reviews --- 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.
Re: [R] CRAN (and crantastic) updates this week
Sorry, we had some problems with the initial sending of our weekly digest which resulted in a rather empty email. Here is the correct version: CRAN (and crantastic) updates this week New packages * atm (0.1.0) Charlotte Maia http://crantastic.org/packages/atm An R package for creating additive models with semiparametric predictors, emphasizing term objects, especially (1) implementation of a term class hierarchy, and (2) interpretation and evaluation of term estimates as functions of explanatories. * gnumeric (0.5-1) Karoly Antal http://crantastic.org/packages/gnumeric Read data files readable into R. Can read whole sheet or a range, from several file formats, including the native format of gnumeric. Reading is done by using ssconvert (a file converter utility included in the gnumeric distribution) to convert the requested part to CSV. * KFAS (0.3.1) Jouni Lehtonen http://crantastic.org/packages/KFAS Fast multivariate Kalman filter, smoother, simulation smoother and forecasting. Uses exact diffuse initialisation when distributions of some or all elements of initial state vector are unknown. * munsell (0.1) Charlotte Wickham http://crantastic.org/packages/munsell Functions for exploring and using the Munsell colour system * oosp (0.1.0) Charlotte Maia http://crantastic.org/packages/oosp An R package designed to support object oriented statistical programming, especially by extending S3 capabilities, providing pointer and component objects, and providing basic support for symbolic-numeric statistical programming. * PLIS (1.0) Zhi Wei http://crantastic.org/packages/PLIS PLIS is a multiple testing procedure for testing several groups of hypotheses. Linear dependency is expected from the hypotheses within the same group and is modeled by hidden Markov Models. It is noted that, for PLIS, a smaller p value does not necessarily imply more significance because of dependency among the hypotheses. A typical applicaiton of PLIS is to analyze genome wide association studies datasets, where SNPs from the same chromosome are treated as a group and exhibit strong linear genomic dependency. * rrv (0.0.1) Charlotte Maia http://crantastic.org/packages/rrv An incomplete R package for working with random return variables. The current package provides limited support for formatting money. More features will be added in the future. * ttrTests (1.0) David St John http://crantastic.org/packages/ttrTests Four core functions evaluate the efficacy of a technical trading rule. - Conditional return statistics - Bootstrap resampling statistics - Reality Check for data snooping bias among parameter choices - Robustness, or Persistence, of parameter choices Updated packages AdMit (1-01.03), alr3 (1.1.9), alr3 (1.1.10), cmprskContin (1.1), dataframes2xls (0.4.3), digeR (1.2), doBy (4.0.1), DoE.base (0.7), FrF2 (0.97-1), FrF2 (0.97-3), hdrcde (2.10), HH (2.1-30), JM (0.4-0), memisc (0.95-21), minet (2.0.0), MLDS (0.2-0), monomvn (1.7-3), mrt (0.3), nsRFA (0.6-9), PBSmodelling (2.21), plink (1.2-0), plotrix (2.7), RaschSampler (0.8-2), RCurl (1.0-0), rgdal (0.6-14), RSiena (1.0.5), rtv (0.3.0), sdef (1.1), SIS (0.2), spdep (0.4-36) New reviews --- * sqldf, by m.e.driscoll http://crantastic.org/reviews/26 * SensoMineR, by padmanabhan.vijayan http://crantastic.org/reviews/25 * plyr, by eamani http://crantastic.org/reviews/24 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. On Mon, Aug 24, 2009 at 4:18 PM, Hadley Wickham crana...@gmail.com wrote: CRAN (and crantastic) updates this week New packages Updated packages New reviews --- 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. [[alternative HTML version deleted]] __ 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.
Re: [R] CRAN (and crantastic) updates this week
I like it. Thanks. 2009/8/24 hadley wickham crana...@gmail.com: Sorry, we had some problems with the initial sending of our weekly digest which resulted in a rather empty email. Here is the correct version: CRAN (and crantastic) updates this week New packages * atm (0.1.0) Charlotte Maia http://crantastic.org/packages/atm An R package for creating additive models with semiparametric predictors, emphasizing term objects, especially (1) implementation of a term class hierarchy, and (2) interpretation and evaluation of term estimates as functions of explanatories. * gnumeric (0.5-1) Karoly Antal http://crantastic.org/packages/gnumeric Read data files readable into R. Can read whole sheet or a range, from several file formats, including the native format of gnumeric. Reading is done by using ssconvert (a file converter utility included in the gnumeric distribution) to convert the requested part to CSV. * KFAS (0.3.1) Jouni Lehtonen http://crantastic.org/packages/KFAS Fast multivariate Kalman filter, smoother, simulation smoother and forecasting. Uses exact diffuse initialisation when distributions of some or all elements of initial state vector are unknown. * munsell (0.1) Charlotte Wickham http://crantastic.org/packages/munsell Functions for exploring and using the Munsell colour system * oosp (0.1.0) Charlotte Maia http://crantastic.org/packages/oosp An R package designed to support object oriented statistical programming, especially by extending S3 capabilities, providing pointer and component objects, and providing basic support for symbolic-numeric statistical programming. * PLIS (1.0) Zhi Wei http://crantastic.org/packages/PLIS PLIS is a multiple testing procedure for testing several groups of hypotheses. Linear dependency is expected from the hypotheses within the same group and is modeled by hidden Markov Models. It is noted that, for PLIS, a smaller p value does not necessarily imply more significance because of dependency among the hypotheses. A typical applicaiton of PLIS is to analyze genome wide association studies datasets, where SNPs from the same chromosome are treated as a group and exhibit strong linear genomic dependency. * rrv (0.0.1) Charlotte Maia http://crantastic.org/packages/rrv An incomplete R package for working with random return variables. The current package provides limited support for formatting money. More features will be added in the future. * ttrTests (1.0) David St John http://crantastic.org/packages/ttrTests Four core functions evaluate the efficacy of a technical trading rule. - Conditional return statistics - Bootstrap resampling statistics - Reality Check for data snooping bias among parameter choices - Robustness, or Persistence, of parameter choices Updated packages AdMit (1-01.03), alr3 (1.1.9), alr3 (1.1.10), cmprskContin (1.1), dataframes2xls (0.4.3), digeR (1.2), doBy (4.0.1), DoE.base (0.7), FrF2 (0.97-1), FrF2 (0.97-3), hdrcde (2.10), HH (2.1-30), JM (0.4-0), memisc (0.95-21), minet (2.0.0), MLDS (0.2-0), monomvn (1.7-3), mrt (0.3), nsRFA (0.6-9), PBSmodelling (2.21), plink (1.2-0), plotrix (2.7), RaschSampler (0.8-2), RCurl (1.0-0), rgdal (0.6-14), RSiena (1.0.5), rtv (0.3.0), sdef (1.1), SIS (0.2), spdep (0.4-36) New reviews --- * sqldf, by m.e.driscoll http://crantastic.org/reviews/26 * SensoMineR, by padmanabhan.vijayan http://crantastic.org/reviews/25 * plyr, by eamani http://crantastic.org/reviews/24 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. On Mon, Aug 24, 2009 at 4:18 PM, Hadley Wickham crana...@gmail.com wrote: CRAN (and crantastic) updates this week New packages Updated packages New reviews --- 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. [[alternative HTML version deleted]] __ 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. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ 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.
Re: [R] CRAN (and crantastic) updates this week
Great idea - thx! On Mon, Aug 24, 2009 at 9:30 AM, hadley wickham crana...@gmail.com wrote: Sorry, we had some problems with the initial sending of our weekly digest which resulted in a rather empty email. Here is the correct version: CRAN (and crantastic) updates this week New packages * atm (0.1.0) Charlotte Maia http://crantastic.org/packages/atm An R package for creating additive models with semiparametric predictors, emphasizing term objects, especially (1) implementation of a term class hierarchy, and (2) interpretation and evaluation of term estimates as functions of explanatories. * gnumeric (0.5-1) Karoly Antal http://crantastic.org/packages/gnumeric Read data files readable into R. Can read whole sheet or a range, from several file formats, including the native format of gnumeric. Reading is done by using ssconvert (a file converter utility included in the gnumeric distribution) to convert the requested part to CSV. * KFAS (0.3.1) Jouni Lehtonen http://crantastic.org/packages/KFAS Fast multivariate Kalman filter, smoother, simulation smoother and forecasting. Uses exact diffuse initialisation when distributions of some or all elements of initial state vector are unknown. * munsell (0.1) Charlotte Wickham http://crantastic.org/packages/munsell Functions for exploring and using the Munsell colour system * oosp (0.1.0) Charlotte Maia http://crantastic.org/packages/oosp An R package designed to support object oriented statistical programming, especially by extending S3 capabilities, providing pointer and component objects, and providing basic support for symbolic-numeric statistical programming. * PLIS (1.0) Zhi Wei http://crantastic.org/packages/PLIS PLIS is a multiple testing procedure for testing several groups of hypotheses. Linear dependency is expected from the hypotheses within the same group and is modeled by hidden Markov Models. It is noted that, for PLIS, a smaller p value does not necessarily imply more significance because of dependency among the hypotheses. A typical applicaiton of PLIS is to analyze genome wide association studies datasets, where SNPs from the same chromosome are treated as a group and exhibit strong linear genomic dependency. * rrv (0.0.1) Charlotte Maia http://crantastic.org/packages/rrv An incomplete R package for working with random return variables. The current package provides limited support for formatting money. More features will be added in the future. * ttrTests (1.0) David St John http://crantastic.org/packages/ttrTests Four core functions evaluate the efficacy of a technical trading rule. - Conditional return statistics - Bootstrap resampling statistics - Reality Check for data snooping bias among parameter choices - Robustness, or Persistence, of parameter choices Updated packages AdMit (1-01.03), alr3 (1.1.9), alr3 (1.1.10), cmprskContin (1.1), dataframes2xls (0.4.3), digeR (1.2), doBy (4.0.1), DoE.base (0.7), FrF2 (0.97-1), FrF2 (0.97-3), hdrcde (2.10), HH (2.1-30), JM (0.4-0), memisc (0.95-21), minet (2.0.0), MLDS (0.2-0), monomvn (1.7-3), mrt (0.3), nsRFA (0.6-9), PBSmodelling (2.21), plink (1.2-0), plotrix (2.7), RaschSampler (0.8-2), RCurl (1.0-0), rgdal (0.6-14), RSiena (1.0.5), rtv (0.3.0), sdef (1.1), SIS (0.2), spdep (0.4-36) New reviews --- * sqldf, by m.e.driscoll http://crantastic.org/reviews/26 * SensoMineR, by padmanabhan.vijayan http://crantastic.org/reviews/25 * plyr, by eamani http://crantastic.org/reviews/24 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. On Mon, Aug 24, 2009 at 4:18 PM, Hadley Wickham crana...@gmail.com wrote: CRAN (and crantastic) updates this week New packages Updated packages New reviews --- 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. [[alternative HTML version deleted]] __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ 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.
