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),"A deterministic algorithm for robust location and scatter", 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 'one-Factor with Durante Generators', 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 networks (i.e. not on CRAN). This might be necessary where hosted packages contain intellectual property owned by a corporation. * matR (0.9) Maintainer: Daniel Braithwaite Author(s): Daniel Braithwaite [aut, cre], Kevin Keegan [aut], University of Chicago [cph] License: BSD_2_clause + file LICENSE http://crantastic.org/packages/matR An analysis platform for metagenomics combining specialized tools and workflows, easy handling of the BIOM format, and transparent access to MG-RAST resources. matR integrates easily with other R packages and non-R software. * openssl (0.1) Maintainer: Jeroen Ooms Author(s): Jeroen Ooms License: MIT + file LICENSE http://crantastic.org/packages/openssl This package interfaces to the OpenSSL libraries libssl and libcrypto. Currently it only implements bindings to the OpenSSL random number generator in order to generate crypto secure random bytes in R. * ore (1.0.1) Maintainer: Jon Clayden Author(s): Jon Clayden, based on Onigmo by K. Kosako and K. Takata License: BSD_3_clause + file LICENCE http://crantastic.org/packages/ore Provides an alternative to R's built-in functionality for handling regular expressions, based on the Oniguruma library. It offers first-class compiled regex objects, partial matching and function-based substitutions, amongst other features. * P2C2M (0.5) Maintainer: Michael Gruenstaeudl Author(s): Michael Gruenstaeudl, Noah Reid License: GPL (>= 2) http://crantastic.org/packages/P2C2M P2C2M is an R package to conduct posterior predictive checks of coalescent models using gene and species trees generated by BEAST and *BEAST, respectively. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites only: genealogicalSorting (http://www.genealogicalsorting.org) and phybase (http://odyssey.bioinformatics.uga.edu/~lliu/phybase/). To use these optional packages, installation of the Python libraries NumPy (>= 1.9.0) and DendroPy (= 3.12.0) is necessary. * PANICr (0.0.0.2) Maintainer: Steve Bronder Author(s): Steve Bronder <sbron...@stevebronder.com> License: GPL-3 http://crantastic.org/packages/PANICr This package contains a methodology that makes use of the factor structure of large dimensional panels to understand the nature of nonstationarity inherent in data. This is referred to as PANIC - Panel Analysis of Nonstationarity in Idiosyncratic and Common Components. PANIC (2004) includes valid pooling methods that allow panel tests to be constructed. PANIC (2004) can detect whether the nonstationarity in a series is pervasive, or variable specific, or both. PANIC (2010) includes two new tests on the idiosyncratic component that estimates the pooled autoregressive coefficient and sample moment, respectively. The PANIC model approximates the number of factors based on Bai and Ng (2002) * PHENIX (1.0) Maintainer: A. J. Muñoz-Pajares Author(s): R. Torices, A. J. Muñoz-Pajares License: GPL (>= 2) http://crantastic.org/packages/PHENIX Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might overestimate the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) and a bootstrapping method to test the significance of both integration indices. * rsml (1.0) Maintainer: Guillaume Lobet Author(s): Guillaume Lobet License: GPL-2 http://crantastic.org/packages/rsml Read and analyse Root System Markup Language (RSML) files. * rtkpp (0.8.3) Maintainer: Serge Iovleff Author(s): Serge Iovleff [aut, cre], Vincent Kubicki [ctb], Quentin Grimonprez [ctb], Parmeet Bhatia [ctb] License: GPL (>= 2) | LGPL (>= 2) | file LICENSE http://crantastic.org/packages/rtkpp STK++ (http://www.stkpp.org) is a collection of C++ classes for statistics, clustering, linear algebra, arrays (with an Eigen-like API), regression, dimension reduction, etc. The integration of the library to R is using Rcpp. Some functionalities of the Clustering project provided by the library are available in the R environment as R functions. . The rtkpp package includes the header files from the STK++ library (currently version 0.8.2). Thus users do not need to install STK++ itself in order to use it. . STK++ is licensed under the GNU LGPL version 2 or later. rtkpp (the stkpp integration into R) is licensed under the GNU GPL version 2 or later. * ruv (0.9.4) Maintainer: Johann Gagnon-Bartsch Author(s): Johann Gagnon-Bartsch <joh...@stat.berkeley.edu> License: GPL http://crantastic.org/packages/ruv The algorithms in this package attempt to adjust for systematic errors of unknown origin in high-dimensional data. The algorithms were originally developed for use with genomic data, especially microarray data, but may be useful with other types of high-dimensional data as well. The algorithms included in this package are RUV-2, RUV-4, RUV-inv, and RUV-rinv, along with various supporting algorithms. These algorithms were proposed by Gagnon-Bartsch and Speed (2012), and by Gagnon-Bartsch, Jacob and Speed (2013). The algorithms require the user to specifiy a set of negative control variables, as described in the references. * saeSim (0.6.0) Maintainer: Sebastian Warnholz Author(s): Sebastian Warnholz <sebastian.warnh...@fu-berlin.de> License: GPL-3 | file LICENSE http://crantastic.org/packages/saeSim Tools for the simulation of data in the context of small area estimation. Combine all steps of your simulation - from data generation over drawing samples to model fitting - in one object. This enables easy modification and combination of different scenarios. You can store your results in a folder or start the simulation in parallel. * scrm (1.3-2) Maintainer: Paul Staab Author(s): Paul Staab [aut, cre, cph], Zhu Sha [aut, cph], Dirk Metzler [ths], Gerton Lunter [aut, cph, ths] License: GPL (>= 3) http://crantastic.org/packages/scrm A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution. * sigloc (0.0.4) Maintainer: Sergey S. Berg Author(s): Sergey S. Berg License: GPL (>= 2) http://crantastic.org/packages/sigloc A collection of tools for estimating the location of a transmitter signal from radio telemetry studies using the maximum likelihood estimation (MLE) approach described in Lenth (1981). * TDboost (1.0) Maintainer: Yi Yang Author(s): Yi Yang <yiy...@umn.edu>, Wei Qian <weiq...@stat.umn.edu>, Hui Zou <h...@stat.umn.edu> License: GPL-3 http://crantastic.org/packages/TDboost A fully nonparametric Tweedie model using the gradient boosting. It is capable of fitting a flexible nonlinear model and capturing interactions among predictors. * traj (1.0) Maintainer: Dan Vatnik Author(s): Marie-Pierre Sylvestre, Dan Vatnik License: GPL-2 http://crantastic.org/packages/traj Implements the three step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters. Updated packages ---------------- AutoSEARCH (1.3), BayesFactor (0.9.9), bio3d (2.1-2), CAMAN (0.72), confidence (1.1-0), DBKGrad (1.6), equate (2.0-3), extracat (1.7-1), FSelector (0.20), GGIR (1.1-3), HiDimDA (0.2-2), highr (0.4), httpuv (1.3.2), imputeYn (1.2), jackknifeKME (1.1), JADE (1.9-92), JMdesign (1.1), logconPH (1.2), logconPH (1.1), MAINT.Data (0.3), MESS (0.3-2), MPTinR (1.6.3), MRH (1.1), nhlscrapr (1.8), npmlreg (0.46-1), ore (1.0.1), pcaPP (1.9-60), PKfit (1.2.4), polyCub (0.5-1), prevalence (0.3.0), rasterVis (0.32), redcapAPI (1.0.1), restlos (0.1-3), rex (0.1.1), RnavGraph (0.1.7), Rook (1.1-1), rpf (0.40), RSQLite (1.0.0), rtkpp (0.8.3), SamplingStrata (1.0-3), scrm (1.3-2), sgof (2.1.1), sparr (0.3-6), spatstat (1.39-1), spatstat (1.39-0), speedglm (0.2-1.0), STARSEQ (1.2.1), stepp (3.0-11), synbreed (0.10-3), tclust (1.2-3), timeordered (0.9.7), TwoStepCLogit (1.2.3), VIM (4.1.0), WRS2 (0.2-0) 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.
