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‎ChangeLog‎

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2014-05-31: Ver. 0.1-7
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2014-06-21: Ver. 0.1-7
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* Migrate to MS-MPI.
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* Get rid of jss.cls and jss.bst.
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2014-02-02: Ver. 0.1-6
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* Add I/O demo to read data and dump clustering results.

‎DESCRIPTION‎

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Package: pmclust
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Version: 0.1-7
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Date: 2014-05-31
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Date: 2014-05-24
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Title: Parallel Model-Based Clustering
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Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
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"[email protected]"), person("George", "Ostrouchov", role = "aut"))
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Depends: R (>= 3.0.0), methods, rlecuyer, pbdMPI (>= 0.2-4), MASS
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Depends: R (>= 3.0.0), methods, rlecuyer, pbdMPI (>= 0.2-3), MASS
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Enhances: MixSim, pbdSLAP (>= 0.1-9), pbdBASE (>= 0.3-0), pbdDMAT (>=
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0.3-0)
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LazyLoad: yes
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BugReports: http://group.r-pbd.org/
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MailingList: Please send questions and comments regarding pbdR to
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[email protected]
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Packaged: 2014-05-24 20:19:44 UTC; snoweye
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Packaged: 2014-06-21 18:25:53 UTC; snoweye
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Author: Wei-Chen Chen [aut, cre],
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George Ostrouchov [aut]
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Maintainer: Wei-Chen Chen <[email protected]>

‎inst/doc/pmclust-guide.Rnw‎

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%\VignetteIndexEntry{pmclust-guide}
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\documentclass[article,shortnames,nojss]{pmclust-include/jss}
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\documentclass[article,shortnames,nojss]{jss}
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\newcommand{\pmclustversion}{0.1-7}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% declarations for jss.cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\author{
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\begin{minipage}{6in}
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\centering
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Wei-Chen Chen$^1$ and George Ostrouchov$^{1,2}$
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Wei-Chen Chen$^1$ and George Ostrouchov$^{2,3}$
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\end{minipage}
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\\
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\\
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$^1$Department of Ecology and Evolutionary Biology, \\
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University of Tennessee, \\
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Knoxville, TN, USA \\
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\\
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$^2$Remote Data Analysis and Visualization Center,\\
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$^2$National Institute for Computational Sciences, \\
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University of Tennessee, \\
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Knoxville, TN, USA \\
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\\
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$^3$Computer Science and Mathematics Division, \\
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Oak Ridge National Laboratory, \\
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Oak Ridge, TN, USA
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}
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%\\ \today}
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\title{A Quick Guide for the \pkg{pmclust} Package}
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\title{A Quick Guide for the \pkg{pmclust} Package {\small (Ver. \pmclustversion)}}
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%\\
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%\vspace{0.2cm} \large (Based on Version 0.1-2)}
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%% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\input{./pmclust-include/my_jss.cls}
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\input{./pmclust-include/00-preamble}
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\begin{document}

‎inst/doc/pmclust-guide.pdf‎

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‎vignettes/build_pdf.sh‎

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#!/bin/sh
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rm *.aux *.bbl *.blg *.log *.out *.toc
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R_HOME=`Rscript -e 'cat(R.home()[1])'`
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JSS_BST=${R_HOME}/share/texmf/bibtex/bst/jss.bst
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JSS_CLS=${R_HOME}/share/texmf/tex/latex/jss.cls
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rm *.aux *.bbl *.blg *.log *.out *.toc *.bst *.cls
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cp ${JSS_BST} ./
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cp ${JSS_CLS} ./
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pdflatex pmclust-guide.Rnw
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bibtex pmclust-guide
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pdflatex pmclust-guide.Rnw
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pdflatex pmclust-guide.Rnw
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pdflatex pmclust-guide.Rnw
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rm *.aux *.bbl *.blg *.log *.out *.toc
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rm *.aux *.bbl *.blg *.log *.out *.toc *.bst *.cls
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mv -f *.pdf ../inst/doc/
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cp -f *.Rnw ../inst/doc/

‎vignettes/pmclust-guide.Rnw‎

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%\VignetteIndexEntry{pmclust-guide}
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\documentclass[article,shortnames,nojss]{pmclust-include/jss}
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\documentclass[article,shortnames,nojss]{jss}
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\newcommand{\pmclustversion}{0.1-7}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% declarations for jss.cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\author{
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\begin{minipage}{6in}
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\centering
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Wei-Chen Chen$^1$ and George Ostrouchov$^{1,2}$
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Wei-Chen Chen$^1$ and George Ostrouchov$^{2,3}$
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\end{minipage}
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\\
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\\
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$^1$Department of Ecology and Evolutionary Biology, \\
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University of Tennessee, \\
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Knoxville, TN, USA \\
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\\
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$^2$Remote Data Analysis and Visualization Center,\\
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$^2$National Institute for Computational Sciences, \\
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University of Tennessee, \\
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Knoxville, TN, USA \\
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\\
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$^3$Computer Science and Mathematics Division, \\
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Oak Ridge National Laboratory, \\
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Oak Ridge, TN, USA
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}
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%\\ \today}
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\title{A Quick Guide for the \pkg{pmclust} Package}
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\title{A Quick Guide for the \pkg{pmclust} Package {\small (Ver. \pmclustversion)}}
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%\\
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%\vspace{0.2cm} \large (Based on Version 0.1-2)}
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%% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\input{./pmclust-include/my_jss.cls}
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\input{./pmclust-include/00-preamble}
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\begin{document}

‎vignettes/pmclust-include/01-acknowledgement.tex‎

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\section*{Acknowledgement}
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\addcontentsline{toc}{section}{Acknowledgement \vspace{-0.3cm}}
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Chen was supported in part by
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the Department of Ecology and Evolutionary Biology at the
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University of Tennessee, Knoxville, and a grant from
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the National Science Foundation (MCB-1120370.)
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\\
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Chen and Ostrouchov were supported in part by the project
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``Visual Data Exploration and Analysis of Ultra-large Climate Data''
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funded by U.S. DOE Office of Science

‎vignettes/pmclust-include/01-introduction.tex‎

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{\color{red} \bf Warning:} This document is written to explain the major
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functions of
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\pkg{pmclust}~\citep{Chen2012pmclustpackage}, version 0.1-5.
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\pkg{pmclust}~\citep{Chen2012pmclustpackage}, version 0.1-7.
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Every effort will be made to insure future versions are consistent with
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these instructions, but new features in later versions may not be explained
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in this document.

‎vignettes/pmclust-include/02-example.tex‎

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\begin{Command}
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mpiexec -np 4 Rscript -e "demo(ex_MixSim,'pmclust',ask=F,echo=F)"
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\end{Command}
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More performance comparison can be found in~\citet{Chen2013}.
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More performance comparison can be found in~\citet{Chen2012a}.
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Further, \code{X.spmd} may be replaced by \code{X.dmat} in a \code{ddmatrix}
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format (block-cyclic) for larger datasets and gaining performance

‎vignettes/pmclust-include/03-algorithm.tex‎

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Five algorithms are implemented in this packages including:
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EM~\citep{Dempster1977}, AECM~\citep{Meng1997}, APECM~\citep{Chen2011},
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APECMa~\citep{Chen2013}, and K-means~\citep{Lloyd1982}.
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APECMa~\citep{Chen2012a}, and K-means~\citep{Lloyd1982}.
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The EM-like algorithms (EM, AECM, APECM, and APECMa) are for model-based
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clusterings~\citep{Fraley2002},
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while K-means is a distance based clustering algorithm.

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