Skip to content

Commit 3b1db00

Browse files
snoweyesnoweye
committed
Merge pull request #8 from snoweye/master
Add dependent back
2 parents 7e84f92 + 3e46fc9 commit 3b1db00

File tree

10 files changed

+98
-18
lines changed

10 files changed

+98
-18
lines changed

‎ChangeLog‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,7 @@
1-
2014-05-24: Ver. 0.1-7
1+
2014-06-21: Ver. 0.1-7
22
* Migrate to MS-MPI.
3+
* Get rid of jss.cls and jss.bst.
4+
* Add pbdSLAP, pbdBASE, pbdDMAT back to dependent and import.
35

46
2014-02-02: Ver. 0.1-6
57
* Add I/O demo to read data and dump clustering results.

‎DESCRIPTION‎

Lines changed: 5 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,10 @@ Date: 2014-05-24
44
Title: Parallel Model-Based Clustering
55
Authors@R: c(person("Wei-Chen", "Chen", role = c("aut", "cre"), email =
66
"[email protected]"), person("George", "Ostrouchov", role = "aut"))
7-
Depends: R (>= 3.0.0), methods, rlecuyer, pbdMPI (>= 0.2-3), MASS
8-
Enhances: MixSim, pbdSLAP, pbdBASE, pbdDMAT
7+
Depends: R (>= 3.0.0), methods, rlecuyer, pbdMPI (>= 0.2-3), MASS,
8+
pbdSLAP (>= 0.1-9), SEXPtools (>= 0.1-0), pbdBASE (>= 0.3-0),
9+
pbdDMAT (>= 0.3-0)
10+
Enhances: MixSim
911
LazyLoad: yes
1012
LazyData: yes
1113
Description: The pmclust aims to utilize model-based clustering (unsupervised)
@@ -24,7 +26,7 @@ URL: http://r-pbd.org/
2426
BugReports: http://group.r-pbd.org/
2527
MailingList: Please send questions and comments regarding pbdR to
2628
[email protected]
27-
Packaged: 2014-02-02 22:05:31 UTC; snoweye
29+
Packaged: 2014-06-21 19:26:18 UTC; snoweye
2830
Author: Wei-Chen Chen [aut, cre],
2931
George Ostrouchov [aut]
3032
Maintainer: Wei-Chen Chen <[email protected]>

‎NAMESPACE‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
useDynLib(pmclust)
22

3-
import(methods, rlecuyer, pbdMPI, MASS)
3+
import(methods, rlecuyer, pbdMPI, MASS, pbdSLAP, SEXPtools, pbdBASE, pbdDMAT)
44

55
# exportPattern("^[[:alpha:]]+")
66
# exportPattern("^[\\.]")

‎inst/doc/pmclust-guide.Rnw‎

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
11
%\VignetteIndexEntry{pmclust-guide}
22

3-
\documentclass[article,shortnames,nojss]{pmclust-include/jss}
3+
\documentclass[article,shortnames,nojss]{jss}
4+
5+
\newcommand{\pmclustversion}{0.1-7}
46

57
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
68
%% declarations for jss.cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -10,20 +12,24 @@
1012
\author{
1113
\begin{minipage}{6in}
1214
\centering
13-
Wei-Chen Chen$^1$ and George Ostrouchov$^{1,2}$
15+
Wei-Chen Chen$^1$ and George Ostrouchov$^{2,3}$
1416
\end{minipage}
1517
\\
1618
\\
1719
$^1$Department of Ecology and Evolutionary Biology, \\
1820
University of Tennessee, \\
1921
Knoxville, TN, USA \\
2022
\\
21-
$^2$Remote Data Analysis and Visualization Center,\\
23+
$^2$National Institute for Computational Sciences, \\
2224
University of Tennessee, \\
2325
Knoxville, TN, USA \\
26+
\\
27+
$^3$Computer Science and Mathematics Division, \\
28+
Oak Ridge National Laboratory, \\
29+
Oak Ridge, TN, USA
2430
}
2531
%\\ \today}
26-
\title{A Quick Guide for the \pkg{pmclust} Package}
32+
\title{A Quick Guide for the \pkg{pmclust} Package {\small (Ver. \pmclustversion)}}
2733
%\\
2834
%\vspace{0.2cm} \large (Based on Version 0.1-2)}
2935

@@ -65,7 +71,7 @@ Knoxville, TN, USA \\
6571

6672
%% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
6773

68-
74+
\input{./pmclust-include/my_jss.cls}
6975
\input{./pmclust-include/00-preamble}
7076

7177
\begin{document}

‎inst/doc/pmclust-guide.pdf‎

-12.2 KB
Binary file not shown.

‎vignettes/build_pdf.sh‎

Lines changed: 9 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,19 @@
11
#!/bin/sh
22

3-
rm *.aux *.bbl *.blg *.log *.out *.toc
3+
R_HOME=`Rscript -e 'cat(R.home()[1])'`
4+
JSS_BST=${R_HOME}/share/texmf/bibtex/bst/jss.bst
5+
JSS_CLS=${R_HOME}/share/texmf/tex/latex/jss.cls
6+
7+
rm *.aux *.bbl *.blg *.log *.out *.toc *.bst *.cls
8+
cp ${JSS_BST} ./
9+
cp ${JSS_CLS} ./
10+
411
pdflatex pmclust-guide.Rnw
512
bibtex pmclust-guide
613
pdflatex pmclust-guide.Rnw
714
pdflatex pmclust-guide.Rnw
815
pdflatex pmclust-guide.Rnw
9-
rm *.aux *.bbl *.blg *.log *.out *.toc
1016

17+
rm *.aux *.bbl *.blg *.log *.out *.toc *.bst *.cls
1118
mv -f *.pdf ../inst/doc/
1219
cp -f *.Rnw ../inst/doc/

‎vignettes/pmclust-guide.Rnw‎

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,8 @@
11
%\VignetteIndexEntry{pmclust-guide}
22

3-
\documentclass[article,shortnames,nojss]{pmclust-include/jss}
3+
\documentclass[article,shortnames,nojss]{jss}
4+
5+
\newcommand{\pmclustversion}{0.1-7}
46

57
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
68
%% declarations for jss.cls %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -10,20 +12,24 @@
1012
\author{
1113
\begin{minipage}{6in}
1214
\centering
13-
Wei-Chen Chen$^1$ and George Ostrouchov$^{1,2}$
15+
Wei-Chen Chen$^1$ and George Ostrouchov$^{2,3}$
1416
\end{minipage}
1517
\\
1618
\\
1719
$^1$Department of Ecology and Evolutionary Biology, \\
1820
University of Tennessee, \\
1921
Knoxville, TN, USA \\
2022
\\
21-
$^2$Remote Data Analysis and Visualization Center,\\
23+
$^2$National Institute for Computational Sciences, \\
2224
University of Tennessee, \\
2325
Knoxville, TN, USA \\
26+
\\
27+
$^3$Computer Science and Mathematics Division, \\
28+
Oak Ridge National Laboratory, \\
29+
Oak Ridge, TN, USA
2430
}
2531
%\\ \today}
26-
\title{A Quick Guide for the \pkg{pmclust} Package}
32+
\title{A Quick Guide for the \pkg{pmclust} Package {\small (Ver. \pmclustversion)}}
2733
%\\
2834
%\vspace{0.2cm} \large (Based on Version 0.1-2)}
2935

@@ -65,7 +71,7 @@ Knoxville, TN, USA \\
6571

6672
%% end of declarations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
6773

68-
74+
\input{./pmclust-include/my_jss.cls}
6975
\input{./pmclust-include/00-preamble}
7076

7177
\begin{document}

‎vignettes/pmclust-include/01-acknowledgement.tex‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,12 @@
22
\section*{Acknowledgement}
33
\addcontentsline{toc}{section}{Acknowledgement \vspace{-0.3cm}}
44

5+
Chen was supported in part by
6+
the Department of Ecology and Evolutionary Biology at the
7+
University of Tennessee, Knoxville, and a grant from
8+
the National Science Foundation (MCB-1120370.)
9+
\\
10+
511
Chen and Ostrouchov were supported in part by the project
612
``Visual Data Exploration and Analysis of Ultra-large Climate Data''
713
funded by U.S. DOE Office of Science

‎vignettes/pmclust-include/01-introduction.tex‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11

22
{\color{red} \bf Warning:} This document is written to explain the major
33
functions of
4-
\pkg{pmclust}~\citep{Chen2012pmclustpackage}, version 0.1-5.
4+
\pkg{pmclust}~\citep{Chen2012pmclustpackage}, version 0.1-7.
55
Every effort will be made to insure future versions are consistent with
66
these instructions, but new features in later versions may not be explained
77
in this document.

‎vignettes/pmclust-include/my_jss.cls‎

Lines changed: 51 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,51 @@
1+
2+
\renewcommand{\makefooter}{%
3+
\vspace{\footerskip}
4+
}
5+
6+
\makeatletter
7+
% \def\maketitle{%
8+
% \par\textbf{\@title}%
9+
% \par{\@author}%
10+
% \par}
11+
\def\maketitle{
12+
{\centering
13+
{\LARGE\bf \@title\par}
14+
% \vskip 0.2in plus 1fil minus 0.1in
15+
\vskip 0.2in
16+
{
17+
\def\and{\unskip\enspace{\rm and}\enspace}%
18+
\def\And{\end{tabular}\hss \egroup \hskip 1in plus 2fil
19+
\hbox to 0pt\bgroup\hss \begin{tabular}[t]{c}\large\bf\rule{\z@}{24pt}\ignorespaces}%
20+
\def\AND{\end{tabular}\hss\egroup \hfil\hfil\egroup
21+
\vskip 0.1in plus 1fil minus 0.05in
22+
\hbox to \linewidth\bgroup\rule{\z@}{10pt} \hfil\hfil
23+
\hbox to 0pt\bgroup\hss \begin{tabular}[t]{c}\large\bf\rule{\z@}{24pt}\ignorespaces}
24+
\hbox to \linewidth\bgroup\rule{\z@}{10pt} \hfil\hfil
25+
\hbox to 0pt\bgroup\hss \begin{tabular}[t]{c}\large\bf\rule{\z@}{24pt}\@author
26+
\end{tabular}\hss\egroup
27+
\hfil\hfil\egroup
28+
}
29+
}
30+
}
31+
\makeatother
32+
33+
\renewcommand{\jsssec}[2][default]{\vskip \preXLskip%
34+
\refstepcounter{section}%
35+
\centerline{\textbf{\Large \thesection. #2}} \nopagebreak
36+
\vskip \postMskip \nopagebreak}
37+
38+
\renewcommand{\jsssubsec}[2][default]{\vskip \preMskip%
39+
\refstepcounter{subsection}%
40+
\textbf{\large \thesubsection. #2} \nopagebreak
41+
\vskip \postSskip \nopagebreak}
42+
43+
\renewcommand{\jsssubsubsec}[2][default]{\vskip \preSskip%
44+
\refstepcounter{subsubsection}%
45+
{\large \textit{#2}} \nopagebreak
46+
\vskip \postSskip \nopagebreak}
47+
48+
\renewcommand{\jsssimplesec}[2][default]{\vskip \preLskip%
49+
\refstepcounter{section}%
50+
\textbf{\large #1} \nopagebreak
51+
\vskip \postSskip \nopagebreak}

0 commit comments

Comments
 (0)