# [R] Sweave

Frank E Harrell Jr fharrell at virginia.edu
Wed Jul 30 17:24:19 CEST 2003

Many of you are using Sweave for making statistical reports.  I thought it might be helpful to some to see an example of the setup I use (in Linux).  For those of you who have not yet discovered the power and productivity gains from using Fritz Leisch's wonderful package, I encourage you to give Sweave a try.

%File: model.nw
%Usage:
% Put library(Hmisc;Design;tools} in .First
% Sweave model   - runs model.nw to produce model.tex and
%                  graphics files in graphics/
% Sweave shell script defined as echo "Sweave(\"$1.nw\")" | R --no-save % latex or pdflatex model; bibtex model; latex or pdflatex model % To get .R file: Stangle model \documentclass{article} \usepackage{relsize,setspace} % used by latex(describe( )) \newcommand{\co}[1]{\texttt{\smaller #1}} \title{Analysis} \author{Frank E Harrell Jr} \begin{document} \SweaveOpts{prefix.string=graphics/plot} \setkeys{Gin}{width=1.0\textwidth} \maketitle <<echo=F>>= Hmisc.version <- package.description('Hmisc')['Version'] Design.version <- package.description('Design')['Version'] @ All calculations were done using \Sexpr{R.version.string} \cite{Roriginal} on RedHat Linux 9.0, using version \Sexpr{Hmisc.version} of the \texttt{Hmisc} package and version \Sexpr{Design.version} of the \texttt{Design} package. \section{Descriptive Statistics} <<results=tex>>= load('mydata.sav') latex(describe(mydata), file='') # generate LaTeX code in place @ The variable clustering diagram below shows which variables in the dataset are interrelated. The$y$-axis is the Spearman$\rho^2\$
(squared rank correlation coefficient).  \co{addon} and
\co{mica} cannot be considered together because of an undefined
correlation between them.  \co{addon} correlates weakly with
\co{sodm} (only).  \co{usedlabd} is always unity when it is not
missing, so it is also omitted from variable clustering.
\begin{center}
<<fig=T>>=
@
\end{center}
\section{Analysis of Dose Effects}
. . . .
\bibliography{/home/feh/bib/feh.bib}
\bibliographystyle{abbrv}
\end{document}