Kurs:Computer für Psychologen/Sitzung7
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\useinnertheme{} \usecolortheme[named=purple]{structure} \usecolortheme{rose}
\title{{\bf Sweave -- Dynamic Interaction of R and \LaTeX{}
}}
\vspace{2cm} \author{Nora Umbach} \date{Dezember 2009}
\begin{document}
\thispagestyle{empty} \frame{\titlepage}
\begin{frame}{Why would I need Sweave?}
\begin{itemize}
\item Creating reports that can be updated automatically
\item Statistic exercises
\item Manuals with embedded examples (like R-help files, etc.)
\item Avoiding copy/paste errors between analysis output and report
file
\item Reproducible research
\end{itemize}
\vfill
\end{frame}
\begin{frame}[fragile]{R package xtable -- create export tables}
\begin{itemize}
\item Function converting an R object to an `xtable' object, which
can then be printed as a LaTeX or HTML table
\item \begin{verbatim}xtable(x, caption=NULL, label=NULL,
align=NULL, digits=NULL, display=NULL, ...)\end{verbatim}
\item Check \verb+print.xtable()+ for useful arguments
\item Example:
\end{itemize}
\lstset{language=R}
\begin{lstlisting}
- Taken from help(lm) in R 1.1.1
- Annette Dobson (1990) "An Introduction to Generalized Linear Models".
- Page 9: Plant Weight Data.
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group <- gl(2,10,20, labels=c("Ctl","Trt")) weight <- c(ctl, trt) lm.D9 <- lm(weight ~ group) print(xtable(lm.D9)) print(xtable(anova(lm.D9)))
\end{lstlisting}
\vfill
\end{frame}
\begin{frame}[fragile]{R package xtable -- example}
\begin{itemize}
\item R output
\end{itemize}
\begin{lstlisting}
> print(xtable(anova(lm.D9))) % latex table generated in R 2.9.2 by xtable 1.5-6 package % Mon Dec 07 14:53:44 2009 \begin{table}[ht] \begin{center} \begin{tabular}{lrrrrr}
\hline & Df & Sum Sq & Mean Sq & F value & Pr($>$F) \\ \hline
group & 1 & 0.69 & 0.69 & 1.42 & 0.2490 \\
Residuals & 18 & 8.73 & 0.48 & & \\ \hline
\end{tabular} \end{center} \end{table}
\end{lstlisting}
\end{frame}
\begin{frame}{R package xtable -- example}
\begin{itemize}
\item LaTeX output
\end{itemize}
% latex table generated in R 2.9.2 by xtable 1.5-6 package
% Mon Dec 07 14:53:44 2009
\begin{table}[ht]
\begin{center}
\begin{tabular}{lrrrrr}
\hline
& Df & Sum Sq & Mean Sq & F value & Pr($>$F) \\
\hline
group & 1 & 0.69 & 0.69 & 1.42 & 0.2490 \\
Residuals & 18 & 8.73 & 0.48 & & \\
\hline
\end{tabular}
\end{center}
\end{table}
\vfill
\end{frame}
\begin{frame}[fragile]{Sweave example}
\begin{lstlisting}
\documentclass[a4paper]{article}
\begin{document}
In this example we embed parts of the examples from the \texttt{kruskal.test} help page into a \LaTeX{} document:
<<>>= data(airquality) kruskal.test(Ozone ~ Month, data = airquality) @ which shows that the location parameter of the Ozone distribution varies significantly from month to month. Finally we include a boxplot of the data:
\begin{center} <<fig=TRUE,echo=FALSE>>= boxplot(Ozone ~ Month, data = airquality) @ \end{center}
\end{document}
\end{lstlisting}
\end{frame}
\begin{frame}[fragile]{How to use Sweave}
\begin{itemize}
\item File will be saved as {\G \verb+filename.Snw+}
\item Then run {\G \verb+Sweave("filename.Snw", stylepath=T)+}
\item R generates {\G \verb+filename.tex+} and possible figures (do not
forget to set working directory in R!)
\item Now compile {\G \verb+filename.tex+}
\item Done!
\item If you want only the R code from your {\G
\verb+filename.Snw+} use {\G \verb+Stangle("filename.Snw")+} and R
will create {\G filename.R} with only R code from the R chunks
\end{itemize}
\vfill
\end{frame}
\begin{frame}[fragile]{Useful options} \begin{verbatim} <<>>= starts an R chunk @ starts a documentation chunk
(ergo ends an R chunk)
\end{verbatim}
\begin{itemize}
\item options are defined by: `\verb+<<option>>=+' and seperated by
commas
\item {\G \verb+echo=false+} to hide R commands
\item {\G \verb+results=hide+} when you do not want to have the
results displayed
\item {\G \verb+results=tex+} when output shall not be displayed as
S output (for example when using {\G \verb+xtable()+})
\item {\G \verb+fig=true+} when you want to insert a figure
\end{itemize}
\vfill
\end{frame}
\begin{frame}{Results of my thesis}
\begin{itemize}
\item Spatial cueing effects and awareness of target location:
Evidence against early selection
\item Subjects had to press a button when they saw a light (simple
reaction time)
\item With or without mirror, cue on right or left ear, light in
right or left eye
\end{itemize}
\vfill
\end{frame}
\begin{frame}[fragile]{Documentation}
On Friedrich Leisch's homepage you will find all the information you
need about Sweave:
{\color{purple}{
\begin{verbatim}
http://www.statistik.lmu.de/~leisch/Sweave/
\end{verbatim}}}
\nocite{Leisch2002}
\nocite{Leisch2002b}
\nocite{Leisch2003}
\nocite{Leisch2003b}
\vfill
\end{frame}
\begin{frame}[fragile]{Exercise} Write your own .Swn-file and compile it into a PDF:
\begin{itemize}
\item Load the dataset {\G \verb+cars+} and write a few short
sentences about it (where can you find information on the dataset?)
\item Create a table with descriptive statistics of the dataset
(use {\G \verb+caption+} and {\G \verb+label+})
\item Plot the data in a scatterplot and draw the regression line
(use {\G \verb+lm()+}, {\G \verb+abline()+})
\item Put the parameters of your regression model in a table in
your report
\item {\sc Hint:} for all tables use {\G \verb+xtable()+}, remember
options: {\G \verb+echo=false+}, {\G \verb+results=hide+}, {\G
\verb+results=tex+}, {\G \verb+fig=true+}
\end{itemize}
\vfill
\end{frame}
\begin{frame}{}
\vfill
\begin{center}\Huge {\color{purple}{\bf Thank you for your attention!}}
\vfill
\small nora.umbach@uni-tuebingen.de
\end{center}
\end{frame}
\renewcommand\refname{} \begin{frame}{References}\small%[allowframebreaks]
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