Sweave

What is Sweave?

Sweave is a tool that enables users to embed R code into reports. It is a powerful tool for Literate programming that is the focus of this web-resource, however there are Alternatives to Sweave for the R statistical environment.

Installing Sweave

The Sweave package is part of R. If you do not already have R installed on your machine then visit the R page. In addition to the R computing envrionment, it is also required that you have \textrm{\LaTeX} installed. If \textrm{\LaTeX} is not yet available on your system or if you wish to learn more visit the LaTeX information page. Finally, before we get into the essentials of Sweave you will have be familiar with and have handy your programming editor.

A simple example

Sometimes in programming it is easiest for learning to jump right in with and example then to go back through that exampled and try to break it apart. Here is a fairly simple example that will run a Fisher’s exact test.

Open an editor and save the following as FishersExactTest.Rnw otherwise use the download link below.

\documentclass{article}
\usepackage{amsmath}
\usepackage[utf8]{inputenc}
\usepackage{textcomp}

\title{Fisher's Exact Test Sweave Example}
\author{Ender Wiggin}

\begin{document}
\maketitle
\section{The Problem}
This is a very simple example of how to use Sweave.  In this problem we are interested in
is testing the null hypothesis that a drug is not related to the proportion of winners and losers.

\section{The Data}
\begin{center}
\begin{tabular}[h]{|c|c|c|}
\hline
        & Winners & Losers \\
\hline
Drug    & 90      & 10     \\
Placebo & 80      & 20     \\
\hline
\end{tabular}
\end{center}

<<data>>=
drug<-as.table(cbind(c(90,80),c(10,20)))
colnames(drug)<-c("Winners","Losers")
rownames(drug)<-c("Drug","Placebo")
print(drug)
@

\section{The Analysis}
<<test>>=
result <- fisher.test(drug)
print(result)
@

\end{document}

Now visit the following to get more familar with the example that you just ran.

Running the code (from a command prompt)

Sweave files look a lot like \textrm{\LaTeX} files. Running the next few commands will produce your Sweave report. R CMD Sweave tells R to use Sweave to evaluate the file and produces a .tex file. The next command pdflatex uses \textrm{\LaTeX} to produce a pdf report and the final line is a shortcut to view the report. For a more detailed explination of this example visit the Sweave example walkthrough. In order to run these commands you must first navigate to the directory containing FishersExactTest.Rnw. It is also nice to let each Sweave report reside in its own directory because both Sweave and \textrm{\LaTeX} produce numerous extra files during compilation.

  • GNU/Linux
    ~$ R CMD Sweave FishersExactTest.Rnw
~$ pdflatex FishersExactTest.tex
~$ evince FishersExactTest.pdf
  • Max OS X
    ~$ R CMD Sweave FishersExactTest.Rnw
~$ pdflatex FishersExactTest.tex
~$ open FishersExactTest.pdf
  • Windows
    ~$ R CMD Sweave FishersExactTest.Rnw
~$ pdflatex FishersExactTest.tex
~$ adobereader FishersExactTest.pdf

Alternatively, we have created a tool (lpEdit) that uses Sweave syntax, but does not require the user to enter the command line. RStudio will also run Sweave documents.

Sweave.sty not found?

In some distributions or operating systems it is possible that the Sweave.sty file will not be found. Ideally, the style file should be installed and included in the system paths so that LaTeX can find it. An alternative short term solution is to download the file and include it in the same directory as your *.rnw file.

Alternatives to Sweave