\documentclass{article}
\title{Sweave Example}
\author{Kate Cowles}
\usepackage{Sweave}
\begin{document}
\maketitle


The {\tt Sweave} function facilitates creation of documents that blend R code, its output, and documentation or other text.  The user begins by creating a {\tt noweb} source file,
which is a text file with
the extension {\tt.Rnw}.  It resembles a {\tt .tex} file, but it has two
kinds of segments (called ``chunks") in it:  \emph{documentation chunks} and \emph{code chunks}.
By default, the document begins with a documentation chunk.  Each code chunk must start
with 
\begin{verbatim}
 <<>>=
\end{verbatim} 
at the beginning of a line.  Optionally, a name for the code chunk may be included in the
angle brackets:
\begin{verbatim}
 <<name>>=
\end{verbatim}
Code chunk names may be used to pass options to Sweave to control the final output.

Each documentation chunk (except the first) begins with
\begin{verbatim}
  @
\end{verbatim}
at the beginning of a line.   
  

In this example, we create a small data frame, run a linear regression model,
and produce diagnostic plots.  Since we do not specify any options in a
code chunk name, the default behavior occurs:  both the code and its output
are included in the final document.

<<>>=
set.seed(15)
x <- 1:5
y <- rnorm(1 -0.5* x )
mydat <- data.frame(cbind(x,y))
print(mydat)
summary( lmout <- lm( y ~ x, data=mydat) )
@

Next we will create plots.  The options {\tt fig} and {\tt echo} in the code chunk name 
tell Sweave to include the actual
plots produced, and to suppress printing (echoing) of the R code.
\begin{center}
<<fig=TRUE,echo=FALSE>>=
par(mfrow=c(2,2))
plot(lmout)
@
\end{center}

This time we will show the code that produces the figure, instead of the figure itself.
\begin{center}
<<fig=FALSE, echo=TRUE>>=
par(mfrow=c(2,2))
plot(lmout)
@
\end{center}

It is also possible to include the scalar results of R expressions in text chunks. 
For example, the logit of 0.237 is \Sexpr{ log( 0.237/( 1-0.237)) }. 

To process this .Rnw file, one goes into R and runs the Sweave function.
\begin{verbatim}
Sweave(file="firsttry.Rnw")
\end{verbatim}
Alternatively, if working in Linux or Unix, one may enter
\begin{verbatim}
echo 'Sweave("firsttry.Rnw")' | R --vanilla --quiet
\end{verbatim}
at the Linux/Unix prompt without having to go into R.

Either way of running the {\tt Sweave} function will create the \LaTeX\ source 
file {\tt firsttry.tex} and the graphics files {\tt firsttry-002.pdf}
and {\tt firsttry-002.ps}.  The final typeset document may be produced by running
\begin{verbatim}
latex firsttry
\end{verbatim}
at the Linux/Unix prompt.  If in Windows, a batch file or the TeXnic Center may 
be used to process the {\tt .tex} file.

\end{document}