% -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
\documentclass[a4paper]{article}

\title{A Test File}
\author{Friedrich Leisch}

\SweaveOpts{echo=F}
\usepackage{a4wide}

\begin{document}

\maketitle

A simple example that will run in any S engine: The integers from 1 to
10 are
<<print=TRUE>>=
1:10
<<results=hide>>=
print(1:20)
@ % the above is just to ensure that 2 code chunks can follow each other

We can also emulate a simple calculator:
<<echo=TRUE,print=TRUE>>=
1 + 1
1 + pi
sin(pi/2)
@ 

Now we look at Gaussian data:

<<>>=
x <- rnorm(20)
print(x)
library(ctest)
print(t1 <- t.test(x))
@ 
Note that we can easily integrate some numbers into standard text: The
third element of vector \texttt{x} is \Sexpr{x[3]}, the 
$p$-value of the test is \Sexpr{format.pval(t1$p.value)}. % $  

Now we look at a summary of the famous iris data set, and we want to
see the commands in the code chunks.  Note that the summary needs to
be \texttt{print()}ed explicetly, because eval would discard it otherwise. I
consider this a feature, because it allows for much finer control on
what gets into the final report.

\SweaveOpts{echo=true}

% the following code is R-specific, as data(iris) will not run in Splus. 
% Hence, we mark it as R code.
<<engine=R>>=
data(iris)
print(summary(iris))
@ %def 


\begin{figure}[htbp]
  \begin{center}
<<fig=TRUE>>=
pairs(iris)
@     
    \caption{Pairs plot of the iris data.}
  \end{center}
\end{figure}

\begin{figure}[htbp]
  \begin{center}
<<fig=true>>=
boxplot(Sepal.Length~Species, data=iris)
@ 
    \caption{Boxplot of sepal length grouped by species.}
  \end{center}
\end{figure}


% R is not Splus, hence this chunk will be ignored:
<<engine=S4>>=
function.that.comes.only.with.Splus(x)
@ 

\end{document}