\documentclass[12pt]{report}

%%
%% This is an Sweave file.  To generate a latex file from this, use (in R): 
%% > library(tools)
%% > Sweave("HVTNscenarios")
%% and then in a regular Unix (or MSDOS, or...) shell, 
%% $ latex HVTNscenarios
%% to generate the results.
%%

%% The following is for creating PDF.
\newif\ifpdf
\ifx\pdfoutput\undefined
  \pdffalse     % not running PDFLaTeX
\else
  \pdfoutput=1  % running PDFLaTeX
  \pdftrue
\fi

%\ifpdf
%  \usepackage{thumbpdf}
%\fi
%\usepackage{html,heqn,htmllist}
%\usepackage[latex2html]{hyperref} 
\ifpdf
  \usepackage[pdftex]{graphicx}
  \usepackage[pdftex]{hyperref} 
\else
  \usepackage[dvips]{graphicx}
  \usepackage[dvips]{hyperref} 
\fi

\usepackage{url}
\usepackage[authoryear,round]{natbib}
\usepackage{graphicx}

\addtolength{\oddsidemargin}{-0.5in}
\addtolength{\textheight}{0.2in}
\addtolength{\textwidth}{1in}

\hypersetup{backref,colorlinks=true,pagebackref=true,
  hyperindex=true}%pdfpagemode=FullScreen,

\ifpdf
  \DeclareGraphicsExtensions{.jpg,.pdf,.png,.mps}
\fi

\title{Analysis}
\author{AJ Rossini}
\date{\today}

\begin{document}

\maketitle

\tableofcontents

\listoffigures

\listoftables

\begin{abstract}
  An example for using Sweave.
\end{abstract}

%% For setting graphics for Sweave
%\setkeys{Gin}{width=5cm}
%\setkeys{Gin}{width=0.8\textwidth}

Possible settings for sweave chunks: 
\begin{itemize}
\item eval=TRUE
\item fig=TRUE, eps=FALSE
\item results=hide, tex
\item echo=TRUE
\item prefix=FALSE
\item include=FALSE
\end{itemize} 

Indexing works.  You can see that from Table~\ref{tab:1} and
Figure~\ref{fig:control}.

<<example data 1>>=
x <- rnorm(10) + 2
y <- x + rnorm(10)
my.lm.fit <- lm(y~x)
@ 


\chapter{Tables}
\label{CHA:tables}

<<Check library existence,echo=FALSE,eval=TRUE>>=
xtableExists <- require(xtable)
@ 

We have our first table

<<example output for data 1,results=tex,echo=FALSE>>=
if (xtableExists) {
   xtable(my.lm.fit)
}
@ 

and the second table, with Caption and \LaTeX{} reference label. 

<<example output for data 1,results=tex,echo=FALSE>>=
if (xtableExists) {
  xtable(my.lm.fit,caption="My First Table Caption",label="tab:1")
}
@ 

\clearpage

We could do the same thing and echo the code, as well:

We have our first table

<<example output for data 1,results=tex,echo=TRUE>>=
if (xtableExists) {
   xtable(my.lm.fit)
}
@ 

\clearpage

and the second table, with Caption and \LaTeX{} reference label. 

<<example output for data 1,results=tex,echo=TRUE>>=
if (xtableExists) {
  xtable(my.lm.fit,caption="My Second Table Caption",label="tab:2")
}
@ 

\chapter{Figures}
\label{CHA:figures}

Normally you can just include plots, by specifying that the chunk
generates a figure.

<<exampleFigureOne,fig=TRUE,echo=FALSE>>=
plot(rnorm(10),rnorm(10))
@ 

\clearpage

However, if you want more control, such as Labels on figures as well
as floating placement (i.e. letting \LaTeX{} place it for you
appropriately), you might:

\begin{figure}[htbp]
  \centering
<<exampleFigureTwo,fig=TRUE,echo=FALSE>>=  
plot(rnorm(10),rnorm(10))
@ 
  \caption{Example of more control}
  \label{fig:control}
\end{figure}

\end{document}