% Hints for those not versed in LaTeX are at
% http://biostat.mc.vanderbilt.edu/LaTeXCollab

\documentclass{article}
\usepackage{spaper}

% Define particular comment commands for each author so as to automatically
% include name/initials
\newcommand{\comfh}[1]{\com{FH}{#1}}
\newcommand{\comfp}[1]{\com{FP}{#1}}
% To cause all comments and marginal notes to be suppressed, 
% uncomment the following line
%\ignorecom

\addbibresource{/home/harrelfe/bib/harrelfe.bib}
\renewcommand{\cite}[1]{\supercite{#1}}   % make citations use superscripts

\title{Example Report}
\author{Frank Harrell\thanks{Department of Biostatistics,
    Vanderbilt University School of Medicine,
    \texttt{f.harrell@vanderbilt.edu}}
  \and
  Fictitious Person\thanks{Department of Irreproducible Research,
    Slapout College, 
    \texttt{fp@sloppy.com}}}
\date{\today}
\begin{document}
\maketitle
\tableofcontents

<<echo=FALSE>>=
require(rms)
knitrSet(echo=TRUE)   # set echo=FALSE to not print code
lan <- function(a, ...) latex(a, file='', table.env=FALSE, ...)
@

\section{Descriptive Statistics}
<<desc,results='asis'>>=
getHdata(FEV)
latex(describe(FEV), file='')
@ 
\comfh{I have a question about the data.  Do all the values make sense?
  Are these data applicable to our research question?  Did we really
  land a man on the moon?}
\comfp{No, I don't think we landed a man on the moon, but I do think
  that hundreds of aliens from an advanced civilization visited us in
  the 1950s and forgot to say hello.}
\comfh{I'm convinced}

\section{FEV vs.\ Age}
Figure~\ref{fig:plot} shows the raw data for some of the key variables.
<<plot,w=5.5,h=3.75,cap='Scatterplot of age vs.\ FEV stratified by sex'>>=
ggplot(FEV, aes(x=age, y=fev, color=sex)) + geom_point()
@ 
\comfh{\textbf{TO DO}:
  \begin{enumerate}
    \item See if other variables need to be accounted for
    \item See if age and sex interact
  \end{enumerate}}

\section{Computing Environment}
These analyses were done using the following versions of R\cite{Rsystem}, the
\snote{CHECK}
operating system, and add-on packages \code{Hmisc}\cite{Hmisc},
\code{rms}\cite{rrms}, and others:
<<sinfo,echo=FALSE,results='asis'>>=
toLatex(sessionInfo(), locale=FALSE)
@
The reproducible research framework \code{knitr}~\cite{knitr} was used.

\printbibliography[title={Bibliography}]

% To print all code in an appendix if you used knitrSet(echo=FALSE),
% use the following
\appendix
\section{\R\ Code}
<<all-code, ref.label=all_labels(), echo=TRUE, eval=FALSE>>=
@ 

\end{document}

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