%Usage: knitr sweaveEx
%       rubber -d sweaveEx
%       (= pdflatex sweaveEx + bibtex sweaveEx sufficiently many times)
% To get .R file: R CMD Stangle sweaveEx.Rnw = Stangle sweaveEx
\documentclass{article}
\usepackage{relsize,setspace}  % used by latex(describe( ))
\usepackage{url}               % used in bibliography
\usepackage[superscript,nomove]{cite} % use if \cite is used and superscripts wanted
% Remove nomove if you want superscripts after punctuation in citations
\usepackage{lscape}            % for landscape mode tables
\usepackage{calc,epic,color}   % used for latex(..., dotchart=TRUE)
\usepackage{moreverb}          % handles verbatiminput

% Macro changes: defines commands \cbstart* to use the changebar
% package to draw vertical change bars for different edits (e.g. on
% different days) having their own color/line thickness.  A key is
% generated in the text at the point at which \changes is called.
% Change marking can be turned off without removing /cbstart* and
% /cbend commands from the text.
%
% Usage: 
%  \def\showchanges{1}    or {0} to turn off change marking
%  \changes{suffix}{color}{thickness in pts}{description}
%  \changes{another suffix}{color}{thickness}{description}
%  . . .
% Note that suffixes must contain only letters (single or multiple).
% Suffixes are appended to \cbstart.  \changes appears after
% \begin{document}.
%
\usepackage[color]{changebar}
\newcommand{\changes}[4]{%
 \ifnum\showchanges=1
 \expandafter\newcommand\csname cbstart#1\endcsname{\cbstart[#3pt]\cbcolor{#2}}%
 \noindent Changes for #4 are marked by %
 \textcolor{#2}{\rule[0.05in]{.25in}{#3pt}} as a vertical line in the
 right margin\\
 \else
 \expandafter\newcommand\csname cbstart#1\endcsname{}%
 \def\cbend{}
 \fi
}


\textwidth 6.75in              % set dimensions before fancyhdr 
\textheight 9.25in
\topmargin -.875in
\oddsidemargin -.125in
\evensidemargin -.125in
\usepackage{fancyhdr}          % this and next line are for fancy headers/footers
\pagestyle{fancy}
\newcommand{\bc}{\begin{center}}  % abbreviate
\newcommand{\ec}{\end{center}}
\newcommand{\code}[1]{{\smaller\texttt{#1}}}
\newcommand{\R}{{\normalfont\textsf{R}}{}}

% Define the following only if you put figures in a figure environment
%\fg{basefilename}{label}{caption}
\newcommand{\fg}[3]{\begin{figure}[htbp]%
 \leavevmode\centerline{\includegraphics{graphics/#1}}%
 \caption{\smaller #3}\label{#2}\end{figure}}

\usepackage{Sweavel}
% Uncomment some of the following to use some alternatives:
% \def\Sweavesize{\normalsize}  (changes size of typeset R code and output)
% \def\Rcolor{\color{black}}
% \def\Routcolor{\color{green}}
% \def\Rcommentcolor{\color{red}}
% To change background color or R code and/or output, use e.g.:
% \def\Rbackground{\color{white}}
% \def\Routbackground{\color{white}}
% To use rgb specifications use \color[rgb]{ , , }
% To use gray scale use e.g. \color[gray]{0.5}
% If you change any of these after the first chunk is produced, the
% changes will have effect only for the next chunk.

<<echo=FALSE>>=
knitrSet(w=5, h=3.5)  # function is defined in my .Rprofile
# To omit code and its output throughout, use
# knitrSet(echo=FALSE, results='hide'}
@ 

%\SweaveOpts{prefix.string=graphics/plot, eps = FALSE, pdf = TRUE}

\title{Example Enhanced Report}
\author{Frank E Harrell Jr\\\smaller Department of Biostatistics\\\smaller Vanderbilt University School of Medicine}
\begin{document}
\maketitle
\def\showchanges{1}
\changes{a}{blue}{1}{2014-10-02}
\changes{b}{red}{2}{2014-10-04}

% Use the following 3 lines for long reports needing navigation
%\tableofcontents
%\listoftables
%\listoffigures     % not used unless figure environments used

\section{Descriptive Statistics}\label{descStats}
<<results='asis'>>=
require(rms)        # Get access to rms and Hmisc packages
getHdata(support)   # Use Hmisc/getHdata to get dataset from VU DataSets wiki
d <- subset(support, select=c(age,sex,race,edu,income,hospdead,slos,dzgroup,
                       meanbp,hrt))
latex(describe(d), file='')
@
Race is reduced to three levels (white, black, OTHER) because of low
frequencies in other levels (minimum relative frequency set to 0.05).
<<>>=
d <- transform(d, race = combine.levels(race, minlev = 0.05))
@
\cbstarta
Summaries of variables stratified by sex are below.
<<results='asis'>>=
latex(summaryM(age + race + edu + income + slos + dzgroup +
                 meanbp + hrt ~ sex, data=d, test=TRUE),
      npct='both', file='', landscape=TRUE, round=1)
@ 
\cbend

\section{Redundancy Analysis and Variable Interrelationships}
\bc
% Note: giving a chunk name to each code chunk that produces a figure
% makes it easy to know which plots to send to a collaborator, and
% will not allow numbered orphan plots to be left when code chunks are
% inserted into the file.  The default in knitr is for plots to be
% numbered by the chunks producing them.

\cbstartb
<<vc>>=
v <- varclus(~., data=d)
plot(v)
redun(~ age + sex + race + edu + income + dzgroup + meanbp + hrt, data=d)
# Alternative: redun(~., data=subset(d, select=-c(hospdead,slos)))
@
\ec
Note that the clustering of black with white is not interesting; this
just means that these are mutually exclusive higher frequency
categories, causing them to be negatively correlated.
\cbend
\section{Logistic Regression Model}
Here we fit a tentative binary logistic regression model.  The
coefficients are not very useful so they are not printed (\dots is
printed in their place).  Artificially create more missing data so
that a dot chart showing frequencies of missings will be printed when
the \code{latex} version of the output appears later.
<<z,eval=FALSE,echo=TRUE>>=
dd <- datadist(d); options(datadist='dd')
d$age[1:10] <- d$meanbp[1:13] <- d$hospdead[1:7] <- NA
f <- lrm(hospdead ~ rcs(age,4) + sex + race + dzgroup + rcs(meanbp,5),
         data=d) # see Section (*\ref{descStats}*) for descriptive statistics
f
<<echo=FALSE>>=
z <- capture.output( {
<<z>>
   } )
prselect(z, 'S.E.') # keep only summary stats; or:
# prselect(z, stop='S.E.', j=-1)  # keep only coefficients
@
Better: Directly output model statistics as \LaTeX\ markup and easily
suppress coefficients. 
<<results='asis'>>=
print(f, latex=TRUE, coefs=FALSE)
@ 

The mean arterial blood pressure effect is shown below, on the
probability scale.   \textbf{Note}: \code{knitr} was told to
automatically use a \LaTeX\ floating \code{figure} environment since a
caption was given.
<<<pmeanbp>>=
p <- Predict(f, meanbp, fun=plogis)
<<meanbp,cap=paste('Partial effect of mean arterial blood pressure adjusted to',attr(p, 'info')$adjust)>>=
plot(p, ylab='Prob[hospital death]', adj.subtitle=FALSE)
# Figure (*\ref{fig:meanbp}*)
<<results='asis'>>=
latex(anova(f), where='h', file='')   # can also try where='htbp'
@
The likelihood ratio $\chi^{2}$ statistic is
\Sexpr{round(f$stats['Model L.R.'],2)} on \Sexpr{f$stats['d.f.']} d.f.
The fitted model in algebraic form is found below.
<<results='asis'>>=
latex(f, file='')
@ 

\section{Computing Environment}
These analyses were done using the following versions of \R\cite{Rsystem}, the
operating system, and add-on packages \code{Hmisc}\cite{Hmisc},
\code{rms}\cite{rrms}, and others:
<<echo=FALSE,results='asis'>>=
toLatex(sessionInfo(), locale=FALSE)
@

% Note: Rsystem reference is defined inside feh.bib.  It is a slightly
% edited version of the output of citation().
\bibliography{/home/harrelfe/bib/harrelfe.bib}
\bibliographystyle{unsrt}
% Use \bibliographystyle{abbrv} if want references alphabetized

\section{Source Code for This Report}
\verbatimtabinput{sweaveEx.Rnw}

\section{\code{Sweavel.sty}}
\verbatimtabinput{/home/harrelfe/doc/latex/texinput/Sweavel.sty}

\end{document}