\RequirePackage{hyperref}
\RequirePackage{url}
\RequirePackage{amsmath}
\RequirePackage{bm}
\newcommand{\Slang}{\textsf{S} language}
\newcommand{\RR}{\textsf{R}}
\newcommand{\email}[1]{\href{mailto:#1}{\normalfont\texttt{#1}}}
%- R programming markup
\newcommand\code{\bgroup\@codex}
\def\@codex#1{{\normalfont\ttfamily\hyphenchar\font=-1 #1}\egroup}
\let\env=\code
\let\command=\code
\newcommand*{\Rfun}[1]{\code{#1()}\index{\RR~function #1}}
\newcommand*{\class}[1]{\code{#1}\index{class #1}}%
\newcommand*{\pkg}[1]{\code{#1}\index{\RR~package #1}}
%
\newcommand{\kbd}[1]{{\normalfont\texttt{#1}}}
\newcommand{\key}[1]{{\normalfont\texttt{\uppercase{#1}}}}
\newcommand\samp{`\bgroup\@noligs\@sampx}
\def\@sampx#1{{\normalfont\texttt{#1}}\egroup'}
\let\option=\samp
\newcommand{\var}[1]{{\normalfont\textsl{#1}}}
\newcommand{\file}[1]{{`\normalfont\textsf{#1}'}}
\newcommand{\dfn}[1]{{\normalfont\textsl{#1}}}
\newcommand{\acronym}[1]{{\normalfont\textsc{\lowercase{#1}}}}
\newcommand{\strong}[1]{{\normalfont\fontseries{b}\selectfont #1}}
\let\pkg=\strong
%
\RequirePackage{alltt}
\newenvironment{example}{\begin{alltt}}{\end{alltt}}
\newenvironment{smallexample}{\begin{alltt}\small}{\end{alltt}}
\newenvironment{display}{\list{}{}\item\relax}{\endlist}
\newenvironment{smallverbatim}{\small\verbatim}{\endverbatim}
% This is already in ``Sweave'' :
%% \RequirePackage{fancyvrb}
%% \DefineVerbatimEnvironment{Sinput}{Verbatim}{fontsize=\small,fontshape=sl}
%% \DefineVerbatimEnvironment{Soutput}{Verbatim}{fontsize=\small}
%% \DefineVerbatimEnvironment{Scode}{Verbatim}{fontsize=\small,fontshape=sl}
%
\newcommand{\FIXME}[1]{\marginpar{ \dots FIXME \emph{#1} \dots}}
\newcommand{\TODO}[1]{\par\noindent\textsc{Todo:} \textit{#1}\par}
%
%% Matrix stuff :
%
\newcommand{\trans}{\ensuremath{^\mathsf{T}}}
\newcommand{\bA}{\ensuremath{\bm{A}}}
\newcommand{\bD}{\ensuremath{\bm{D}}}
\newcommand{\bDelta}{\ensuremath{\bm{\Delta}}}
\newcommand{\bI}{\ensuremath{\bm{I}}}
\newcommand{\bL}{\ensuremath{\bm{L}}}
\newcommand{\LXXi}[1]{\ensuremath{\bL_{\mathit{XX}({#1})}}}
\newcommand{\LXX}{\ensuremath{\bL_\mathit{XX}}}
\newcommand{\LXZi}[1]{\ensuremath{\bL_{\mathit{XZ}({#1})}}}
\newcommand{\LXZ}{\ensuremath{\bL_\mathit{XZ}}}
\newcommand{\LZZi}[1]{\ensuremath{\bL_{\mathit{ZZ}({#1})}}}
\newcommand{\LZZ}{\ensuremath{\bL_\mathit{ZZ}}}
\newcommand{\LZZoo}{\ensuremath{\bL_{\mathit{ZZ}11}}}
\newcommand{\LZZot}{\ensuremath{\bL_{\mathit{ZZ}12}}}
\newcommand{\LZZtt}{\ensuremath{\bL_{\mathit{ZZ}22}}}
\newcommand{\bOmega}{\ensuremath{\bm{\Omega}}}
\newcommand{\bPhi}{\ensuremath{\bm{\Phi}}}
\newcommand{\bR}{\ensuremath{\bm{R}}}
\newcommand{\bX}{\ensuremath{\bm{X}}}
\newcommand{\bZ}{\ensuremath{\bm{Z}}}
\newcommand{\bbeta}{\ensuremath{\bm{\beta}}}
\newcommand{\bb}{\ensuremath{\bm{b}}}
\newcommand{\beps}{\ensuremath{\bm{\epsilon}}}
\newcommand{\dX}{\ensuremath{\bm{d}_{\mathit{X}}}}
\newcommand{\dZ}{\ensuremath{\bm{d}_{\mathit{Z}}}}
\newcommand{\dy}{\ensuremath{d_{\mathit{y}}}}
\newcommand{\lyXi}[1]{\ensuremath{\bm{\ell}_{\mathit{yX}(#1)}}}
\newcommand{\lyX}{\ensuremath{\bm{\ell}_\mathit{yX}}}
\newcommand{\lyZi}[1]{\ensuremath{\bm{\ell}_{\mathit{yZ}(#1)}}}
\newcommand{\lyZ}{\ensuremath{\bm{\ell}_\mathit{yZ}}}
\newcommand{\lyyi}[1]{\ensuremath{\bm{\ell}_{\mathit{yy}(#1)}}}
\newcommand{\lyy}{\ensuremath{\ell_\mathit{yy}}}
\newcommand{\btheta}{\ensuremath{\bm{\theta}}}
\newcommand{\by}{\ensuremath{\bm{y}}}
\newcommand{\bzer}{\ensuremath{\bm{0}}}