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4mbapreamble.tex
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4mbapreamble.tex
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%% page layout
\textheight 9in
\textwidth 6.5in
\topmargin -0.5in
\oddsidemargin 0in
\evensidemargin 0in
%\hoffset=-0.5in
\voffset=-0.25in
%% packages
\usepackage{scrtime} % for \thistime (this package MUST be listed first!)
\usepackage{amsmath} % essential for cases environment
\usepackage{amsthm} % for theorems and proofs
\usepackage{amsfonts} % mathbb
\usepackage{graphics,graphicx}
\usepackage{multirow} % fancy tables
\usepackage{wasysym} % circle symbols (including half-filled circles)
\usepackage{enumerate} % fancier enumeration (e.g., a,b,c, ...)
%\usepackage{xcolor}
\usepackage{color}
\newcommand{\de}[1]{{\color{red}{\bfseries DE:} #1}}
%% for solutions to multiple choice questions:
\newcommand{\correct}{{\color{blue}\fbox{\color{red}\checkmark} }}
%% macros
\newcommand{\reals}{\mathbb{R}}
\newcommand{\term}[1]{{\bfseries\slshape #1}}
\newcommand{\Ker}{{\text{Ker}\,}}
\newcommand{\Range}{{\text{Range}\,}}
\newcommand{\diag}{{\text{diag}}}
\newcommand{\alg}{{\text{alg}}}
\newcommand{\geom}{{\text{geom}}}
\newcommand{\norm}[1]{\left\|#1\right\|}
\newcommand{\abs}[1]{\left|#1\right|}
\newcommand{\R}{{\cal R}}
\newcommand{\G}{{\cal G}}
\newcommand{\eps}{\varepsilon}
\newcommand{\B}{\cal B}
\newcommand{\Tinf}{T_\textrm{inf}}
\newcommand{\Shat}{{\hat{S}}}
\newcommand{\Ihat}{{\hat{I}}}
\newcommand{\ie}{\emph{i.e., }}
\newcommand{\eg}{\emph{e.g., }}
\newcommand{\Rlogo}{\protect\includegraphics[height=2ex,keepaspectratio]{images/Rlogo.pdf}\xspace}
\newcommand{\XPPAUT}{\texttt{XPPAUT}\xspace}
\newcommand{\etal}{\textit{et al}.\xspace}
\newcommand\emphblue[1]{\emph{\color{blue}#1}}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% from feverpreamble.tex %%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage{amssymb,latexsym,amsmath,setspace}
%%\usepackage[colorlinks,linkcolor=blue]{hyperref}
\usepackage[colorlinks=true,allcolors=blue]{hyperref}
%%\usepackage[colorlinks]{hyperref}
\usepackage{xspace}
\usepackage{graphics,graphicx}
\usepackage{subfigure}
\usepackage{lineno}
\usepackage{fancyhdr}
\usepackage[english]{babel} %% for texi2dvi ~ bug
\usepackage[normalem]{ulem}
\usepackage{tikz} % http://www.texample.net/tikz/examples/tikzdevice-demo/
% N.B. version 0.6.3 of tikzDevice from Rforge is required!!
%% improve figure caption typsetting: (see ~/tex/caption.pdf for manual)
\usepackage[footnotesize,bf]{caption}
\usepackage{placeins} % \FloatBarrier
% citation macros
\newcommand{\citen}[1]{\cite{#1}}
% comment macros
\usepackage{color}
\newcommand{\comment}[3]{\textcolor{#1}{\textbf{[#2: }\textit{#3}\textbf{]}}}
\newcommand{\david}[1]{\comment{blue}{DE}{#1}}
\newcommand{\paul}[1]{\comment{cyan}{PA}{#1}}
\newcommand{\ben}[1]{\comment{magenta}{BB}{#1}}
\newcommand{\needref}{{\textcolor{red}{[NEED REF]}}}
\newcommand{\TBD}{{\textcolor{red}{{\bf TBD}}}}
% remove comments
%\renewcommand{\comment}[3]{\relax}
% remove section headings
%\def\subsubsection*#1{\relax\nobreak}
% other macros
\newcommand{\avg}[1]{{\left\langle#1\right\rangle}}
\newcommand{\var}[1]{\textrm{var}\left(#1\right)}
\newcommand{\sem}[1]{\textrm{sem}\left(#1\right)}
\newcommand{\natinf}{{\mathcal I}}
\newcommand{\find}{f_{\textrm{i}}}
\newcommand{\fpop}{f_{\textrm{p}}}
\newcommand{\logit}{\textrm{logit}}
\newcommand{\sign}{\textrm{sign}}
\newcommand{\logistic}{\textrm{logistic}}
\def\AJE{{\it American Journal of Epidemiology\/}}
\newcommand{\code}[1]{{\tt #1}}
\newcommand{\magcode}[1]{{\tt\color{magenta}#1}}
\newcommand{\redcode}[1]{{\tt\color{red}#1}}
\newcommand{\blackcode}[1]{{\tt\color{black}#1}}
%%%%%%%%%%%%%%%%%%%
%% JOURNAL NAMES %%
%%%%%%%%%%%%%%%%%%%
\def\PNAS{PNAS}
\def\JAMA{JAMA}
\def\BMB{{\it Bulletin of Mathematical Biology\/}}
% references
\newcommand{\eref}[1]{Equation~\eqref{E:#1}}
\newcommand{\fref}[1]{Figure~\ref{F:#1}}
\newcommand{\tref}[1]{Table~\ref{T:#1}}
\newcommand{\sref}[1]{\S\ref{S:#1}}
% other macros
\newcommand{{\Reff}}{{\mathcal{R}}_{\rm eff}}
\newcommand{{\Sinit}}{S_{\rm init}}
\newcommand{\supp}{Supplementary Information}
\newcommand{\StoppedHere}{\bigskip\bigskip{\textcolor{red}{\hrule\centerline{\bfseries STOPPED HERE}\hrule}}\bigskip\bigskip}
\newcommand{\colvec}[2]{\begin{pmatrix}#1\\#2\end{pmatrix}}
\newcommand{\diagmat}[3]{\begin{pmatrix}#1&0&0\\0&0\\0&0\end{pmatrix}}
\newcommand{\solution}[1]{{\hfill\break\vspace{-0.5\baselineskip}\break\color{blue}\emph{Solution: }#1}}
\newcommand{\tr}{\text{tr}}
\newcommand{\thickredline}{\bigskip{\color{red}\hrule height 5pt}\bigskip}
%% for assignment 3:
\newtheorem{theorem}{Theorem}
\newtheorem{remark}{Remark}
\newcommand{\openset}{{\mathcal O}}
\newcommand{\C}{{\mathcal C}}
% Journal Names
% -------------
% \def\MNRAS{{\it Mon.\ Not.\ R.\ astr.\ Soc.\/}}
\def\MNRAS{{\it Monthly Notices of the Royal Astronomical Society\/}}
% \def\ApJ{{\it Astrophys.~J.\/}}
\def\ApJ{{\it The Astrophysical Journal\/}}
% \def\Interface{{\it J.\ R.\ Soc.\ Lond.\/ \rm Interface}}
\def\Interface{{\it Journal of the Royal Society of London, \rm Interface}}
% \def\ProcA{{\it Proc.\ R.\ Soc.\ Lond.\/ \rm A}}
\def\ProcA{{\it Proceedings of the Royal Society of London, Series\/ \rm A}}
% \def\ProcB{{\it Proc.\ R.\ Soc.\ Lond.\/ \rm B}}
\def\ProcB{{\it Proceedings of the Royal Society of London, Series\/ \rm B}}
% \def\TransB{{\it Phil.\ Trans.\ R.\ Soc.\ Lond.\/ \rm B}}
\def\TransB{{\it Philosophical Transactions of the Royal Society of London, Series\/ \rm B}}
\def\TREE{{\it Trends in Ecology and Evolution\/}}
% \def\JTB{{\it J.\ theor.\ Biol.\/}}
\def\JTB{{\it Journal of Theoretical Biology\/}}
% \def\BE{{\it Behav.\ Ecol.\/}}
\def\BE{{\it Behavioural Ecology\/}}
% \def\BES{{\it Behav.\ Ecol.\ Sociobiol.\/}}
\def\BES{{\it Behavioural Ecology and Sociobiology\/}}
% \def\BJLS{\it Biol.\ J.\ Linn.\ Soc.\/}}
\def\BJLS{{\it Biological Journal of the Linnean Society\/}}
\def\Nature{{\it Nature\/}}
\def\Science{{\it Science\/}}
\def\Lancet{{\it The Lancet\/}}
\def\LancetID{{\it Lancet Infectious Diseases\/}}
% \def\PNAS{{\it Proc.\ Natl.\ Acad.\ Sci.\ USA}}
\def\PNAS{{\it PNAS -- Proceedings of the National Academy of Sciences of the
U.S.A.}}
\def\PLoSMed{{\it PLoS Medicine\/}}
\def\PLoSCB{{\it PLoS Computational Biology\/}}
\def\EID{{\it Emerging Infectious Diseases\/}}
\def\BMB{{\it Bulletin of Mathematical Biology\/}}
\def\AJE{{\it American Journal of Epidemiology\/}}
\def\TPB{{\it Theoretical Population Biology\/}}
\def\JRSS{{\it Journal of the Royal Statistical Society\/}}
\def\JRSSB{{\it Journal of the Royal Statistical Society Series B\/}}
\def\IRV{{\it Influenza and Other Respiratory Viruses\/}}
\def\JAMA{{\it JAMA -- Journal of the American Medical Association\/}}
\def\JGLR{{\it Journal of Great Lakes Research\/}}
\def\NEJM{{\it New England Journal of Medicine\/}}
\def\JMB{{\it Journal of Mathematical Biology\/}}
\def\Interface{{\it Journal of the Royal Society Interface\/}}
\def\THEE{{\it Theoretical Ecology\/}}
\def\Annals{{\it Annals of Internal Medicine\/}}
\def\PRL{{\it Physical Review Letters\/}}
\def\PRX{{\it Physical Review X\/}}
\def\NAMS{{\it Notices of the American Mathematical Society\/}}