header.tex

\usepackage{amsmath,amsfonts,amssymb,graphicx}
\usepackage{pict2e}
\usepackage{curve2e}

%%%% parameters %%%%%%%%%%5
\newcommand\Wsat{W_{\mathrm{sat}}}
\newcommand\muIR{\mu_{IR}}
\newcommand\muEI{\mu_{EI}}
\newcommand\transmission{\beta}
\newcommand\seasAmplitude{a}
\newcommand\rainfallExponent{r}
\newcommand\muRS{\mu_{RS}}
\newcommand\vaccineEfficacy{\theta}
\newcommand\muBirth{\mu_S}
\newcommand\muDeath{\delta}
\newcommand\choleraDeath{\delta_{C}}
\newcommand\symptomFrac{f}
\newcommand\asymptomRelativeInfect{\epsilon}
\newcommand\asymptomRelativeShed{\epsilon_{W}}
\newcommand\Wbeta[1]{\beta_{W#1}}
\newcommand\Wremoval{\delta_W}
\newcommand\Wshed{\mu_W}
\newcommand\mixExponent{\nu}
\newcommand\sigmaProc{\sigma_{\mathrm{proc}}}
\newcommand\reportRate{\rho}
\newcommand\obsOverdispersion{\psi}
\newcommand\phaseParm{\phi}
\newcommand\transmissionTrend{\zeta}
\newcommand\Binit{\xi}
\newcommand\vaccClass{Z}
\newcommand\vaccCounter{z}
\newcommand\modelCounter{m}
\newcommand\Whur[1]{\beta_{W#1}^{hm}}
\newcommand\hHur[1]{h_{#1}^{hm}}
\newcommand\Iinit{I_{0,0}}
\newcommand\Einit{E_{0, 0}}
\newcommand\reportChange{\delta}
\newcommand\NBintercept{\alpha}
\newcommand\NBsize{\varphi}

\newcommand\figTitle{\bf}

\newcommand\missing{\hspace{6mm} ---}
\newcommand\fixed{\color{blue}}
\newcommand\demography{\bullet}

\newcommand\mytitle{Informing policy via dynamic models: Cholera in Haiti}
\newcommand\comma{{\hspace{-0.25mm},\hspace{-0.2mm}}}

%%%%%%%%%%%%%%%% START OF USER DEFINITIONS %%%%%%%%%%%%%%%5

\newcommand\siOnly[1]{} %% redefined for the supplement
\newcommand\msOnly[1]{#1} %% redefined for the supplement

\newcommand\code[1]{\texttt{#1}}
\usepackage{xurl}
% \usepackage[breaklinks]{hyperref}
\usepackage{makecell}
\usepackage{multirow}
\usepackage{multicol}
\usepackage[ruled,noline,linesnumbered]{algorithm2e}
% \usepackage{setspace}

%% EDITING MACROS
\usepackage{color}
\usepackage[section]{placeins}
\usepackage[normalem]{ulem}% to use \sout in feedback commands
\usepackage{bm}
% orange for EI
\definecolor{orange}{rgb}{1,0.5,0}
\newcommand\ei[2]{\sout{#1} \textcolor{orange}{#2}}
\newcommand\eic[1]{\textcolor{orange}{[#1]}}
% green for JW
\definecolor{green}{rgb}{0,0.5,0}
\newcommand\jw[2]{\sout{#1} \textcolor{green}{#2}}
\newcommand\jwc[1]{\textcolor{green}{[#1]}}
% purple for JJ
\definecolor{purple}{rgb}{0.5,0,1}
\newcommand\jj[2]{\sout{#1} \textcolor{purple}{#2}}
\newcommand\jjc[1]{\textcolor{purple}{[#1]}}
% cyan for AR
\definecolor{cyan}{rgb}{0,.5,.5}
\newcommand\ar[2]{\sout{#1} \textcolor{cyan}{#2}}
% \newcommand\arc[1]{\textcolor{cyan}{#1}}
% light brown for KT
\definecolor{lightbrown}{rgb}{0.5,0.5,0}
\newcommand\kt[2]{\sout{#1} \textcolor{lightbrown}{#2}}
\newcommand\ktc[1]{\textcolor{lightbrown}{#1}}

%% basic POMP definitions
\newcommand\Xspace{{\mathbb X}}
\newcommand\Yspace{{\mathbb Y}}
\newcommand\Thetaspace{\R^{\Thetadim}}
\newcommand\Xunitspace{{\scriptsize{\mathcal X}}}
\newcommand\Yunitspace{{\tiny{\mathcal Y}}}
\newcommand\hatTheta{\widehat{\Theta}}
\newcommand\Xdim{{\mathrm{dim}}(\Xspace)}
\newcommand\Ydim{{\mathrm{dim}}(\Yspace)}
\newcommand\Thetadim{P}
\newcommand\thetadim{p}
\newcommand\timeSet{{\mathbb T}}
\newcommand\data[1]{#1^*}

\newcommand\unitSpecific{\hspace{0.1mm}\mathrm{us}}
\newcommand\shared{\hspace{0.15mm}\mathrm{sh}}

% for algorithm pseudocode
\SetKwFor{For}{for}{:}{end}

%% for particle filters
\newcommand\unit{u}
\newcommand\altUnit{\tilde u}
\newcommand\Unit{U}
\newcommand\rep{i}
\newcommand\Rep{\mathcal{I}}
\newcommand\island{\rep}
\newcommand\Island{\Rep}
%\newcommand\txtisland{replicate}
\newcommand\altIsland{\tilde i}
\usepackage[mathscr]{euscript}

\renewcommand\time{n}
\newcommand\myvec[1]{\boldsymbol{#1}}
\newcommand\altTime{\tilde n}
\newcommand\Time{N}
\newcommand\Np{J}
\newcommand\np{j}
\newcommand\altNp{k}
\newcommand\altAltNp{\tilde j}
\newcommand\resampleIndex{r}
\newcommand\unitWeight{w}

%% for all iterated filtering algorithms
\newcommand\Nit{M}
\newcommand\nit{m}

%% customized math macros
\newcommand\prob{\mathbb{P}}
\newcommand\E{\mathbb{E}}
\newcommand\dd[1]{\mathrm{d}{#1}}
\newcommand\given{{\,\vert\,}}
\newcommand\equals{{{\,}={\,}}}
\newcommand\myequals{\hspace{0.5mm}{=}\hspace{0.5mm}}
\newcommand\myto{{\;:\;}}
\newcommand\seq[2]{{#1}\!:\!{#2}}
\newcommand\mydot{{\,\cdot\,}}
\newcommand\cp[2]{N_{\mathrm{#1}\mathrm{#2}}}
\newcommand\giventh{{\hspace{0.5mm};\hspace{0.5mm}}}
\newcommand\normal{\mathcal{N}}
\newcommand\argequals{{\,=\,}}
\newcommand\lags{c}
\newcommand\maxlag{\overline{c}}
\newcommand\nlfList{C}
\newcommand\bigO{\mathcal{O}}
\newcommand\loglik{\lambda}
\newcommand\loglikMC{\MC{\loglik}}
\newcommand\R{\mathbb{R}}
\newcommand\param{\,;}
\newcommand\mycolon{{\hspace{0.6mm}:\hspace{0.6mm}}}
\newcommand\MC[1]{#1^{\,\mbox{\tiny MC}}}
\newcommand\EMC{{\E}}
\newcommand\Var{\mathrm{Var}}
\newcommand\var{\Var}
\newcommand\Cov{\mathrm{Cov}}
\newcommand\cov{\Cov}
\newcommand\iid{\mathrm{iid}}
\newcommand\dist{d}
\newcommand\transpose{\top}

\newcommand\gnsep{,}

\def\lik{L}
\def\loglik{\ell}

%% THEOREM-LIKE ENVIRONMENTS
\usepackage{amsthm}
\newtheorem{prop}{Proposition}
\newtheorem{theorem}{Theorem}
\newtheorem{lemma}{Lemma}
\newtheorem{example}{Example}
\newtheorem{remark}{Remark}
\newtheorem{cor}{Corrolary}
\newtheorem{fact}{Fact}
\newtheorem{assumption}{Assumption}
\newtheorem{assumptionB}{Assumption}
\renewcommand\theassumption{A\arabic{assumption}}
\renewcommand\theassumptionB{B\arabic{assumptionB}}

\makeatletter
\AtBeginDocument{%
  \expandafter\renewcommand\expandafter\subsection\expandafter{%
    \expandafter\@fb@secFB\subsection
  }%
}
\makeatother

%% FOR PSEUDOCODE SETUP
\newcommand\mystretch{\rule[-2mm]{0mm}{5mm} }
\newcommand\asp{\hspace{4mm}}
\newcommand\codeIndent{\hspace{4mm}}

%%%%%%%%%%%%%%%% END OF USER DEFINITIONSS %%%%%%%%%%%%%%%

% \bibliographystyle{apalike}
\bibliographystyle{plos2015}
% \usepackage{natbib}
\usepackage{cite}
\usepackage{fullpage}
% \usepackage[aboveskip=1pt,labelfont=bf,labelsep=period,justification=raggedright,singlelinecheck=off]{caption}
% \usepackage[labelfont=bf,labelsep=period]{caption} % For some reason this doesn't work with .Rnw file, but it does with just the tex file, so after compiling you can edit this so that it works.
\renewcommand{\figurename}{Fig}

\newcommand\myeqref[1]{(\ref{#1})}

\renewcommand{\contentsname}{Supplementary Content}
\renewcommand{\refname}{References}
\renewcommand\thefigure{S-\arabic{figure}}
\renewcommand\thetable{S-\arabic{table}}
\renewcommand\thesection{S\arabic{section}}
% \renewcommand\thesection{\makebox[0.8em][l]{S}\arabic{section}}
\renewcommand\theequation{S\arabic{equation}}
\renewcommand\theprop{S\arabic{prop}}
\renewcommand\thelemma{S\arabic{lemma}}
\renewcommand\thealgocf{S\arabic{algocf}}

\makeatletter
\renewcommand*\l@section[2]{%
  \ifnum \c@tocdepth >\z@
    \addpenalty\@secpenalty
    % Space for the number
    \setlength\@tempdima{2.3em}%
    \begingroup
      \parindent \z@ \rightskip \@pnumwidth
      \parfillskip -\@pnumwidth
      % No bold in ToC
      \leavevmode \bfseries
      \advance\leftskip\@tempdima
      \hskip -\leftskip
      % Insert "S" before the section number
      #1\nobreak\hfil \nobreak\hb@xt@\@pnumwidth{\hss #2}\par
      \addvspace{1.15em}% Adjust space after each entry (double space)
    \endgroup
  \fi}
% Similar redefinition can be done for \l@subsection if needed.
\makeatother