config.tex

% \input{markdraft} # DRAFT
% \usepackage{showframe}\def\ShowFrameColor{\color{lightgray}} % DEBUG
%---------------------------------------------------------------------------------------------------
% fonts
\usepackage{mathtools,bm,newtxsf,underscore}
\usepackage[tabular,osf,sfdefault]{gandhi}
\usepackage[italic]{mathastext}
\usepackage[scale=.8]{FiraMono}
\usepackage{microtype}\DisableLigatures{shape=sc}
\let\obfseries\bfseries\renewcommand\bfseries{\boldmath\obfseries}
\usepackage[T1]{fontenc}
%---------------------------------------------------------------------------------------------------
% spacing
\frenchspacing
\setlength{\parskip}{1ex plus .2ex minus .2ex}
\setlength{\parindent}{0ex}
\renewcommand{\topfraction}{.85}
\renewcommand{\bottomfraction}{.7}
\renewcommand{\textfraction}{.15}
\renewcommand{\floatpagefraction}{.67}
\widowpenalty9999
\clubpenalty9999
%---------------------------------------------------------------------------------------------------
% footnotes + sections
\usepackage[marginal,bottom,stable]{footmisc}
\addtolength{\skip\footins}{2ex plus 1ex minus 1ex}
\setcounter{secnumdepth}{4}
\renewcommand{\paragraph}[1]{\par\textbf{#1.}\ }
%---------------------------------------------------------------------------------------------------
% frontmatter
\usepackage{xpatch}
\xpatchcmd{\maketitle}{\@title}%
  % {\@title\vfill\vfill\vfill\vfill}{}{} % for ProQuest
  {\@title\vfill\vfill\includegraphics[height=.2\textheight]{ut-crest}\vfill}{}{}
\newcommand{\singlespaced}[1]{%
  \pretocmd{#1}{\begingroup\singlespacing}{}{}%
  \apptocmd{#1}{\endgroup}{}{}}
\singlespaced{\tableofcontents}
\singlespaced{\listoffigures}
\singlespaced{\listoftables}
\newenvironment{acknowlist}
  {\begin{itemize}[leftmargin=2em,itemindent=-2em,parsep=0pt,label=]}{\end{itemize}}
\newcommand{\ack}[2]{\item #1 --- #2}
\let\contributions\acknowledgements
\let\endcontributions\endacknowledgements
\xpatchcmd{\contributions}{Acknowledgements}{Contributions}{}{}
%---------------------------------------------------------------------------------------------------
% headers
\makeatletter
\renewcommand{\headerstyle}[1]{\footnotesize\textsc{#1}}
\renewcommand*{\ps@headings}%
 {\let\@mkboth\markboth
  \let\@oddfoot\@empty
  \let\@evenfoot\@empty
  \def\@oddhead{\headerstyle{\rightmark\hfil\thepage}}%
  \def\sectionmark##1{\markright{%
      \if@mainmatter\headerstyle{\thesection\hskip.8em##1}\fi}}}
\makeatother
%---------------------------------------------------------------------------------------------------
% bibliography
\usepackage[
  style=numeric-comp,
  sorting=none,
  date=year,
  doi=false,
  url=true,
  isbn=false,
  eprint=false,
  natbib=true,
  backend=biber,
]{biblatex}
\addbibresource{/home/jesse/refs/library.bib}
\renewcommand{\bibfont}{\footnotesize}
\renewcommand*{\multicitedelim}{\addcomma\,}
\DeclareSourcemap{\maps[datatype=bibtex]{%
  \map{\step[fieldset=abstract,null]}}}
\DeclareSourcemap{\maps[datatype=bibtex]{%
  \map{\step[typesource=techreport,typetarget=report]}}}
\DeclareFieldFormat{url}{\url{#1}}
\renewbibmacro{in:}{}
\newcommand{\printchapterbibliography}[1][]{} % TODO: (~) remove
\defbibnote{bibhead}{\markboth{\refname}{\refname}}
\newcommand{\printfullbibliography}{%
  \printbibliography[prenote=bibhead,heading=bibintoc,title=\refname]}
%---------------------------------------------------------------------------------------------------
% colors
\usepackage{xcolor}
\input{colors}
%---------------------------------------------------------------------------------------------------
% hyperlinks
\usepackage[
  colorlinks,
  linkcolor=link,
  citecolor=cite,
  urlcolor=url,
]{hyperref}
\usepackage{nameref}
\makeatletter
\hypersetup{pdftitle={\@title},pdfauthor={\@author}}
\makeatother
%---------------------------------------------------------------------------------------------------
% floatfoot
\newcommand{\floatfoot}[2][1]{\nopagebreak\vskip\abovecaptionskip\par
  \parbox{#1\linewidth}{\footnotesize#2}}
\newcommand{\ffpbar}[1][calibration target]{points and error bars: mean and 95\%~CI for each #1}
\newcommand{\ffbox}[1][model fits]{whiskers, boxes, and midlines: 95\%~CI, 50\%~CI, median of #1}
\newcommand{\ffribbon}[1][model fits]{ribbon and curve: range and median of #1}
\newcommand{\ffast}[1]{Asterisks denote significance of #1, where $p < 0.1$: *, $p < 0.01$: **, etc.}
\newcommand{\fffsw}[1]{%
  \foreach \year/\status in {2011/serologic,2014/self-reported}{
  \foreach \var/\lab in {f/factor,c/continuous}{
  \sfref{#1.\year.\var} \year, \status\ HIV status, \lab\ variables;}}}
\newcommand{\ffpops}{Low: lowest activity; Med: medium activity;
  LR/HR: lower/higher risk; FSW: female sex workers; Clients: of FSW}
\newcommand{\ffpopz}{Lower Risk: all women and men not involved in sex work;
  FSW: female sex workers; Clients: of FSW}
\newcommand{\fffit}{1000 model fits (top 1\% by likelihood among 100,000 sampled parameter sets)}
\newcommand{\ffpar}{Table~\ref{tab:par.defs} givs parameter definitions}
\newcommand{\fffoi}{Table~\ref{tab:foi.models} gives approach definitions}
\newcommand{\ffart}{Base case: \cashi by 2020;
  ``left behind'' counterfactual scenarios: \casmd overall by 2020,
  with reduced cascade (\caslo) among FSW, clients of FSW, both, or neither}
\newcommand{\ffcas}{PLHIV: people living with HIV; VLS: viral load unsuppressed}
\newcommand{\ffwiw}{median numbers of infections across all model fits shown}
\newcommand{\fftpaf}{TPAF: transmission population attributable fraction, \sref{foi.exp.model.tpaf}}
%---------------------------------------------------------------------------------------------------
% figures
\usepackage{subcaption,graphicx,lscape}
\graphicspath{
  {front/fig/}
  {intro/fig/}
  {sr/fig/}
  {model/fig/}{model/fig/fsw/}{model/fig/fit/}
  {foi/fig/}{foi/fig/fit/}
  {art/fig/}}
\newcommand{\subcapoverlap}{\captionsetup[subfigure]{skip=-\baselineskip,margin=0pt}}
\newcommand{\iterfig}[6][]{\vskip\textfloatsep
  \setcaptiontype{figure}
  \foreach \var/\cap in #4{
    \parbox[t]{\dimexpr#3\linewidth-1em}{%
      \includegraphics[width=\linewidth]{#2.\var}
      \subcaption{\cap}\label{fig:#2.\var}}\ifx1#3\par\fi}
  \caption{#5}\label{fig:#2#1}\floatfoot{#6}}
\def\fitscale{.475}
%---------------------------------------------------------------------------------------------------
% tables
\usepackage{booktabs,longtable,rotating,multicol,multirow,csvsimple}
\newcommand{\tn}[1]{\textsuperscript{\rlap{\,#1}}}
\newcommand{\tnt}[2][*]{\textsuperscript{#1\,}{#2}}
\newcommand{\tabitem}{{\textbullet}\hskip.5em}
\renewcommand{\d}{\hphantom{0}}
\newcommand{\m}{\hphantom{-}}
\newcommand{\s}{\rlap{\tsup{*}}}
\newcommand{\vsig}{\llap{$<$}0.001\s\xspace}
\makeatletter
\let\olongtable\longtable\let\oendlongtable\endlongtable
\renewenvironment{longtable}[5][]{% fmt,cols,caption,header,footer
  \begingroup\singlespacing#1
  \olongtable[#1]{#2}\caption{#3} \\
  \toprule #4 \\ \midrule \endfirsthead
  \multicolumn{\LT@cols}{l}{\dots~continued} \\ \midrule #4 \\ \midrule \endhead
  \midrule \multicolumn{\LT@cols}{l}{continued~\dots} \endfoot
  \bottomrule \noalign{\vskip\abovecaptionskip} \multicolumn{\LT@cols}{l}{%
    \begin{minipage}{\dimexpr\linewidth-2\tabcolsep} \footnotesize#5 \end{minipage}} \endlastfoot
  }{\oendlongtable\endgroup}
\makeatother
%---------------------------------------------------------------------------------------------------
% acronyms & symbols
\usepackage{xspace,pifont}
\newcommand{\eg}{{e.g.,}\xspace}
\newcommand{\ie}{{i.e.,}\xspace}
\newcommand{\nb}{{n.b.}\xspace}
\newcommand{\vs}{{vs.}\xspace}
\newcommand{\ttilde}{\textasciitilde\,}
\newcommand{\hivp}{HIV$+$\xspace}
\newcommand{\hivn}{HIV$-$\xspace}
\newcommand{\hivu}{HIV\,?\,\xspace}
\newcommand{\REF}{\textsc{ref}\xspace}
\newcommand{\wph}{\textsc{wph}\xspace}
\newcommand{\bph}{\textsc{bph}\xspace}
\newcommand{\ir}{\textsc{ir}\xspace}
\newcommand{\ip}{\textsc{ip}\xspace}
\newcommand{\covid}{COVID-19\xspace}
\newcommand{\ird}{\textcolor{ird}{\textsc{ird}}\xspace}
\newcommand{\iry}{\textcolor{iry}{\textsc{iry}}\xspace}
\newcommand{\ipy}{\textcolor{ipy}{\textsc{ipy}}\xspace}
\newcommand{\epa}{\textcolor{epa}{\textsc{epa}}\xspace}
\newcommand{\caslo}{\textcolor{caslo}{\mbox{60-40-80}}\xspace}
\newcommand{\casmd}{\textcolor{casmd}{\mbox{80-80-90}}\xspace}
\newcommand{\cashi}{\textcolor{cashi}{\mbox{95-95-95}}\xspace}
\newcommand{\yes}{\ding{51}\xspace}
\newcommand{\no}{\ding{55}\xspace}
\renewcommand{\ast}{\raisebox{-.5ex}{*}\xspace}
\newcommand{\p}{\bar{p}}
\newcommand{\E}{\txn{E}}
%---------------------------------------------------------------------------------------------------
% short text styles
\newcommand{\tdef}[2]{#1{\,:\,}\txn{#2}}
\newcommand{\opname}[1]{\operatorname{#1}\,}
\newcommand{\tsub}[1]{\textsubscript{#1}}
\newcommand{\tsup}[1]{\textsuperscript{#1}}
\newcommand{\shortquote}[1]{``\emph{#1}''}
\newcommand{\hreftt}[2][https://]{\href{#1#2}{\texttt{#2}}}
\newcommand{\sref}[1]{\S\,\ref{#1}}
\newcommand{\sfref}[1]{(\subref{#1})}
\renewcommand{\eqref}[1]{Eq.~(\ref{#1})}
\newcommand{\eqrefs}[2]{Eqs.~(\ref{#1})~and~(\ref{#2})}
\newcommand{\eqrefr}[2]{Eqs.~(\ref{#1})--(\ref{#2})}
\newcommand{\ifempty}[3]{\if\relax\detokenize{#1}\relax#2\else#3\fi}
\newcommand{\cdf}[2]{\ifempty{#2}{CD4\,$>$\,#1}{\ifempty{#1}{}{#1\,$<$\,}CD4\,$<$\,#2}}
\renewenvironment{quote}{\list{}{\rightmargin=\leftmargin\topsep=0pt}\item\relax\itshape}{\endlist}
\let\txn\textnormal
%---------------------------------------------------------------------------------------------------
% itemize & enumerate
\usepackage{enumitem}
\setitemize{itemsep=0pt,topsep=0pt}
\setenumerate{itemsep=0pt,topsep=0pt}
%---------------------------------------------------------------------------------------------------
% systematic review styles
\usepackage{tikz}
\newcommand{\srds}[1]{Dataset~\hyperref{}{sr.dataset}{#1}{#1}}
\newcommand{\srt}[1]{{\ttfamily#1}}
\newcommand{\srcite}[1]{\quad\tabitem
    \parbox{3em}{\parencite{#1}}
    \parbox{3em}{\citeyear{#1}}
    \citeauthor{#1}}
\newenvironment{srcites}%
  {\begin{multicols}{2}\footnotesize\setlength\parskip{0pt}}%
  {\end{multicols}}
\usepackage{pdfpages}
% end