Thesis.tex

% Unfortunately for the contents to contain  the "Parts" lines successfully, hyperref needs to be disabled.
\documentclass[nohyper,nobib,a4,16pt]{tufte-book} %nobib

% There are usefull references heres: https://github.com/lalider/tufte-latex-thesis/blob/master/main.pdf

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% BOOK DATA %%%%%%%%%%%%%%
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\title[PhD Thesis: infectious disease dynamics modeling towards informed control decisions]{Modeling infectious disease \\ dynamics towards informed \\ public health interventions: \\ applications on \textsc{covid}-19 and cholera}

\date{\today}
\author[Joseph Lemaitre]{Joseph \ Lemaitre}
\publisher{REMOVE THIS TITLE PAGE AND REPLACE WITH OFFICIAL, PLEASE :)}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% PACKAGES %%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[utf8]{inputenc}
 \usepackage{pdfpages} % Include pdfs directly
 \usepackage[ruled,vlined]{algorithm2e} % algorithms
 \usepackage{nameref} % named references 
 \usepackage{url}
 \usepackage{ebgaramond} % Font I use, let's go baroque
 \usepackage[cmintegrals,cmbraces]{newtxmath}
 \usepackage{ebgaramond-maths} %exist for math too
\usepackage{booktabs}  % For nicely typeset tabular material
\usepackage{tabularx}
\usepackage{units}
\usepackage{xargs} % several argument in functions (needed for cite)
\usepackage[toc,page]{appendix}
%\usepackage{emoji} % I'd love to have emojis, but it doesn't work
%\setemojifont{TwemojiMozilla}
  % Set up the spacing using fontspec features
%\renewcommand\allcapsspacing[1]{{\addfontfeature{LetterSpace=15}#1}}
% \renewcommand\smallcapsspacing[1]{{\addfontfeature{LetterSpace=10}#1}}
\renewcommand{\epsilon}{\varepsilon} % because eb garamond doesn't have epsilon

% math stuff:
%\usepackage{amssymb} % does not play well with garamond math
\usepackage{amsbsy}
\usepackage{makecell}
\usepackage{amsmath}
\usepackage{bm}

%\usepackage[multiple]{footmisc} % several footnotes with delimiters --> breaks stuff

% For graphics / images
\usepackage{graphicx}
\setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio}

% https://tex.stackexchange.com/questions/5017/center-column-with-specifying-width-in-table-tabular-enviroment define x for centered p in tabularx
\usepackage{array}
\newcolumntype{x}[1]{>{\centering\arraybackslash\hspace{0pt}}p{#1}}


%  margin figure caption header should to be smaller to remove this weird size diperempty:
% adapted from https://tex.stackexchange.com/questions/319345/change-font-size-in-caption-for-selected-figures, should post it there
\usepackage{caption}
\newcommand{\margincaption}[2][1={}]{%
  \captionsetup{font=footnotesize}%
  \caption[#1]{#2}}
% The fancyvrb package lets us customize the formatting of verbatim
% environment, so a slightly smaller font is used.
\usepackage{fancyvrb}
\fvset{fontsize=\normalsize}

% provide \FloatBarrier and ensure that floats are placed within their section (can remove this option \usepackage[section]{placeins})
\usepackage{placeins}


% lower case label for figure and tables:
\usepackage[tablename=tab., figurename=fig.]{caption}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%% FRONTMATTER %%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% section in table of content
\setcounter{tocdepth}{3}
% pdf bookmarks, that are open to level 2
\usepackage[open,openlevel=2]{bookmark} %open up to level 2 by default
% Numbered chapters 
\setcounter{secnumdepth}{0}
%No link in TOC, that breaks tuftebook
\makeatletter
\let\Hy@linktoc\Hy@linktoc@none
\makeatother

% Prints an epigraph and speaker in sans serif, all-caps type.
\newcommand{\openepigraph}[2]{%
  %\sffamily\fontsize{14}{16}\selectfont
  \begin{fullwidth}
  \sffamily\large
  \begin{doublespace}
  \noindent\allcaps{#1}\\% epigraph
  \noindent\allcaps{#2}% author
  \end{doublespace}
  \end{fullwidth}
}
% Inserts a blank page
\newcommand{\blankpage}{\newpage\hbox{}\thispagestyle{empty}\newpage}

%%%% Kevin Godny's code for title page and contents from https://groups.google.com/forum/#!topic/tufte-latex/ujdzrktC1BQ
\makeatletter
\renewcommand{\maketitlepage}{%
\begingroup%
\setlength{\parindent}{0pt}
{\fontsize{20}{20}\selectfont\textit{\@author}\par}

%\vspace{1.75in}{\fontsize{36}{54}\selectfont\@title\par}
\vspace{1.75in}{\fontsize{30}{44}\selectfont\@title\par}

\vspace{0.5in}{\fontsize{14}{14}\selectfont\textsf{\smallcaps{\@date}}\par}

\vfill{\fontsize{14}{14}\selectfont\text{\@publisher}\par}

\thispagestyle{empty}
\endgroup
}
\makeatother

\titlecontents{part}%
    [0pt]% distance from left margin
    {\addvspace{0.25\baselineskip}}% above (global formatting of entry)
    {\allcaps{Part~\thecontentslabel}\allcaps}% before w/ label (label = ``Part I'')
    {\allcaps{Part~\thecontentslabel}\allcaps}% before w/o label
    {}% filler and page (leaders and page num)
    [\vspace*{0.5\baselineskip}]% after

\titlecontents{chapter}%
    [4em]% distance from left margin
    {}% above (global formatting of entry)
    {\contentslabel{2em}\textit}% before w/ label (label = ``Chapter 1'')
    {\hspace{0em}\textit}% before w/o label
    {\qquad\thecontentspage}% filler and page (leaders and page num)
    [\vspace*{0.5\baselineskip}]% after
%%%% End additional code by Kevin Godby


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%% BIBLIOGRAPHY & CITATION %%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\usepackage[backend=biber,doi=false,isbn=false,url=false,eprint=false,style=verbose,citestyle=authoryear,maxbibnames=999,maxcitenames=1,citetracker=true,pagetracker=true,uniquename=false]{biblatex}%,firstinits=true, before: authoryear-comp; unique name is false :)
\addbibresource{../ZoteroLibUpdated/ZoteroLibUpdated.bib}
%\addbibresource{references.bib}

% Remove the In: if there is no journal title. But if not in my defined shortcite, it means that the publication type is ill-defined (should be online, or something without journal)
% Thanks to https://tex.stackexchange.com/questions/502657/how-to-remove-in-from-bibliography-if-there-is-no-journal-information
\renewbibmacro*{in:}{%
  \iffieldundef{journaltitle}
    {}
    {\printtext{\bibstring{in}\intitlepunct}}}
% remove it altogher
%\renewbibmacro*{in:}{;}
% a fullcite command described by removing stuff
\DeclareCiteCommand{\fullcite}
  {\usebibmacro{prenote}}
  {\clearfield{month}\clearfield{day}\clearfield{pages}\clearfield{volume}\clearfield{number}\clearfield{issue}\clearfield{urlyear}\clearfield{urlmonth}\clearfield{url}\clearfield{pagetotal}%\clearfield{title}\clearfield{journaltitle}%
   \usedriver
     {\DeclareNameAlias{sortname}{default}}
     {\thefield{entrytype}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}
  
    \DeclareCiteCommand{\fullcite}
  {\usebibmacro{prenote}}
  {%
     \printnames[family]{labelname}% \printnames[given-family]{labelname}
     \setunit{\addcomma\space}%
     \printfield{title}%
     \setunit{\addspace}%addedme
  \usebibmacro{in:}%addedme
  \setunit{\addspace}%addedme
     \printfield{journaltitle}%
     \setunit{\addspace}%
     \printtext[parens]{%
       \printfield{year}}}%printdate
  {\multicitedelim}
  {\usebibmacro{postnote}}
  
  % a fullcite command described by adding stuff
  % Thanks https://tex.stackexchange.com/questions/490049/towards-a-concise-fullcite-command (also:https://tex.stackexchange.com/questions/479590/change-journaltitle-to-italics-in-fullcite, https://tex.stackexchange.com/questions/339681/abbreviate-journal-title-in-fullcite-command)
  \DeclareCiteCommand{\fullciteshorta}
  {\usebibmacro{prenote}}
  {%
     \printnames[family]{labelname}% \printnames[given-family]{labelname}
     \setunit{\addcomma\space}%
  %
     \printfield{journaltitle}%
     \setunit{\addspace}%
     \printtext[parens]{%
       \printfield{year}}}%printdate
  {\multicitedelim}
  {\usebibmacro{postnote}}
  
  \newbibmacro{aycite}{%
  \defcounter{maxnames}{1}%
  \ifnameundef{labelname}
    {\printfield{labeltitle}%
     \setunit{\printdelim{nonameyeardelim}}}
    {\printnames[family]{labelname}%
     \setunit{\printdelim{nameyeardelim}}}
  \printtext[bibhyperref]{\printlabeldateextra}}
  
\DeclareCiteCommand{\fullciteshortb}
  {\usebibmacro{prenote}}%
  {\usebibmacro{citeindex}%
   \usebibmacro{aycite}}
  {\multicitedelim}
  {\usebibmacro{postnote}} 

  %[][-\value{listtotal}]
  % from me: Remove the visited on https://tex.stackexchange.com/questions/400384/how-to-disable-biblatex-showing-visited-on-on-the-references
%\AtEveryBibitem{
  %  \clearfield{urlyear}
    %\clearfield{urlmonth}
%}
% Only year
%\AtEveryBibitem{\clearfield{month}}
%\AtEveryBibitem{}
%\AtEveryCitekey{\clearfield{month}\clearfield{day}\clearfield{pages}\clearfield{volume}\clearfield{number}\clearfield{issue}\clearfield{urlyear}\clearfield{urlmonth}\clearfield{pagetotal}\clearfield{publication}} % Remove day only in fullcite

\renewcommandx{\cite}[3][1={0pt},2={}]{\sidenote[][#1]{\fullcite[#2]{#3}.}}
\newcommandx{\shortcite}[3][1={0pt},2={}]{\sidenote[][#1]{\fullciteshortb[#2]{#3}.}}

% from me: short citation in sideline: https://tex.stackexchange.com/questions/414716/options-for-styling-fullcite
% No space: https://tex.stackexchange.com/questions/25891/fullcite-without-indent-in-biblatex ---> DELETED

%% Define \longfullcite to include all authors (https://tex.stackexchange.com/questions/142148/typeset-one-citation-with-all-authors)
\makeatletter
\DeclareCiteCommand{\longfullcite}
  {\usebibmacro{prenote}}
  {\usedriver
     {\c@maxnames\blx@maxbibnames\relax
      \DeclareNameAlias{sortname}{default}}
     {\thefield{entrytype}}}
  {\multicitedelim}
  {\usebibmacro{postnote}}
\makeatother

% Maybe this, but seems overkill: https://tex.stackexchange.com/questions/71526/repeat-the-same-reference-in-footnote-on-different-pages/71566#71566

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%% HEADINGS %%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% --> I want titles ittle in Small capitals
\usepackage{titlesec}
%\usepackage{titletoc}
% Display instead of hang makes it on two line: Chapter 1\\blabla
\makeatletter
\titleformat{\chapter}[display]{\huge\scshape}{\@chapapp~\thechapter}{1em}{}%[\vspace{2ex}\titlerule]
\titleformat{\section}{\Large\scshape}{\thesection}{1em}{}
\titleformat{\subsection}{\large\scshape}{\thesubsection}{1em}{}
\titleformat{\paragraph}[runin]{\scshape}{\theparagraph}{}{}
\makeatother

% Table of contents. works well but should not use tocloft with titlesec
\usepackage[titles]{tocloft}
\renewcommand\cftchapfont{\scshape}
\renewcommand\cftsecfont{\scshape}
\renewcommand\cftsubsecfont{\scshape}
\renewcommand{\cftdot}{} %if fot inside, will put dots

%part from Kevin Godby, 
\titlecontents{part}%
    [0pt]% distance from left margin
    {\addvspace{0.25\baselineskip}}% above (global formatting of entry)
    {\allcaps{Part~\thecontentslabel}\allcaps}% before w/ label (label = ``Part I'')
    {\allcaps{Part~\thecontentslabel}\allcaps}% before w/o label
    {}% filler and page (leaders and page num)
    [\vspace*{0.5\baselineskip}]% after


% manual list of abbreviation https://tex.stackexchange.com/questions/149708/simple-list-of-abbreviations-manually
\usepackage{calc}
\makeatletter
\newcommand{\tocfill}{\cleaders\hbox{$\m@th \mkern\@dotsep mu . \mkern\@dotsep mu$}\hfill}
\makeatother
\newcommand{\abbrlabel}[1]{\makebox[3cm][l]{#1\ \tocfill}}
\newenvironment{abbreviations}{\begin{list}{}{\renewcommand{\makelabel}{\abbrlabel}%
        \setlength{\labelwidth}{3cm}\setlength{\leftmargin}{\labelwidth+\labelsep}%
                                              \setlength{\itemsep}{0pt}}}{\end{list}}
%% This code creates the groups
% -----------------------------------------
\usepackage{etoolbox}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%% FULLFIGURE %%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% as per https://tex.stackexchange.com/questions/57413/change-caption-in-tufte-class-full-page-figure and https://tex.stackexchange.com/questions/229308/combining-tufte-latex-and-threeparttable/229419#229419 I want normal caption for full page figure... To do this: (I could have also used the fixed pull request by 
\RequirePackage{etoolbox}
\makeatletter
\newif\if@tufte@margtab\@tufte@margtabfalse
\AtBeginEnvironment{margintable}{\@tufte@margtabtrue}
\AtEndEnvironment{margintable}{\@tufte@margtabfalse}
\newcommand{\classiccaptionstyle}{%
    \long\def\@caption##1[##2]##3{%
        \par
        \addcontentsline{\csname ext@##1\endcsname}{##1}%
        {\protect\numberline{\csname the##1\endcsname}{\ignorespaces ##2}}%
        \begingroup
        \@parboxrestore
        \if@minipage
        \@setminipage
        \fi
        \normalsize
        \@makecaption{\csname fnum@##1\endcsname}{\ignorespaces ##3}\par
        \endgroup}
    \long\def\@makecaption##1##2{%
        \vskip\abovecaptionskip
        \sbox\@tempboxa{\@tufte@caption@font##1: ##2}%
        \ifdim \wd\@tempboxa >\hsize
        \@tufte@caption@font\if@tufte@margtab\@tufte@caption@justification\fi##1: ##2\par
        \else
        \global \@minipagefalse
        \hb@xt@\hsize{\hfil\box\@tempboxa\hfil}%
        \fi
        \vskip\belowcaptionskip}
       \setcaptionfont{\normalfont} % To have the rigght captio.n size
    \let\caption\@tufte@orig@caption%
    \let\label\@tufte@orig@label}
\makeatother


\newenvironment{fwfigure}{%
    \begin{figure*}[h!]
        \classiccaptionstyle
  }{\end{figure*}}
  \newenvironment{fwtable}{%
    \begin{table*}[h!]
        \classiccaptionstyle
  }{\end{table*}}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%% MISC %%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Prints argument within hanging parentheses (i.e., parentheses that take
% up no horizontal space).  Useful in tabular environments.
\newcommand{\hangp}[1]{\makebox[0pt][r]{(}#1\makebox[0pt][l]{)}}
% Prints an asterisk that takes up no horizontal space.
% Useful in tabular environments.
\newcommand{\hangstar}{\makebox[0pt][l]{*}}
% Prints a trailing space in a smart way.
\usepackage{xspace}
\newcommand{\hairsp}{\hspace{1pt}}% hair space
\newcommand{\ie}{\textit{i.\hairsp{}e.}\xspace}
\newcommand{\eg}{\mbox{\textit{e.\hairsp{}g.}}\xspace}
\newcommand{\na}{\quad--}% used in tables for N/A cells

\newcommand{\eqname}[1]{\tag*{#1}} %tag equations by name
% boxes
\usepackage[most]{tcolorbox}
\newtcolorbox{mybox}[1]{
    tikznode boxed title,
    enhanced,
    breakable, 
    arc=0mm,
    interior style={white},
    attach boxed title to top center= {yshift=-\tcboxedtitleheight/2},
    fonttitle=\bfseries,
    colbacktitle=white,coltitle=black,
    boxed title style={size=normal,colframe=white,boxrule=0pt},
    title={#1}}
%longer pages
\usepackage{geometry}
 \geometry{
 a4paper,
textheight=690pt,
 }

%Hyperref likes to be loaded last
\usepackage{hyperref}
 % prevent hyperref from destroying my lettrines https://tex.stackexchange.com/questions/561651/eb-garamond-initials-and-hyperref-package
%\DeclareTextFontCommand{\textin}{\initials}
%\usepackage{lettrine}
%\setcounter{DefaultLines}{5}
%\renewcommand{\LettrineFontHook}{\initials}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%% YAML LISTING %%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% from https://tex.stackexchange.com/questions/152829/how-can-i-highlight-yaml-code-in-a-pretty-way-with-listings
\usepackage[dvipsnames]{xcolor}
\usepackage{listings}
\newcommand\YAMLcolonstyle{\color{darkgray}\mdseries\small}
\newcommand\YAMLkeystyle{\color{darkgray}\mdseries\ttfamily\small}
\newcommand\YAMLvaluestyle{\color{orange}\mdseries\small}
\makeatletter
% here is a macro expanding to the name of the language
% (handy if you decide to change it further down the road)
\newcommand\language@yaml{yaml}
\expandafter\expandafter\expandafter\lstdefinelanguage
\expandafter{\language@yaml}
{
  keywords={true,false,null,y,n},
  keywordstyle=\color{darkgray}\bfseries,
  basicstyle=\YAMLkeystyle,                                 % assuming a key comes first
  sensitive=false,
  comment=[l]{\#},
  morecomment=[s]{/*}{*/},
  commentstyle=\color{purple}\ttfamily,
  stringstyle=\YAMLvaluestyle\ttfamily,
  moredelim=[l][\color{orange}]{\&},
  moredelim=[l][\color{magenta}]{*},
  moredelim=**[il][\YAMLcolonstyle{:}\YAMLvaluestyle]{:},   % switch to value style at :
  morestring=[b]',
  morestring=[b]",
  literate =    {---}{{\ProcessThreeDashes}}3
                {>}{{\textcolor{red}\textgreater}}1     
                {|}{{\textcolor{red}\textbar}}1 
                {\ -\ }{{\mdseries\ -\ }}3,
}
% switch to key style at EOL
\lst@AddToHook{EveryLine}{\ifx\lst@language\language@yaml\YAMLkeystyle\fi}
\makeatother
\newcommand\ProcessThreeDashes{\llap{\color{cyan}\mdseries-{-}-}}

%https://tex.stackexchange.com/questions/560991/change-font-color-of-appendices-page-that-appears-with-the-appendix-package
\renewcommand\appendixpagename{\normalfont  \Huge \textsc{Appendices}}


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%% DOC %%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}

\frontmatter

\input{frontmatter}
\begin{fullwidth}
\pdfbookmark[chapter]{\contentsname}{toc}
\tableofcontents
\addcontentsline{toc}{chapter}{List of Figures}\markboth{List of Figures}{}
\listoffigures
\addcontentsline{toc}{chapter}{List of Tables}\markboth{List of Tables}{}
\listoftables
\end{fullwidth}
\mainmatter
\input{introduction}
%%\input{matmet}
\input{cholera} % 1
\input{cholera-rainfall} % 2
\input{cholera-haiti-ocv} % 3
\input{covid-pipeline-reports} % 4
\input{covid-switzerland-npi} % 5
\input{covid-italy-ocp} % 6
\input{conclusions}

%%input{abbreviations}

\backmatter
\begin{appendices}\input{appendices}\end{appendices}


\begin{fullwidth}\addcontentsline{toc}{chapter}{Bibliography}\markboth{Bibliography}{}\printbibliography\end{fullwidth}

\blankpage

\addcontentsline{toc}{chapter}{Curriculum Vitae}\markboth{Curriculum Vitae}{}\includepdf[pages=-, pagecommand={\thispagestyle{empty}}]{academic_jl.pdf}

\end{document}