template.tex

% This is the default LaTeX template (default-1.17.0.2.tex) from the RMarkdown package, from:
% https://github.com/rstudio/rmarkdown/blob/master/inst/rmd/latex/default-1.17.0.2.tex
%
% New additions to the template are marked with "LCR"

%\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(papersize)$$papersize$paper,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$} %LCR
$if(book_size)$ % if the book is being rendered for print, force twoside option
\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(papersize)$$papersize$paper,twoside,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$} %LCR
$else$ % if not, force the oneside and a4paper options, which seem to be the only reasonable defaults
\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$a4paper,oneside,$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$} %LCR
$endif$
$if(fontfamily)$
\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
$else$
\usepackage{lmodern}
$endif$
$if(linestretch)$
\usepackage{setspace}
\setstretch{$linestretch$}
$endif$
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
  \usepackage[utf8]{inputenc}
$if(euro)$
  \usepackage{eurosym}
$endif$
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
$if(euro)$
  \newcommand{\euro}{€}
$endif$
$if(mainfont)$
    \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
$endif$
$if(sansfont)$
    \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
$endif$
$if(monofont)$
    \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$endif$]{$monofont$}
$endif$
$if(mathfont)$
    \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
$endif$
$if(CJKmainfont)$
    \usepackage{xeCJK}
    \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
$endif$
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(book_size)$ % LCR
\usepackage[paperwidth=170mm,paperheight=240mm]{geometry} % LCR %set to standard thesis size
$endif$
$if(geometry)$
$if(book_size)$ % LCR % if we've already invoked geometry
\geometry{$for(geometry)$$geometry$$sep$,$endfor$} %LCR % don't call usepackage again
$else$ %LCR
\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
$endif$
$endif$ %LCR
\usepackage{hyperref}
$if(colorlinks)$
\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
$endif$
\hypersetup{unicode=true,
$if(title-meta)$
            pdftitle={$title-meta$},
$endif$
$if(author-meta)$
            pdfauthor={$author-meta$},
$endif$
$if(keywords)$
            pdfkeywords={$for(keywords)$$keywords$$sep$; $endfor$},
$endif$
$if(colorlinks)$
            colorlinks=true,
            linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
            citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
            urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
$else$
            pdfborder={0 0 0},
$endif$
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
$if(lang)$
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
$if(babel-newcommands)$
  $babel-newcommands$
$endif$
\else
  \usepackage{polyglossia}
  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
$endfor$
\fi
$endif$
$if(natbib)$
\usepackage$if(natbiboptions)$[$for(natbiboptions)$$natbiboptions$$sep$,$endfor$]$endif${natbib}
\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
$endif$
$if(biblatex)$
\usepackage$if(biblio-style)$[style=$biblio-style$]$endif${biblatex}
$if(biblatexoptions)$\ExecuteBibliographyOptions{$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$}$endif$
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(listings)$
\usepackage{listings}
\newcommand{\passthrough}[1]{#1}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
$endif$
$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
$endif$
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
$if(indent)$
$else$
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
$endif$
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
$if(numbersections)$
\setcounter{secnumdepth}{5}
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(subparagraph)$
$else$
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
$endif$
$if(dir)$
\ifxetex
  % load bidi as late as possible as it modifies e.g. graphicx
  $if(latex-dir-rtl)$
  \usepackage[RTLdocument]{bidi}
  $else$
  \usepackage{bidi}
  $endif$
\fi
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \TeXXeTstate=1
  \newcommand{\RL}[1]{\beginR #1\endR}
  \newcommand{\LR}[1]{\beginL #1\endL}
  \newenvironment{RTL}{\beginR}{\endR}
  \newenvironment{LTR}{\beginL}{\endL}
\fi
$endif$

%%% Use protect on footnotes to avoid problems with footnotes in titles
\let\rmarkdownfootnote\footnote%
\def\footnote{\protect\rmarkdownfootnote}

%%% This fixes a TexLive 2019 change that broke pandoc template. Will also be fixed in pandoc 2.8 %LCR
% https://github.com/jgm/pandoc/issues/5801
\renewcommand{\linethickness}{0.05em}

$for(header-includes)$
$header-includes$
$endfor$


%%%%%%%%%%%%% BEGIN DOCUMENT %%%%%%%%%%%%%
\begin{document}

%% Page 0: cover  % LS 

% for some reason this cannot be in the preamble
\setlength{\abstitleskip}{-\absparindent}

$if(book_size)$
% No cover
\pagestyle{empty}
$else$
% Include the cover page
\pagestyle{empty}
\renewcommand{\thepage}{\CoverName} % make sure this page is "numbered" with a name, not as page 1 or I
\includepdf{./cover/thesis_cover.pdf}
$endif$

%% Page I: the half-title / "Franse pagina" %LCR
\frontmatter
\thispagestyle{empty}
\def\drop{.1\textheight}

\vspace*{\drop}
\begin{center}
\Huge \textsc{$if(title)$$title$$else$[…Title Doctoral Thesis…]$endif$}
\end{center}

%% Page II: Colophon %LCR
\clearpage
\thispagestyle{empty}
\vspace*{\fill}
\begingroup % to change formatting only temporarily
\small
\setlength{\parskip}{\baselineskip} % add space between paragraphs
\setlength\parindent{0pt} % no indents
$if(funder)$
The investigations in this thesis were supported by $if(grant)$a $grant$ from $endif$
$if(funder)$$funder$.$endif$
$endif$

This thesis was typeset using (R) Markdown, the \LaTeX\, \verb+bookdown+ R-package, and the \verb+bookdown+ template developed by Leon Reteig (\textit{amsterdown}).

\begin{itemize}[label={}, itemsep=0pt, partopsep=3pt, topsep=-\parskip, parsep=0pt, leftmargin=1em]
  $if(ISBN)$\item ISBN: $ISBN$ $endif$
  $if(printing)$\item Printing: $printing$ $endif$
  $if(cover)$\item Cover art: $cover$ $endif$
\end{itemize}

$if(thesis_url)$
\noindent An online version of this thesis is available at $thesis_url$$if(license)$, licensed under a $license$.$endif$
$endif$
\endgroup

%% Page III: `Title page' mandated by University of Amsterdam %LCR
\clearpage
\thispagestyle{empty}
\vspace*{\drop}
\begin{center}
\Huge\textbf{$if(title)$$title$$else$[… Title Doctoral Thesis…]$endif$}\par
$if(subtitle)$
\vspace{\baselineskip}
\Large\textit{$subtitle$}\par
$endif$
\vfill % this space will be whatever is left on the page
\large \textsc{Academisch Proefschrift}\par
\vspace{\baselineskip}
\linespread{1.3}{\normalsize ter verkrijging van de graad van doctor\\
aan de Universiteit van Amsterdam\\
op gezag van de Rector Magnificus\\
prof. dr. ir. K.I.J. Maex\\ % make sure this is the current rector magnificus
\mbox{ten overstaan van een door het College voor Promoties ingestelde commissie,}\\
in het openbaar te verdedigen in de $if(aula)$Aula der Universiteit$else$Agnietenkapel$endif$\\
op $if(date)$$date$$else$[………]dag […date…] […month…] 20[..]$endif$, te 13.00 uur \\ }\par %
\vspace{\baselineskip}
{\large door}\par
\vspace{\baselineskip}
{\Large $if(author)$$author$$else$[…given names in full…] [… surname…]$endif$}\par
\vspace{\baselineskip}
{\large geboren te $if(birthplace)$$birthplace$$if(country_of_birth)$, $country_of_birth$$endif$$else$[…place of birth…]$endif$}
\end{center}

%% Page IV: info on thesis committee %LCR
\clearpage
\thispagestyle{empty}
\noindent\textbf{Promotiecommissie:}\\
\\
\noindent\begin{tabular}{@{}lll}

$if(one_promotor)$Promotor:$else$Promotores:$endif$
$for(promotores)$
& $if(promotores.title)$ $promotores.title$$else$ […full title…]$endif$$if(promotores.initials)$ $promotores.initials$$else$ […initials…]$endif$$if(promotores.surname)$ $promotores.surname$$else$ […surname…]$endif$$if(promotores.affiliation)$ & $promotores.affiliation$$else$ & […affiliation…]$endif$\\
$endfor$

$if(copromotores)$
$if(one_copromotor)$Copromotor:$else$Copromotores:$endif$
$for(copromotores)$
& $if(copromotores.title)$ $copromotores.title$$else$ […full title…]$endif$$if(copromotores.initials)$ $copromotores.initials$$else$ […initials…]$endif$$if(copromotores.surname)$ $copromotores.surname$$else$ […surname…]$endif$$if(copromotores.affiliation)$ & $copromotores.affiliation$$else$ & […affiliation…]$endif$\\
$endfor$
$endif$

\\
Overige leden:
$for(members)$
& $if(members.title)$ $members.title$$else$ […full title…]$endif$$if(members.initials)$ $members.initials$$else$ […initials…]$endif$$if(members.surname)$ $members.surname$$else$ […surname…]$endif$$if(members.affiliation)$ & $members.affiliation$$else$ & […affiliation…]$endif$\\
$endfor$
\end{tabular}\\

\noindent Faculteit: $if(faculty)$$faculty$$else$[…name faculty…]$endif$

%% Page V (dedication)  % LS
\clearpage
\vspace*{\fill}
\begin{center}
\begin{minipage}{.6\textwidth}
\centerline{\emph{\Large Voor pap}}
\end{minipage}
\end{center}
\vfill % equivalent to \vspace{\fill}
\cleardoublepage

%%%%%%%%%%%%%%%%%%

$if(abstract)$
\begin{abstract}
$abstract$
\end{abstract}
$endif$

$for(include-before)$
$include-before$

$endfor$
$if(toc)$
\clearpage
\pagestyle{empty}
{
$if(colorlinks)$
\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$black$endif$}
$endif$
\setcounter{tocdepth}{$toc-depth$}
\tableofcontents
}
$endif$
$if(lot)$
\listoftables
$endif$
$if(lof)$
\listoffigures
$endif$
\pagestyle{\defstyle}
\mainmatter
$body$

\pagestyle{\defstyle}
\backmatter
$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}

$endif$
$endif$
$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$
$endif$

$for(include-after)$
$include-after$

$endfor$

\end{document}