template.tex

% From https://github.com/UWIT-IAM/UWThesis
\documentclass[print]{nuthesis}
\usepackage{amssymb, amsthm, amsmath, amsfonts}
\usepackage{wasysym}
\usepackage{mathrsfs}
% \usepackage{hyperref}
\usepackage{graphicx}
\usepackage{lineno}
\usepackage[colorinlistoftodos]{todonotes}
\usepackage{listings}
%\usepackage{breqn}
\usepackage{cancel, enumerate}
\usepackage{rotating, environ}
\usepackage{caption}
\usepackage{subcaption}
\usepackage[inline]{enumitem}
\usepackage{dirtree}

\newtheorem{thm}{Theorem}
\newtheorem{defn}{Definition}
\newtheorem{prop}{Proposition}
\newtheorem{lemma}{Lemma}
\newtheorem{cor}{Corollary}

% Syntax highlighting #22
$if(highlighting-macros)$
  $highlighting-macros$
$endif$

%% https://github.com/rstudio/rmarkdown/issues/1649
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newenvironment{CSLReferences}[2]%
{\setlength{\parindent}{0pt}%
\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces}%
{\par}

% fix for pandoc 1.14
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

%% something about tables, from https://github.com/ismayc/thesisdown/issues/122
\usepackage{calc}

%% for copyright symbol
\usepackage{textcomp}

%% to allow to rotate pages to landscape
\usepackage{lscape}
%% to adjust table column width
\usepackage{tabularx}

% suppress bottom page numbers on first page of each chapter
% because they overlap with text
\usepackage{etoolbox}
\patchcmd{\chapter}{plain}{empty}{}{}

%% for more attractive tables
\usepackage{booktabs}
\usepackage{longtable}


\usepackage{graphicx}


% Double spacing, if you want it.
\def\dsp{\def\baselinestretch{2.0}\large\normalsize}
% \dsp

% If the Grad. Division insists that the first paragraph of a section
% be indented (like the others), then include this line:
\usepackage{indentfirst}

%%%%%%%%%%%%%%%%%%
% If you want to use "sections" to partition your thesis
% un-comment the following:
%
% \counterwithout{section}{chapter}
% \setsecnumdepth{subsubsection}
% \def\sectionmark#1{\markboth{#1}{#1}}
% \def\subsectionmark#1{\markboth{#1}{#1}}
% \renewcommand{\thesection}{\arabic{section}}
% \renewcommand{\thesubsection}{\thesection.\arabic{subsection}}
% \makeatletter
% \let\l@subsection\l@section
% \let\l@section\l@chapter
% \makeatother
% 
% \renewcommand{\thetable}{\arabic{table}}
% \renewcommand{\thefigure}{\arabic{figure}}

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


%% Stuff from https://github.com/suchow/Dissertate

% The following line would print the thesis in a postscript font

% \usepackage{natbib}
% \def\bibpreamble{\protect\addcontentsline{toc}{chapter}{Bibliography}}

\setcounter{tocdepth}{1} % Print the chapter and sections to the toc
% controls depth of table of contents (toc): 0 = chapter, 1 = section, 2 = subsection

\usepackage{natbib}


% commands and environments needed by pandoc snippets
% extracted from the output of `pandoc -s`
%% Make R markdown code chunks work
\usepackage{array}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\ifxetex
  \usepackage{fontspec,xltxtra,xunicode}
  \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
\else
  \ifluatex
    \usepackage{fontspec}
    \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
  \else
    \usepackage[utf8]{inputenc}
  \fi
\fi
\usepackage{color}
\usepackage{fancyvrb}


\ifxetex
  \usepackage[setpagesize=false, % page size defined by xetex
              unicode=false, % unicode breaks when used with xetex
              xetex,
              colorlinks=false,
              hidelinks=true]{hyperref}
\else
  \usepackage[unicode=true,
              colorlinks=false,
              hidelinks=true]{hyperref}
\fi
\hypersetup{breaklinks=true, pdfborder={0 0 0}}
\setlength{\parindent}{20pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\setcounter{secnumdepth}{2} %% controls section numbering, e.g. 1 or 1.2, or 1.2.3


\input{preamble.tex}

\begin{document}
% \linenumbers{}
%% Start formatting the first few special pages
%% frontmatter is needed to set the page numbering correctly
\frontmatter
%% from thesisdown
% To pass between YAML and LaTeX the dollar signs are added by CII
\title{$title$}
\author{$author$}
\adviser{$adviser$}
\adviserAbstract{$adviserAbstract$}
\major{$major$}
\degreemonth{$month$}
\degreeyear{$year$}
% \copyrightpage
%%
%% For most people the defaults will be correct, so they are commented
%% out. To manually set these, just uncomment and make the needed
%% changes.
%% \college{Your college}
%% \city{Your City}
%%
%% For most people the following can be changed with a class
%% option. To manually set these, just uncomment the following and
%% make the needed changes.
%% \doctype{Thesis or Dissertation}
%% \degree{Your degree}
%% \degreeabbreviation{Your degree abbr.}
%%
%% Now that we know everything we need, we can generate the title page
%% itself.
%%
\maketitle


\begin{abstract}
    $abstract$
\end{abstract}

%% Optional
\begin{copyrightpage}
\end{copyrightpage}

%% Optional
% \begin{dedication}
% $dedication$
% \end{dedication}

%%%%%%%%%%%%%%%%%%%
% Acknowledgments
%%%%%%%%%%%%%%%%%%%
\begin{acknowledgments}
$acknowledgments$
\end{acknowledgments}
%%%%%%%%%%%%%%%%%%%

%%%%%%%%%%%%%%%%%%%
% Grant Information
%%%%%%%%%%%%%%%%%%%
% \begin{grantinfo}
%     % Add any grant info here
% \end{grantinfo}

%%%%%%%%%%%%%%%%%%%
% ToC
%%%%%%%%%%%%%%%%%%%
\tableofcontents

%%%%%%%%%%%%%%%%%%%
% List of Figures
%%%%%%%%%%%%%%%%%%%
\listoffigures
\listoftables

%%%%%%%%%%%%%%%%%%%
% Start of the document
%%%%%%%%%%%%%%%%%%%
\mainmatter


$body$


%% backmatter is needed at the end of the main body of your thesis to
%% set up page numbering correctly for the remainder of the thesis
\backmatter

%% Start the correct formatting for the appendices
% \appendix
%% Input each appendix here
% \input{./appendix_a}

%% Bibliography goes here (You better have one)
%% BibTeX is your friend

% \bibliographystyle{alpha}  % or use  abbrv to abbreviate first names and use numerical indices
\bibliographystyle{abbrv}  % or use  abbrv to abbreviate first names and use numerical indices
%% Add your BibTex file here (don't include the .bib)
\bibliography{./references}



%% Index go here (if you have one)
\end{document}