Multi Paper Dissertation

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\documentclass[12pt]{report}

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% PACKAGES
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% package for projects with multiple files
\usepackage{subfiles}

% formatting packages
\usepackage[
    left=1.5in,     % left margin
    right=1.0in,    % right margin
    top=1.0in,      % top margin
    bottom=1.0in,   % bottom margin
    includefoot     % page number does not protrude into bottom margin
    ]{geometry}     % set margins
\usepackage{titlesec}	                    % custom section titles
\usepackage{appendix}                       % customizable appendices
\usepackage{caption}                        % table and figure captions
\usepackage[nodisplayskipstretch]{setspace} % double spacing
\usepackage[hidelinks]{hyperref} 	        % clickable links/toc
\usepackage[titles]{tocloft}                % table of contents extension
\usepackage[sectionbib]{bibunits}           % separate bib by chapter
\usepackage[
    section,    % bibliographies are sections, not chapters
    numbib,     % bibliographies are numbered
    nottoc,     % do not change table of contents
    notlof,     % do not change list of figures
    notlot,     % do not change list of tables
    ]{tocbibind} % include bibliographies in table of contents

% symbol packages
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{amssymb}
\usepackage{mathtools}
\usepackage{stmaryrd}

% tables and lists
\usepackage{enumerate}
\usepackage{array}
\usepackage{tabularx}
\usepackage{multirow}
\usepackage{dcolumn}

% images and figures
\usepackage[dvips,dvipdf]{graphicx}

% additional packages (uncomment/add as needed)
\usepackage[usenames,dvipsnames]{color}
\usepackage{lipsum}

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% FORMATTING
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% chapter, section, subsection titles
\titleformat{\chapter}[hang]{\bfseries\normalsize\centering}{\thechapter.}{5pt}{}[]
\titleformat{\section}[hang]{\bfseries}{\thesection.}{5pt}{}[]
\titleformat{\subsection}[runin]{\bfseries}{\thesubsection.}{5pt}{}[:]

% front matter format
\newcommand\frontstuff[1]{
    \chapter*{#1}
    \addcontentsline{toc}{chapter}{#1}
}

% add periods to numbers in toc
\let \savenumberline \numberline
\def \numberline#1{\savenumberline{#1.}}

% add dots to toc (from name to page number)
\renewcommand{\cftchapleader}{\cftdotfill{\cftdotsep}}

% bibliography name and style
\renewcommand{\bibname}{References}
\defaultbibliographystyle{abbrv}

% set caption font size
\captionsetup[figure]{font=footnotesize,labelfont=footnotesize}
\captionsetup[table]{font=footnotesize,labelfont=footnotesize}

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% MACROS
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% https://github.com/samreynoldsmath/texmf
\input{preamble/macros.tex}

\usepackage{chapterheader}

\newcommand\PSU{Fariborz Maseeh Department of Mathematics and Statistics,
Portland State University, Portland, OR 97201}

\makeatletter
\newcommand\footnoteref[1]{\protected@xdef\@thefnmark{\ref{#1}}\@footnotemark}
\makeatother

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% THEOREM ENVIRONMENTS
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% https://github.com/samreynoldsmath/texmf
\def\theoremnumberstyle{chaptersection}
\input{sams-theorems.tex}

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% TITLEPAGE
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\begin{document}

% help prevent text from jutting into margins
\sloppy

% due to bibunits package
\bibliographyunit[\chapter]

% no page number on title page
\pagenumbering{gobble}

% title page content
\input{src/front-matter/title-page.tex}

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% FRONT MATTER
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\pagebreak
\pagenumbering{roman}
\doublespacing

\frontstuff{Abstract}
\input{src/front-matter/abstract.tex}

\frontstuff{Dedication}
\input{src/front-matter/dedication.tex}

\frontstuff{Acknowledgements}
\input{src/front-matter/acknowledgements.tex}

% table of contents
\singlespacing
\tableofcontents

% list of figures
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{\listfigurename}
\listoffigures

% list of tables
\cleardoublepage
\phantomsection
\addcontentsline{toc}{chapter}{\listtablename}
\listoftables

\doublespacing

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% MAIN BODY
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\input{src/introduction.tex}
\input{src/paper1/paper1.tex}
\input{src/paper2/paper2.tex}
\input{src/conclusion.tex}

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% APPENDIX
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% exclude appendix from lists of tables and figures
\let\svaddcontentsline\addcontentsline
\renewcommand\addcontentsline[3]{%
  \ifthenelse{\equal{#1}{lof}}{}%
  {\ifthenelse{\equal{#1}{lot}}{}{\svaddcontentsline{#1}{#2}{#3}}}}

% add the "Appendix" to the appendix titles
\titleformat{\chapter}[hang]{\bfseries\normalsize\centering}{Appendix \thechapter.}{5pt}{}[]
\renewcommand{\appendixname}{Appendix}
\appendixtitleon    % puts \appendixname before each appendix title
\appendixtitletocon % puts \appendixname before each TOC entry

\begin{appendices}
    \input{src/appendix-a/extensions.tex}
\end{appendices}

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\end{document}