Template for NAU dissertations (manuscript chapters style).
\begin
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% Template for NAU "manuscript" style dissertation Mar 2023. Feel free to use with no guarantees or warranties.
\documentclass{book}
\usepackage[utf8]{inputenc}
\usepackage[bookmarks=true,
pdfnewwindow=true, % links in new window
colorlinks=true, % false: boxed links; true: colored links
linkcolor=black, % color of internal links; black to blue, 6/10/22 COC % black per NAU EDT 7/27/2022 COC
citecolor=xlinkcolor, % color of links to bibliography
filecolor=xlinkcolor, % color of file links
urlcolor=xlinkcolor, % color of external links
final=true,
]{hyperref}
\usepackage[nointegrals]{wasysym}
\usepackage{siunitx}
\usepackage{mathtools} % loads amsmath also
\usepackage[letterpaper, portrait, margin=1in]{geometry}
\pagestyle{plain}
\raggedbottom % CTU 22/12/12 get rid of space between paragraphs at end of chapters
\setcounter{secnumdepth}{3}
\usepackage{setspace}
\usepackage{lipsum}
\usepackage{float}
\usepackage{graphicx}
\usepackage{lscape}
\usepackage[printonlyused]{acronym}
\makeatletter
\newcommand*{\org@overidelabel}{}
\let\org@overridelabel\@verridelabel
\@ifpackagelater{acronym}{2015/03/21}{% v1.41
\renewcommand*{\@verridelabel}[1]{%
\@bsphack
\protected@write\@auxout{}{\string\AC@undonewlabel{#1@cref}}%
\org@overridelabel{#1}%
\@esphack
}%
}{% older versions
\renewcommand*{\@verridelabel}[1]{%
\@bsphack
\protected@write\@auxout{}{\string\undonewlabel{#1@cref}}%
\org@overridelabel{#1}%
\@esphack
}%
}
\makeatother
\acrodef{ac}{Acronym}
% \usepackage{amssymb} % leftrightsquiggle, etc.
\usepackage{textcomp,gensymb} % degree, etc. CTU 10/20/22
\usepackage{xcolor}
\definecolor{xlinkcolor}{cmyk}{0,0,0,1} % per NAU EDT 7/27/2022 COC
\PassOptionsToPackage{hyphens}{url}
\usepackage[percent]{overpic}
\usepackage{color}
% \usepackage{cleveref}
% \crefformat{footnote}{#2\footnotemark[#1]#3}
\usepackage{url}
\usepackage{natbib}
\bibliographystyle{aasjournal} % Add different bib style .bst file if you'd like
\usepackage{enumitem}
\usepackage{makecell} % 12/27/2017 COC for multi-lined entries in tables
\usepackage{longtable} % spanning pages
\usepackage{multirow} % CJTU 12/15/22
% Wrapped figures and caption shenanigans 11/07/2022 CTU for inline figures
\usepackage[skip=5pt]{caption}
\DeclareCaptionFormat{boldtitle}
{%
\textbf{#1#2} #3
}
\captionsetup{format=boldtitle,font={stretch=1.2}}
\usepackage{wrapfig} % for inline figures
\usepackage{etoolbox} % To fix misaligned wrapfigures
\BeforeBeginEnvironment{wrapfigure}{\setlength{\intextsep}{0pt}}
\BeforeBeginEnvironment{figure}{\setlength{\intextsep}{12.0pt plus 2.0pt minus 2.0pt}}
% Aliases
\newcommand{\dissertationTitle}{!YOUR TITLE ALL CAPS!}
\newcommand{\degr}{$\degree$}
\newcommand{\hho}{H$_2$O}
\newcommand{\ohhho}{OH / \hho}
%%%%%%%%%%%%
\usepackage{sectsty} % 6/26/2022 COC: control style of sectioning (e.g., font size)
% \allsectionsfont{\sffamily}
\chapternumberfont{\large}
\chaptertitlefont{\large}
\chapterfont{\large}
\allsectionsfont{\large}
\subsectionfont{\large}
\subsubsectionfont{\normalsize}
\paragraphfont{\normalsize}
% \sectionnumberfont{\large}
% \sectiontitlefont{\large}
%%%%%%%%%%%%%%%%%
\usepackage{calc}
\newcounter{rownumber}%12/26/2017 COC
%\renewcommand{\therownumber}{\thetable.\arabic{rownumber}}
%\newcounter{rtaskno}
%\newcommand{\rtask}[1]{\refstepcounter{rtaskno}\label{#1}}
\newcommand{\rlabel}[1]{\refstepcounter{rownumber}\label{#1}}
\setcounter{rownumber}{-36}
\newcounter{tabfoot}
\newcommand{\flabel}[1]{\refstepcounter{tabfoot}\label{#1}}
\renewcommand{\thetabfoot}{\alph{tabfoot}}
\setcounter{tabfoot}{-6}
\newcommand{\fakechapter}[1]{%
\par\refstepcounter{chapter}% Increase chapter counter
% \chaptermark{#1}% Add chapter mark (header)
\addcontentsline{toc}{chapter}{\protect\numberline{\thechapter}#1}% Add section to ToC
}
\newcommand{\fakesection}[1]{%
\par\refstepcounter{section}% Increase section counter
% \sectionmark{#1}% Add section mark (header)
\addcontentsline{toc}{section}{\protect\numberline{\thesection}#1}% Add section to ToC
}
\usepackage[figuresleft]{rotating} % forces all clockwise rotation per NAU EDT guidelines
\usepackage{pdflscape} % CTU 11/18/22 use for landscape figures/tables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\frontmatter % Roman numerals
\begingroup % Begin start chapter on any page
\let\cleardoublepage\clearpage % Allow chapters to start on even pages
\doublespacing
\include{0_title_page}
\include{1_abstract}
\include{1_copyright}
\include{1_acknowledgements}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\singlespacing
\setcounter{tocdepth}{2}
\renewcommand{\contentsname}{Table of Contents}
\tableofcontents
\doublespacing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{List of Tables}
\listoftables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\phantomsection
\addcontentsline{toc}{chapter}{List of Figures}
\listoffigures
\endgroup % End start chapter on any page
\doublespacing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\include{1_dedication}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\include{1_preface}
%%%%%%%%%%%%%%%%%%%% INTRO & METHODS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\mainmatter % Regular numbers
\include{2_overall_introduction}
%%%%%%%%%%%%%%%%%%%% MANUSCRIPT CHAPTERS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\include{3_chapter1}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \clearpage
% \include{4_chapter2}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \clearpage
% \include{5_chapter3}
%%%%%%%%%%%%%%%%%%%% DISCUSSION %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\include{9_overall_discussion}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\singlespacing
\include{z_acronyms}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\clearpage
\doublespacing
\include{zz_appendix}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% \clearpage
\singlespacing
\renewcommand{\bibname}{References}
\phantomsection
\addcontentsline{toc}{chapter}{References}
\bibliography{references.bib}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\end{document}