master.tex

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% PHD DISSERTATION
%
%
% Michael Malick
% 2017-05-23
% v3.0
%
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% ----------------------------
% Pre-amble
% ----------------------------
% {{{

\documentclass[11pt]{report}
\usepackage{float}
\usepackage{natbib}
\usepackage{pdflscape}
\usepackage{fancyhdr}
\usepackage{graphicx}
\usepackage{setspace}
\usepackage{pdfpages}
\usepackage{longtable}
\usepackage{booktabs}        % provides cmidrule
\usepackage{threeparttable}  % provides tablenotes
\usepackage{threeparttablex} % enables table notes with long tables
\usepackage[margin=1cm]{caption}
\usepackage[showframe=false,
            includefoot,       % ensure page numbers do not extend into margins
            includehead,       % ensure page numbers do not extend into margins
            headheight=13.6pt, % need for fancyhdr
            top=1.0in,
            bottom=1.0in,
            left=1.25in,
            right=1.25in ]{geometry}
\usepackage{hyperref}
\hypersetup{pdfstartview=FitH,
            bookmarksopen=false,
            colorlinks,
            linkcolor=black,
            urlcolor=black,
            citecolor=black}
\usepackage{amstext}
\usepackage{amsmath}

%% Latin Modern Font
% \usepackage[T1]{fontenc}
% \usepackage{lmodern}
% \usepackage{cfr-lm} % latin-modern with old-style numbers

%% Free Bembo
% \usepackage[full]{textcomp}
% \usepackage[sups,osf]{fbb} % osf (or tosf) for text, not math
% \usepackage[scaled=.95]{cabin} % sans serif
% \usepackage[varqu,varl]{inconsolata} % sans serif typewriter
% \usepackage[libertine,bigdelims,vvarbb]{newtxmath} % bb from STIX
% \usepackage[cal=boondoxo]{mathalfa} % mathcal

%% Libertine font
%% http://get-software.net/fonts/newtx/doc/newtxdoc.pdf (pg. 7)
\usepackage[lining,semibold]{libertine} % a bit lighter than Times--no osf in math
\usepackage[T1]{fontenc} % best for Western European languages
\usepackage{textcomp} % required to get special symbols
\usepackage[varqu,varl]{inconsolata}% a typewriter font must be defined
\usepackage{amsthm}% must be loaded before newtxmath
\usepackage[libertine,cmintegrals,bigdelims,vvarbb]{newtxmath}
\usepackage[scr=rsfso]{mathalfa}
\usepackage{bm}% load after all math to give access to bold math
%% After loading math package, switch to osf in text.
\useosf % for osf in normal text


% Customize section heading text
\renewcommand{\listfigurename}{List of figures}
\renewcommand{\listtablename}{List of tables}

% Left justify the captions
\usepackage{caption}
\captionsetup{justification=justified,
              singlelinecheck=false}

\widowpenalty=1000
\clubpenalty=1000



% 1.5 line spacing
\onehalfspacing

% Line numbers
% \usepackage{lineno}
% \linenumbers

% change font of hyperlinks
\usepackage{url}
\urlstyle{rm}



\begin{document}
% \raggedright
\setlength{\parindent}{1cm}
\bibpunct{(}{)}{;}{a}{}{;}


% }}}



% ----------------------------
% Includes
% ----------------------------
% \phantomsection is needed for
% certain sections to have proper
% links in the toc


%% Title page
\pagenumbering{gobble}
\input{./0_frontmatter/titlepage.tex}
\clearpage
\pagenumbering{roman}
\setcounter{page}{2}

%% Approval
\phantomsection
\input{./0_frontmatter/approval.tex}
\clearpage

%% Partial copyright
% \phantomsection
% \addcontentsline{toc}{chapter}{Partial Copyright License}
% \includepdf[pagecommand={\thispagestyle{plain}}, pages={1}]
%   {./0_frontmatter/partial-copyright.pdf}

%% Abstract
\input{./0_frontmatter/abstract.tex}
\clearpage

%% Quote
% \input{./0_frontmatter/quote.tex}
% \clearpage

%% Acknowledgments
\input{./0_frontmatter/acknowledgements.tex}
\clearpage

%% TOC
\phantomsection
\addcontentsline{toc}{chapter}{Contents}
\tableofcontents
\clearpage

%% List of tables
\phantomsection
\addcontentsline{toc}{chapter}{List of tables}
\listoftables
\clearpage

%% List of figures
\phantomsection
\addcontentsline{toc}{chapter}{List of figures}
\listoffigures
\clearpage
\pagenumbering{arabic}
\setcounter{page}{1}

%%%%%

%% Fancy Headers
\fancyhf{}
\renewcommand{\headrulewidth}{0pt} % remove header rule
\pagestyle{fancy}
\lhead{\small \textit{\leftmark}}
\rhead{\small \thepage}
% \pagestyle{headings} % default latex header


%% Introduction
\input{./1_introduction/intro.tex}
\clearpage

%% Spring-bloom
\input{./2_springbloom/springbloom.tex}
\clearpage

%% North Pacific Current
\input{./3_npcurrent/npcurrent.tex}
\clearpage

%% Bayesian-network
\input{./4_bayesnetwork/bayesnetwork.tex}
\clearpage

%% Policy
\input{./5_policy/policy.tex}
\clearpage

%% Discussion
\input{./6_discussion/discussion.tex}
\clearpage


%% Bibliography
\singlespacing
\phantomsection
\addcontentsline{toc}{chapter}{Bibliography}
\bibliographystyle{apalike}
\bibliography{library}

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\end{document}
% vim:fdm=marker