dissertation.brew.tex

\documentclass[PhD]{dissertation_duke}
%\documentclass[economy,twoside,bind]{dukedissertation}
% Use the second for a single-spaced copy suitable for duplex printing
% and binding.

% Other useful options (there are more options documented in Chapter 2):
%  * draft -- don't actually include images, print a black bar on overful
%             hboxes
%  * MS    -- Format for a Master's Thesis.  No UMI abstract page, some 
%             textual changes to title page.  

% Useful packages for dissertation writing:
\usepackage{amsmath, amssymb, amsfonts, amsthm}
\usepackage{graphicx}
\usepackage{natbib}
\usepackage{color}
\usepackage{bm}
\usepackage{subfigure}
\usepackage{graphicx}
\usepackage{mathabx}
\usepackage{multirow}
\usepackage{setspace}
% \usepackage{cite}  % If you include this, hyperlink cites will
                     % break.  It's nice to use this package if your bibstyle
  						% sorts entries by order-of-use, rather than
							% alphabetically (as plain does).
							
%Theorem, Lemma, etc. environments
\newtheorem{theorem}{Theorem}%[section]
\newtheorem{lemma}[theorem]{Lemma}
\newtheorem{proposition}[theorem]{Proposition}
\newtheorem{corollary}[theorem]{Corollary}
\newtheorem{result}[theorem]{Result}

%-----------------------------------------------------------------------------%
% HYPERREF: plain black hypertext references for ref's and cite's.
%-----------------------------------------------------------------------------%
% \usepackage[pdftex, pdfusetitle, plainpages=false,
\usepackage[pdfusetitle, plainpages=false, 
  			letterpaper, bookmarks, bookmarksnumbered,
				colorlinks, linkcolor=black, citecolor=black,
	         filecolor=black, urlcolor=black]
				{hyperref}

% Personal commands and abbreviations.
%Define and personal commands here

%-----------------------------------------------------------------------------%
% extra pandoc packages from default.tex
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[utf8]{inputenc}
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
    \usepackage{xltxtra,xunicode}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase}
  \newcommand{\euro}{€}
\fi
\usepackage{listings}
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
\usepackage{fancyvrb}
\usepackage{longtable,booktabs}
\usepackage{graphicx}
% Redefine \includegraphics so that, unless explicit options are
% given, the image width will not exceed the width of the page.
% Images get their normal width if they fit onto the page, but
% are scaled down if they would overflow the margins.
\makeatletter
\def\ScaleIfNeeded{%
  \ifdim\Gin@nat@width>\linewidth
    \linewidth
  \else
    \Gin@nat@width
  \fi
}
\makeatother
\let\Oldincludegraphics\includegraphics
{%
 \catcode`\@=11\relax%
 \gdef\includegraphics{\@ifnextchar[{\Oldincludegraphics}{\Oldincludegraphics[width=\ScaleIfNeeded]}}%
}%
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\VerbatimFootnotes % allows verbatim text in footnotes
%-----------------------------------------------------------------------------%

%-----------------------------------------------------------------------------%
% bbest customized to enable pandoc --highlight-style. Shading borrowed from https://groups.google.com/d/msg/knitr/Ll21P9TC2jc/4wqLl7XUzRUJ

\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
% Add ',fontsize=\small' for more characters per line
\usepackage{framed}
\definecolor{shadecolor}{RGB}{248,248,248}
\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{{#1}}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{{#1}}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{{#1}}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{{#1}}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{{#1}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{{#1}}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{{#1}}}
\newcommand{\RegionMarkerTok}[1]{{#1}}
\newcommand{\ErrorTok}[1]{\textbf{{#1}}}
\newcommand{\NormalTok}[1]{{#1}}
%-----------------------------------------------------------------------------%


%Graphics Path to find your pictures
\graphicspath{{./fig/}}


%-----------------------------------------------------------------------------%
% PREAMBLE 
%-----------------------------------------------------------------------------%
\author{<%= author %>}
\title{<%= title %>}
\supervisor{<%= supervisor %>}
\department{<%= department %>} % Appears as Department of \department
% Declare dissertation subject used on UMI abstract page.  List of
% categories: http://dissertations.umi.com/duke/subject_categories.html
%\subject{[Your Subject Here]}

\date{<%= format(Sys.Date(), '%Y') %>} % Anything but the year is ignored.

% Copyright text.  If undefined, default is 'All rights reserved'
% (Example sets the text to a hyperlinked Creative Commons Licence)
\copyrighttext{ All rights reserved except the rights granted by the\\
   \href{http://creativecommons.org/licenses/by-nc/3.0/us/}
        {Creative Commons Attribution-Noncommercial Licence}
}

% Committee Members other than supervisor.  No more than five beyond the
% supervisor allowed.
\member{<%= member1 %>}
\member{<%= member2 %>}
\member{<%= member3 %>}
%-----------------------------------------------------------------------------%

\begin{document}

%-----------------------------------------------------------------------------%
% TITLE PAGE -- provides UMI abstract title page & copyright if appropriate
%-----------------------------------------------------------------------------%
\maketitle

%-----------------------------------------------------------------------------%
% ABSTRACT -- included file should start with '\abstract'.
%-----------------------------------------------------------------------------%
\include{{./a_abstract}}

%-----------------------------------------------------------------------------%
% DEDICATION -- OPTIONAL.  Put the text inside the braces.
%               (Long 'dedications' probably belong in the acknowledgements)
%-----------------------------------------------------------------------------%
\dedication{Dedicated to the open source scientific community who made all the great tools and data freely available that make this thesis possible.}

%-----------------------------------------------------------------------------%
% FRONTMATTER -- ToC is required, LoT and LoF are required if you have any
% tables or figures, respectively. List of Abbreviations and Symbols is 
% optional.
%-----------------------------------------------------------------------------%
\tableofcontents % Automatically generated
\listoftables	   % If you have any tables, automatically generated
\listoffigures	 % If you have any figures, automatically generated
%\include{{./duke_template/listofabbr}} % List of Abbreviations. Start file with '\abbreviations'

%-----------------------------------------------------------------------------%
% ACKNOWLEDGEMENTS -- included file should start with '\acknowledgements'
%-----------------------------------------------------------------------------%
\include{{./a_acknowledgements}}

%==============================================================================
%-----------------------------------------------------------------------------%
%
% MAIN BODY OF PAPER
%
%
%-----------------------------------------------------------------------------%
\include{{./body}} % including appendix, which are just chapters enumerated by Appendix A, Appendix B, Appendix C...
%==============================================================================

%-----------------------------------------------------------------------------%
% APPENDICES -- OPTIONAL. 
%-----------------------------------------------------------------------------%
% \appendix
% \include{{./duke_template/chLorem3}} % appendix. Start with '\chapter{Title}'
%You can always add more appendices here if you want

%-----------------------------------------------------------------------------%
% BIBLIOGRAPHY -- uncomment \nocite{*} to include items in 'mybib.bib' file
% that aren't cited in the text.  Change the style to match your
% discipline's standards.  Of course, if your bibliography file isn't called
% 'mybib.bib' you might want to change that here too :)
%-----------------------------------------------------------------------------%
%\nocite{*} - if you use this it will put EVERYTHING in your .bib file into the references even if you don't cite it in the text
% \bibliographystyle{./duke_template/jasa} % Formats bibliography
% \cleardoublepage
% \normalbaselines %Fixes spacing of bibliography
% \addcontentsline{toc}{chapter}{Bibliography} %adds Bibliography to your table of contents
% \bibliography{./duke_template/References} %your bibliography file - change the path if needed
%-----------------------------------------------------------------------------%

%-----------------------------------------------------------------------------%
% BIOGRAPHY -- Start file with '\biography'.  Mandatory for Ph.D.
%-----------------------------------------------------------------------------%
\include{{./x_biography}}

%-----------------------------------------------------------------------------
% You're done :)
\end{document}