thesis.tex

% This is a template for Ph.D. dissertations in the UCI format.
% 
% All fonts, including those for sub- and superscripts, must be 10
% points or larger.  Recommended sizes are 14-point for chapter
% headings, 12-point for the main body of text and figure/table
% titles, and 10-point for footnotes, sub- and super-scripts, and text
% in figures and tables.
%
% Notes: Add short title to figures, sections, via square brackets,
% e.g. \section[short]{long}.
%
\documentclass[12pt,fleqn]{ucithesis}

% A few common packages
\usepackage{amsmath}
\usepackage{amsthm}
\usepackage{array}
\usepackage{graphicx,subfigure}
\usepackage{natbib}
\usepackage{relsize}

% Some other useful packages
\usepackage{caption}
%\usepackage{subcaption}  % \begin{subfigure}...\end{subfigure} within figure
\usepackage{multirow} 
\usepackage{tabularx}
\usepackage{nameref}

\usepackage{epstopdf}
\usepackage{booktabs}
\usepackage{enumerate}
\usepackage{longtable}
\usepackage{array}
\usepackage[table]{xcolor}
\usepackage{hhline}

% plainpages=false fixes the "duplicate ignored" error with page counters
% Set pdfborder to 0 0 0 to disable colored borders around PDF hyperlinks
\usepackage[plainpages=false,pdfborder={0 0 0}]{hyperref}

% Uncomment the following two lines to use the algorithm package,
% which provides an algorithm environment similar to figure and table
% ("\begin{algorithm}...\end{algorithm}"). A list of algorithms will
% automatically be added in the preliminary pages. Note that you
% probably want a package for the actual code to go with this (e.g.,
% algorithmic).
%\usepackage{algorithm}
%\renewcommand{\listalgorithmname}{\protect\centering\protect\Large LIST OF ALGORITHMS}

% Uncomment the following line to enable Unicode support. This will allow you
% to enter non-ASCII characters (such as accented characters) directly without
% having to use LaTeX's awkward escape syntax (e.g., \'{e})
% NOTE: You may have to install the ucs.sty package for this to work. See:
% http://www.unruh.de/DniQ/latex/unicode/
%\usepackage[utf8x]{inputenc}

% Uncomment the following to avoid "widowing", where page breaks cause
% single lines of paragraphs to float onto the next page (this is not
% a UCI requirement but more of an aesthetic choice).
%\widowpenalty=10000
%\clubpenalty=10000

% Modify or extend these at will.
\newtheorem{theorem}{{\sc Theorem}}[chapter]
\newtheorem{definition}{{\sc Definition}}[chapter]
\newtheorem{example}{{\sc Example}}[chapter]

% Uncomment the following to have numbered subsubsections (by default
% numbering goes only to subsections).
%\setcounter{secnumdepth}{4}


% Set this to only select a subset of the includes directives below.
% Very handy to speed up compilation if you're working on a certain
% part of your thesis. It conserves page numbers, references, etc.
% even for non-included files.

\makeatletter
\def\@cline#1-#2\@nil{%
  \omit
  \@multicnt#1%
  \advance\@multispan\m@ne
  \ifnum\@multicnt=\@ne\@firstofone{&\omit}\fi
  \@multicnt#2%
  \advance\@multicnt-#1%
  \advance\@multispan\@ne
  \leaders\hrule\@height\arrayrulewidth\hfill
  \cr
  \noalign{\nobreak\vskip-\arrayrulewidth}}
\makeatother

\begin{document}

% Preliminary pages are always loaded (TOC, CV, etc.)
\input{preliminaries}
\preliminarypages

% Include the different components of your thesis, in separate files.
\include{Introduction}
\include{Motivation}
\include{CalicoVersionOne}
%\include{NotationPaper}
\include{CalicoVersionTwo}
\include{Evaluation}
\include{Discussion}
\include{RelatedWork}
\include{Conclusions}
%\include{FutureWork}
% ... and so on

% These commands fix an odd problem in which the bibliography line
% of the Table of Contents shows the wrong page number.
\clearpage
\phantomsection

% "References should be formatted in style most common in discipline",
% abbrv is only a suggestion.
\bibliographystyle{abbrv}
\bibliography{thesis}

% The Thesis Manual says not to include appendix figures and tables in
% the List of Figures and Tables, respectively, so these commands from
% the caption package turn it off from this point onwards. If needed,
% it can be re-enabled later (using list=yes argument).
\captionsetup[figure]{list=no}
\captionsetup[table]{list=no}

% If you have an appendix, it should come after the references.
\include{appendix}

\end{document}