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{amssymb}
\usepackage{array}

\usepackage{graphicx}
\usepackage{url}

\usepackage{natbib}
\usepackage{relsize}

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

\usepackage{listings}

\usepackage{color}  %to leave some notes

\makeatletter
\newif\if@restonecol
\makeatother
\let\algorithm\relax
\let\endalgorithm\relax
\usepackage[linesnumbered]{algorithm2e}

\usepackage[normalem]{ulem}

\makeatletter
\newcommand{\nosemic}{\renewcommand{\@endalgocfline}{\relax}}% Drop semi-colon ;
\newcommand{\dosemic}{\renewcommand{\@endalgocfline}{\algocf@endline}}% Reinstate semi-colon ;
\newcommand{\pushline}{\Indp}% Indent
\newcommand{\popline}{\Indm\dosemic}% Undent
\makeatother

% 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}


% 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.
%\includeonly{chapter1}

\begin{document}

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

% Include the different components of your thesis, in separate files.
% Using \include allows you to set \includeonly above.
\include{chapter1}
\include{chapter2}
\include{chapter3}
\include{chapter4}
\include{chapter5}
\include{chapter6}
\include{conclusion}
% ... 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}