thesis.tex

%-- This is a template for Ph.D. dissertations in the UCI format.
%-- https://github.com/tsutterley/uci-thesis-latex
%--
%-- 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.
%--
%-- UCI Theses and Dissertations Manual
%-- http://special.lib.uci.edu/dissertations/electronic/td2e.html#2.3
%--
%-- Notes: Add short title to figures, sections, via square brackets,
%-- e.g. \section[short]{long}.

%\documentclass[fleqn]{ucithesis}    % Orig: left-justified (indented) equations
\documentclass[fancy,strict]{ucithesis}   % Version that was handed in to the library
%%\documentclass[fancy]{ucithesis}        % Version with headers, etc
%%\documentclass[fancy,twoside,fliplr]{ucithesis}    % Version with headers, etc (flipped!)
%\documentclass[fancy,twoside,openright]{ucithesis}  % Alternate two-sided layout (NOT for official submission!)
%\documentclass[fancy,openright]{ucithesis}          % One sided layout that matches two-sided layout
% Options:
%   fancy: use fancyhdr to create headings, and also add nicer title pages and section headings
%   noLoF, noLoT, noLoA:  suppress List of Figures, Tables, or Algorithms in output
%   twoside: use two-sided layout (note: not allowed by the UCI dissertation standard)
%   openright: force chapters to start on an odd page (on the "right" of a book layout)

% Set a section symbol (default: black square) 
% Example: place graphic "sectionmark.pdf" (or other extension) before each numbered section
% \sectionsymbol{\protect\includegraphics[height=1.5ex]{sectionmark}} 
\sectionsymbol{\protect\includegraphics[height=1.5ex]{graybox}}

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

% Some other useful packages
\usepackage{caption}
\usepackage{subcaption}  % \begin{subfigure}...\end{subfigure} within figure
%\usepackage{multirow}
\usepackage{tabularx}
\usepackage[bottom,symbol]{footmisc}


% My added packages
\usepackage{enumerate}% http://ctan.org/pkg/enumerate
\usepackage{verbatim}
\usepackage{amsfonts, amssymb, mathrsfs}
%\usepackage[round,authoryear]{natbib}
%\usepackage[numbers]{natbib}
%\usepackage{natbibspacing}
%\usepackage[colorlinks,citecolor=blue,lin  kcolor=blue]{hyperref}  % hyperlink  \url \href{}{}  \hyperref[]{}
\usepackage{array}
%\usepackage{showlabels}
%\usepackage[inline]{showlabels}
\usepackage{wrapfig}
\usepackage{afterpage}
\usepackage{tikz}
\usetikzlibrary{%
	calc,%
	decorations.pathmorphing,%
	fadings,%
	shadings%
}

\usepackage{float}   % include this if also including hyperref and algorithm

% 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}, colorlinks,citecolor=blue,linkcolor=blue]{hyperref}
\usepackage[plainpages=false,pdfborder={0 0 0}, colorlinks,citecolor=black,linkcolor=black,urlcolor=black]{hyperref}
\usepackage{cleveref}

% If statement for using chapterbib package (default is false)
\newif\ifchapterbib
% Uncomment the following two lines to use the chapterbib package,
% which allows for individual bibliographies for each chapter rather than a
% combined bibliography for the entire thesis.
%\usepackage{chapterbib}
%\chapterbibtrue

% 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, algorithmic}
%\renewcommand{\listalgorithmname}{\protect\centering\protect\Large LIST OF ALGORITHMS}
\usepackage[chapter]{algorithm}
\usepackage{algorithmic}
\renewcommand{\listalgorithmname}{LIST OF ALGORITHMS}  % Match style in cls file!


% 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}

% Caption label with bold font
%\captionsetup{labelfont=bf}

% 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}{\textsc{Theorem}}[chapter]
\newtheorem{definition}{\textsc{Definition}}[chapter]
\newtheorem{example}{\textsc{Example}}[chapter]

% Figure Subdirectories
%\graphicspath{{chapter1.dir/}{chapter1.dir/}}

% 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}

% include thesis-specific info (title, committee, etc.)
\include{preliminaries}

% Add PDF document info fields
\hypersetup{
	pdftitle={\Thesistitle},
	pdfauthor={\Authorname},
	pdfsubject={\Degreefield},
}

% include Optional Dedication and Thesis Acknowledgments
\include{acknowledgments}

% include Curriculum Vitae
\include{curriculumvitae}

% include Thesis Abstract
\include{thesisabstract}

% Preliminary pages are always loaded
\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}
% ... 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

\ifchapterbib
    % using chapterbib to create chapter specific bibliographies.
\else
    % "References should be formatted in style most common in discipline",
    % abbrvnat is only a suggestion.
    \bibliographystyle{abbrvnat}
    \bibliography{thesis-bib-2016}
\fi

% 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.
\newcommand{\RNum}[1]{\uppercase\expandafter{\romannumeral #1\relax}}

\appendix
\include{appendix_entropy_matchKKT}
\include{appendix_marginalmap}
%\include{appendix_mmap_FactorGraph}
\include{appendix_meu}
\end{document}