template.tex

%
%
% UCSD Doctoral Dissertation and Masters Thesis Template
% -----------------------------------
% https://github.com/ucsd-thesis/ucsd-thesis
%
%
% ----------------------------------------------------------------------
% WARNING: 
%
%   This template has not endorsed by OGS or any other official entity.
%   The official formatting guide can be obtained from OGS.
%   It can be found on the web here:
%   http://grad.ucsd.edu/_files/academic-affairs/Dissertations_Theses_Formatting_Manual.pdf
%
%   No guarantee is made that this LaTeX class conforms to the official UCSD guidelines.
%   Make sure that you check the final document against the Formatting Manual.
%  
%   That being said, this class has been routinely used for successful 
%   publication of doctoral theses.  
%
%   The ucsd.cls class files are valid for doctoral dissertations and
%    masters theses.
%
% ----------------------------------------------------------------------
% GETTING STARTED:
%
%   Lots of information can be found on the project wiki:
%   http://code.google.com/p/ucsd-thesis/wiki/GettingStarted
%
%
%   To make a pdf from this template use the command:
%     pdflatex template
%
%
%   To get started please read the comments in this template file 
%   and make changes as appropriate.
%
%   If you successfully submit a thesis with this package please let us
%   know.
%
%
% ----------------------------------------------------------------------
% KNOWN ISSUES:
%
%   Currently only the 12pt size conforms to the UCSD requirements.
%   The 10pt and 11pt options make the footnote fonts too small.
%
%
% ----------------------------------------------------------------------
% HELP/CONTACT:
%
%   If you need help try the ucsd-thesis google group:
%   http://groups.google.com/group/ucsd-thesis
%
%
% ----------------------------------------------------------------------
% BUGS:
%
%   Please report all bugs at:
%   https://github.com/ucsd-thesis/ucsd-thesis/issues
%
%
% ----------------------------------------------------------------------
% More control of the formatting of your thesis can be achieved through
% modifications of the included LaTeX class files:
%
%   * ucsd.cls    -- Class file
%   * uct10.clo   -- Configuration files for font sizes 10pt, 11pt, 12pt
%     uct11.clo                            
%     uct12.clo
%
% ----------------------------------------------------------------------



% Setup the documentclass 
% default options: 12pt, oneside, final
%
% fonts: 10pt, 11pt, 12pt -- are valid for UCSD dissertations and theses.
% sides: oneside, twoside -- note that two-sided theses are not accepted 
%                            by OGS.
% mode: draft, final, lulu -- 
%                            draft mode switches to single spacing, 
%                            removes hyperlinks, and places a black box
%                            at every overfull hbox (check these before
%                            submission).
%
%                            lulu mode prints to 6x9, single spacing, and ready for 
%                            double-sided printing.
%
% degree: phd, masters --
%                            this changes the template to conform to (dissertation or thesis needs)
%
% chapterheads            -- Include this if you want your chapters to read:
%                              Chapter 1
%                              Title of Chapter
%
%                            instead of
%                              1 Title of Chapter
%
% en                      (default) you can add translations to languages/[lang].tex,
%                           then switch languages.
%
\documentclass[12pt,final,phd,chapterheads]{ucsd}  % or masters instead of phd


% Include all packages you need here.  
% Some standard options are suggested below.
%
% See the project wiki for information on how to use 
% these packages. Other useful packages are also listed there.
%
%   http://code.google.com/p/ucsd-thesis/wiki/GettingStarted



%% AMS PACKAGES - Chances are you will want some or all 
%    of these if writing a dissertation/thesis that includes equations.
%  \usepackage{amsmath, amscd, amssymb, amsthm}

%% GRAPHICX - This is the standard package for 
%    including graphics for latex/pdflatex.
%\usepackage{scrextend}
%\usepackage{pslatex}
%\usepackage{graphicx}


%% SUBFIG - Use this to place multiple images in a
%    single figure.  Subfig will handle placement and
%    proper captioning (e.g. Figure 1.2(a))
% \usepackage{subfig}

%% TIMES FONT - replacements for Computer Modern
%%   This package will replace the default font with a
%%   Times-Roman font with math support.
% \usepackage[T1]{fontenc}
% \usepackage{mathptmx}

%% INDEX
%   Uncomment the following two lines to create an index: 
% \usepackage{makeidx}
% \makeindex
%   You will need to uncomment the \printindex line near the
%   bibliography to display the index.  Use the command
% \index{keyword} 
%   within the text to create an entry in the index for keyword.
%   To compile a LaTeX document with an index the 'makeindex'
%   command will need to be run.  See the wiki for more details.



%% CITATIONS
% Sets citation format
% and fixes up citations madness
\usepackage{microtype}  % avoids citations that hang into the margin

%% String comparisons
\usepackage{pdftexcmds}

%% FOOTNOTE-MAGIC
% Enables footnotes in tables, re-referencing the same footnote multiple times.
\usepackage{footnote}
\makesavenoteenv{tabular}
\makesavenoteenv{table}


%% TABLE FORMATTING MADNESS
% Enable all sorts of fun table tricks
\usepackage{rotating}  % Enables the sideways environment (NCPW)
\usepackage{array}  % Enables "m" tabular environment http://ctan.org/pkg/array
\usepackage{booktabs}  % Enables \toprule  http://ctan.org/pkg/array


%% HYPERLINKS
%   To create a PDF with hyperlinks, you need to include the hyperref package.
%   THIS HAS TO BE THE LAST PACKAGE INCLUDED!
%   Note that the options plainpages=false and pdfpagelabels exist
%   to fix indexing associated with having both (ii) and (2) as pages.
%   Also, all links must be black according to OGS.
%   See: http://www.tex.ac.uk/cgi-bin/texfaq2html?label=hyperdupdest
%   Note: This may not work correctly with all DVI viewers (i.e. Yap breaks).
%   NOTE: hyperref will NOT work in draft mode, as noted above.
\usepackage[colorlinks=true, pdfstartview=FitV, 
            linkcolor=black, citecolor=black, 
            urlcolor=black, plainpages=false,
            pdfusetitle, pdfpagelabels]{hyperref}
\urlstyle{same}
\usepackage{bookmark}

\begin{document}

%% FRONT MATTER
%
%  All of the front matter.
%  This includes the title, degree, dedication, vita, abstract, etc..
%  Modify the file template_frontmatter.tex to change these pages.
\include{template_frontmatter}





%% DISSERTATION

% A common strategy here is to include files for each of the chapters. I.e.,
% Place the chapters is separate files: 
%   chapter1.tex, chapter2.tex
% Then use the commands:
%   \include{chapter1}
%   \include{chapter2}
%
% Of course, if you prefer, you can just start with
%   \chapter{My First Chapter Name}
% and start typing away.  
\chapter{Just a Test}
This is only a test.
\section{A section}
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nulla odio
sem, bibendum ut, aliquam ac, facilisis id, tellus. Nam posuere pede
sit amet ipsum. Etiam dolor. In sodales eros quis pede.  Quisque sed
nulla et ligula vulputate lacinia. In venenatis, ligula id semper
feugiat, ligula odio adipiscing libero, eget mollis nunc erat id orci.
Nullam ante dolor, rutrum eget, vestibulum euismod, pulvinar at, nibh.
In sapien. Quisque ut arcu. Suspendisse potenti. Cras consequat cursus
nulla.

\subsection{A Figure Example}
\label{ssec:figure_example}

This subsection shows a sample figure.

\begin{figure}[h] 
  \centering
  \includegraphics[width=0.5\textwidth]{sandiego}
  \caption[Short figure caption (must be \protect{$< 4$} lines in the list of figures)]{A picture of San Diego.  Note that figures must be on their own line (no neighboring text) and captions must be single-spaced and appear \protect\textit{below} the figure.  Captions can be as long as you want, but if they are longer than 4 lines in the list of figures, you must provide a short figure caption.\protect\index{SanDiego}} 
  \label{fig:sandiego}
\end{figure}

\subsection{A Table Example}

While in Section \ref{ssec:figure_example} Figure \ref{fig:sandiego} we had a majestic figure, here we provide a crazy table example.


%%%% TABLE 1 %%%%
\vspace{0.25in}  % Tweak this to give more margin between text and your table caption
\begin{table}[!ht]
\caption[Short figure caption (must be \protect{$< 4$} lines in the list of tables)]{A table of when I get hungry.  Note that tables must be on their own line (no neighboring text) and captions must be single-spaced and appear \protect\textit{above} the table.  Captions can be as long as you want, but if they are longer than 4 lines in the list of figures, you must provide a short figure caption.}
\vspace{-0.15in}  % Tweak this to reduce margin between the caption and your table

\begin{center}
% Better to define these in relative terms; makes printing 
% various sizes / formats easier.
\begin{tabular}{|p{0.2\textwidth}|p{0.35\textwidth}|p{0.35\textwidth}|}

\hline
Time of day & Hunger Level & Preferred Food \\

\hline
8am & high & IHOP (French Toast) \\

\hline
noon & medium & Croutons (Tomato Basil Soup \& Granny Smith Chicken Salad) \\

\hline
5pm & high & Bombay Coast (Saag Paneer) or Hi Thai (Pad See Ew) \\

\hline
8pm & medium & Yogurt World (froyo!) \\

\hline
\end{tabular}
\end{center}
\label{tab:analysis3}
\end{table}



%% APPENDIX
\appendix
\chapter{Final notes}
What to do about things \cite{Martin_1983}.  What did he say \cite{Rilling_Insel_1999}.
  Remove me in case of abdominal pain.



%% END MATTER
% \printindex %% Uncomment to display the index
% \nocite{}  %% Put any references that you want to include in the bib 
%               but haven't cited in the braces.
\bibliographystyle{alpha}  %% This is just my personal favorite style. 
%                              There are many others.
%\setlength{\bibleftmargin}{0.25in}  % indent each item
%\setlength{\bibindent}{-\bibleftmargin}  % unindent the first line
%\def\baselinestretch{1.0}  % force single spacing
%\setlength{\bibitemsep}{0.16in}  % add extra space between items
\bibliography{template}  %% This looks for the bibliography in template.bib 
%                          which should be formatted as a bibtex file.
%                          and needs to be separately compiled into a bbl file.
\end{document}