McMaster Thesis Example

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% McMaster Masters/Doctoral Thesis 
% LaTeX Template
% Version 2.2 (11/23/15)
%
% This template has been downloaded from:
% http://www.LaTeXTemplates.com
% Then subsequently from http://www.overleaf.com
%
% Version 2.0 major modifications by:
% Vel (vel@latextemplates.com)
%
% Original authors:
% Steven Gunn  (http://users.ecs.soton.ac.uk/srg/softwaretools/document/templates/)
% Sunil Patel (http://www.sunilpatel.co.uk/thesis-template/)
%
% Modified to McMaster format by Benjamin Furman (contact: https://www.xenben/com; Most up 
% to date template at https://github.com/benjaminfurman/McMaster_Thesis_Template, 
% occasionally updated on Overleaf template page)
%
% License:
% CC BY-NC-SA 3.0 (http://creativecommons.org/licenses/by-nc-sa/3.0/)
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%----------------------------------------------------------------------------------------
% DOCUMENT CONFIGURATIONS
%----------------------------------------------------------------------------------------

\documentclass[
11pt, % The default document font size, options: 10pt, 11pt, 12pt
oneside, % Two side (alternating margins) for binding by default, uncomment to switch to one side
english, % other languages available
singlespacing, % Single line spacing, alternatives: onehalfspacing or doublespacing
%draft, % Uncomment to enable draft mode (no pictures, no links, overfull hboxes indicated)
%nolistspacing, % If the document is onehalfspacing or doublespacing, uncomment this to set spacing in lists to single
%liststotoc, % Uncomment to add the list of figures/tables/etc to the table of contents
%toctotoc, % Uncomment to add the main table of contents to the table of contents
]{McMasterThesis} % The class file specifying the document structure


%----------------------------------------------------------------------------------------
% Import packages here
%----------------------------------------------------------------------------------------
\usepackage[utf8]{inputenc} % Required for inputting international characters
\usepackage[T1]{fontenc} % Output font encoding for international characters

\usepackage{lmodern} % could change font type by calling a different package
\usepackage{lastpage} % count pages
\usepackage{siunitx} % for scientific units (micro-liter, etc)
\setcounter{tocdepth}{2} % so that only section and sub sections appear in Table of Contents. Remove or set depth to 3 to include sub-sub-sections

%----------------------------------------------------------------------------------------
% Handling Citations
%----------------------------------------------------------------------------------------
\usepackage[backend=biber, giveninits=true, doi=false, natbib=true, url=false, eprint=false, style=authoryear, sorting=nyt, maxcitenames=2, maxbibnames=99, uniquename=false, uniquelist=false, dashed=false]{biblatex} % can change the maxbibnames to cut long author lists to specified length followed by et al., currently set to 99.
\DeclareFieldFormat[article,inbook,incollection,inproceedings,patent,thesis,unpublished]{title}{#1\isdot} % removes quotes around title
\renewbibmacro*{volume+number+eid}{%
  \printfield{volume}%
%  \setunit*{\adddot}% DELETED
  \printfield{number}%
  \setunit{\space}%
  \printfield{eid}}
\DeclareFieldFormat[article]{number}{\mkbibparens{#1}}
%\renewcommand*{\newunitpunct}{\space} % remove period after date, but I like it. 
\renewbibmacro{in:}{\ifentrytype{article}{}{\printtext{\bibstring{in}\intitlepunct}}} % this remove the "In: Journal Name" from articles in the bibliography, which happens with the ynt 
\renewbibmacro*{note+pages}{%
    \printfield{note}%
    \setunit{,\space}% could add punctuation here for after volume
    \printfield{pages}%
    \newunit}    
\DefineBibliographyStrings{english}{% clears the pp from pages
  page = {\ifbibliography{}{\adddot}},
  pages = {\ifbibliography{}{\adddot}},
} 
\DeclareNameAlias{sortname}{last-first}
\renewcommand*{\nameyeardelim}{\addspace} % remove comma in text between name and date
\addbibresource{Bibliography.bib} % The filename of the bibliography
\usepackage[autostyle=true]{csquotes} % Required to generate language-dependent quotes in the bibliography

% you'll have to play with the citation styles to resemble the standard in your field, or just leave them as is here. 
% or, if there is a bst file you like, just get rid of all this biblatex stuff and go back to bibtex. 

%----------------------------------------------------------------------------------------
% Collect all your header information from the chapters here, things like acronyms, custom commands, necessary packages, etc. 
%----------------------------------------------------------------------------------------
\usepackage{parskip} %this will put spaces between paragraphs
\setlength{\parindent}{15pt} % this will create and indent on all but the first paragraph of each section. 
% should maybe change to glossaries package
\usepackage{acro}
\DeclareAcronym{est}{
	short = EST,
	long  = expressed sequence tags
}

\DeclareAcronym{Xl}{
	short = \textit{X.~laevis},
	long  = \textit{Xenopus~laevis}
}
\DeclareAcronym{Xg}{
	short = \textit{X.~gilli},
	long  = \textit{Xenopus~gilli}
}

\usepackage{etoolbox}
\preto\chapter{\acresetall} % resets acronyms for each chapter

\usepackage{xspace} %helps spacing with custom commands. 
\newcommand{\oddname}{{\sc SoME goOfY LonG ThiNg With an AwkWarD NAme}\xspace}


\usepackage{pgfplotstable} % a much better way to handle tables
\pgfplotsset{compat=1.12}

% \usepackage{float} % if you need to demand figure/table placement, then this will allow you to use [H], which demands a figure placement. Beware, making LaTeX do things it doesn't want may lead to oddities.  


%%%%
% LINK COLORS
% You can control the link colors at the end of the McMasterThesis.cls file. There is also a true/false option there to turn off all link colors.  
%%%%


%----------------------------------------------------------------------------------------
%	THESIS INFORMATION
%----------------------------------------------------------------------------------------

\thesistitle{Thesis Title} % Your thesis title, print it elsewhere with \ttitle
\supervisor{Dr. Jane \textsc{Smith}} % Your supervisor's name, print it elsewhere with \supname
\examiner{} % Your examiner's name, print it elsewhere with \examname
\degree{Doctor of Philosophy} % Your degree name, print it elsewhere with \degreename
\author{John \textsc{Smith}} % Your name, print it elsewhere with \authorname
\addresses{} % Your address, print it elsewhere with \addressname

\subject{Biological Sciences} % Your subject area, print it elsewhere with \subjectname
\keywords{} % Keywords for your thesis, print it elsewhere with \keywordnames
\university{\href{http://www.mcmaster.ca/}{McMaster University}} % Your university's name and URL, print it elsewhere with \univname
\department{\href{http://www.biology.mcmaster.ca/}{Department of Biology}} % Your department's name and URL, print it elsewhere with \deptname
\group{\href{http://researchgroup.university.com}{Research Group Name}} % Your research group's name and URL, print it elsewhere with \groupname
\faculty{\href{http://www.science.mcmaster.ca/}{Faculty of Science}} % Your faculty's name and URL, print it elsewhere with \facname

% this sets up hyperlinks
\hypersetup{pdftitle=\ttitle} % Set the PDF's title to your title
\hypersetup{pdfauthor=\authorname} % Set the PDF's author to your name
\hypersetup{pdfkeywords=\keywordnames} % Set the PDF's keywords to your keywords

\begin{document}

 \frontmatter % Use roman page numbering style (i, ii, iii, iv...) for the pre-content pages

\pagestyle{plain} % Default to the plain heading style until the thesis style is called for the body content

%----------------------------------------------------------------------------------------
%	Half Title (lay title)
%----------------------------------------------------------------------------------------
%\begin{halftitle} % could not get this environment working
%\vspace*{\fill}
\vspace{6cm}
\begin{center}
A short 60 character title % ideally, but it doesn't seem to matter
\end{center}
%\vspace*{\fill}
\pagenumbering{gobble} % leave this here, McMaster doesn't want this page numbered
%\end{halftitle}
\clearpage

%----------------------------------------------------------------------------------------
%	TITLE PAGE
%----------------------------------------------------------------------------------------
\pagenumbering{gobble}
\begin{center}

\vfill
\textsc{\Large \ttitle} \\

\vfill
By \authorname, \\%% -----> List prior degrees after comma  <----

 \vfill
{\large \textit{A Thesis Submitted to the School of Graduate Studies in the Partial Fulfillment of the Requirements for the Degree \degreename}}\\

\vfill
{\large \univname\, \copyright\, Copyright by \authorname\, \today}\\[4cm] % replace \today with the submission date

\end{center}


%----------------------------------------------------------------------------------------
%	Descriptive note numbered ii
%----------------------------------------------------------------------------------------
% Need to add below info
\newpage
\pagenumbering{roman} % leave to turn numbering back on
\setcounter{page}{2} % leave here to make this page numbered ii, a Grad School requirement

\noindent % stops indent on next line
\univname \\ 
\degreename\, (\the\year) \\
Hamilton, Ontario (\deptname) \\[1.5cm]
TITLE: \ttitle \\
AUTHOR: \authorname\,  %list previous degrees
(\univname)  \\
SUPERVISOR: \supname\, \\ 
NUMBER OF PAGES: \pageref{lastoffront}, \pageref{LastPage}  % put in iv and number

\clearpage

%----------------------------------------------------------------------------------------
%	Lay abstract number iii
%----------------------------------------------------------------------------------------
% not actually included in most theses, though requested by the GSA
% uncomment below lines if you want to include one
%\section*{Lay Abstract}
%\addchaptertocentry{Lay Abstract}
% Type it here
%\clearpage
%----------------------------------------------------------------------------------------
%	ABSTRACT PAGE
%----------------------------------------------------------------------------------------

\section*{\Huge Abstract} 
\addchaptertocentry{Abstract}
% Type your abstract here. 
An abstract! 
\clearpage
%----------------------------------------------------------------------------------------
%	ACKNOWLEDGEMENTS
%----------------------------------------------------------------------------------------

\begin{acknowledgements}
\addchaptertocentry{\acknowledgementname} % Add the acknowledgments to the table of contents

The acknowledgments and the people to thank go here, don't forget to include your project adviser\ldots

\end{acknowledgements}

%----------------------------------------------------------------------------------------
%	LIST OF CONTENTS/FIGURES/TABLES PAGES
%----------------------------------------------------------------------------------------

\tableofcontents % Prints the main table of contents

\listoffigures % Prints the list of figures

\listoftables % Prints the list of tables

%----------------------------------------------------------------------------------------
%	ABBREVIATIONS
%----------------------------------------------------------------------------------------
% many theses don't use this section, as it will be declared at first use and again each chapter. Uncomment these four lines to activate if you want
%\clearpage
%\section*{\Huge Acronyms}
%\addchaptertocentry{Acronyms}
%\printacronyms[name] % name without an option stops the header

%----------------------------------------------------------------------------------------
%	DECLARATION PAGE
%----------------------------------------------------------------------------------------

\begin{declaration}
\addchaptertocentry{\authorshipname}

\noindent I, \authorname, declare that this thesis titled, \enquote{\ttitle} and the work presented in it are my own. I confirm that:

\begin{itemize} 
\item List each chapter
\item and what you have done for it
\end{itemize}
 
\end{declaration}


%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% optional page stuff
%----------------------------------------------------------------------------------------
% can do physical constraints and symbols pages, see the original thesis example on overleaf if you want to include them at https://www.overleaf.com/latex/templates/template-for-a-masters-slash-doctoral-thesis/mkzrzktcbzfl#.VlPeicorpE4
%----------------------------------------------------------------------------------------

%----------------------------------------------------------------------------------------
%	QUOTATION PAGE
%----------------------------------------------------------------------------------------

%\vspace*{0.2\textheight}

%\noindent\enquote{\itshape Thanks to my solid academic training, today I can write hundreds of words on virtually any topic without possessing a shred of information, which is how I got a good job in journalism.}\bigbreak

%\hfill Dave Barry

%----------------------------------------------------------------------------------------
%	DEDICATION
%----------------------------------------------------------------------------------------

% \dedicatory{For/Dedicated to/To my\ldots} 

%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%



%----------------------------------------------------------------------------------------
% The following bit is just here to make sure we end up on a new page and get the total number of roman numeral
\label{lastoffront}
\clearpage
% make sure this command is on the last of your frontmatter pages, i.e. only this command, a \clearpage then \mainmatter
% should be fine without modification
%----------------------------------------------------------------------------------------

%----------------------------------------------------------------------------------------
%	THESIS CONTENT - CHAPTERS
%----------------------------------------------------------------------------------------

\mainmatter % Begin numeric (1,2,3...) page numbering

\pagestyle{thesis} % Return the page headers back to the "thesis" style

% Include the chapters of the thesis as separate files from the Chapters folder
\input{Chapters/Chapt1}      
\input{Chapters/Chapt2} 

% I suggest only compiling one chapter at a time, and comment out the others. That way, the document will typeset faster. When your done with all the chapters, then uncomment them all. Don't worry about the numbering of chapters/figures/etc. LaTeX will take care of that. 

%----------------------------------------------------------------------------------------
%	THESIS CONTENT - APPENDICES
%----------------------------------------------------------------------------------------

\appendix % Cue to tell LaTeX that the following "chapters" are Appendices
\renewcommand{\thetable}{A\arabic{chapter}.\arabic{table}} % adds an A to table names in appendix (Table A1.1, A1.2...)
\renewcommand{\thefigure}{A\arabic{chapter}.\arabic{figure}} % same for figures
\renewcommand{\thesection}{A\arabic{section}}

% Include the appendices of the thesis as separate files from the Appendices folder
\input{Appendix/Supp_Chap1.tex}

%----------------------------------------------------------------------------------------
%	BIBLIOGRAPHY
%----------------------------------------------------------------------------------------

\printbibliography[heading=bibintoc]

%----------------------------------------------------------------------------------------

\end{document}