University of Manchester thesis and dissertation (muthesis)

# LaTeX thesis template
This is a template for typesetting theses at the University of Manchester.

This document is adapted from the template provided by the School of Mathematics, University of Manchester (last updated 13th August, 2013). It was merged with another document, originally provided by Electronics & Computer Science at the University of Southampton, but was extensively modified by a number of postgraduates in Geography & Environment at the University of Southampton through the years. These folks include Chris Hackney, followed by Tom Bishop and Robin Wilson. Gerard Capes and Tom Bishop produced this version of the template in 2016.

All of the materials here are licenced under CC-BY-SA v4.0 in lieu of any explicit licencing of the original material; see: https://creativecommons.org/licenses/by-sa/4.0/ for more details.

## BibTeX branch
This branch uses BibTeX for referencing, while the other branch uses Biber.
Biber is newer and has more advanced features.
BibTeX can be simpler to set up, especially for teaching where the desktop environment is more controlled than on a typical user's machine.

\chapter{Figures and Tables}
\section{Figures}
Figures are included using the code below. Remember there are environments for sideways figures and subfigures. 

\begin{figure}[tbp]
	\centering
		\includegraphics[width=1.00\textwidth]{example-image-a}
	\caption[Example image.]{An example images that uses the MWE package functions to call a dummy image.}
	\label{fig:editapic}
\end{figure}

\section{Tables}
Tables are complicated in \LaTeX. Table \ref{tab:itraxsetupsummary} is a simple example.

\begin{table}[tbp]
	\centering
		\begin{tabular}{lr}
		 \hline
		 Parameter     & Setting       \\ \hline
		 Tube          & Mo            \\
		 Voltage       & 30kV          \\
		 Current       & 30mA          \\
	   Exposure time & 30s           \\
		 Step size     & 400$\mu$m     \\
		 \hline			
		\end{tabular}
	\caption[Summary of parameters used in Itrax XRF data aquisition.]{Summary of parameters used in Itrax XRF data aquisition.}
	\label{tab:itraxsetupsummary}
\end{table}

\chapter{Introduction}
\section{The University Thesis Document}
This document is adapted from the template provided by the School of Mathematics, University of Manchester (last updated 13\textsuperscript{th} August, 2013. It was merged with another document, originally provided by Electronics \& Computer Science at the University of Southampton, but was extensively modified by a number of postgraduates in Geography \& Environment at the University of Southampton through the years. These folks include Chris Hackney, followed by Tom Bishop and Robin Wilson. Gerard Capes and Tom Bishop produced this version of the template in 2016.

\section{How to Use This Document}
Keep a copy of this in its original form for reference --- we have tried to include a few key examples of code from our own theses. Otherwise, simply modify as appropriate.

\section{Structure}
The thesis style sheet tells \LaTeX \ how to produce the output. The thesis document is where you define the variables, for example the title, your name and the chapters. The individual chapters are usually separate files (although you may combine and split them as you see fit), and images are stored as individual files. You can modify where you store these in the thesis document. Remember that paths can be relative or absolute --- relative paths are always relative to the location of the thesis document. This is recommended as it makes everything rather more portable.

@article{Payne2011,
author = {Payne, Richard J. and Lamentowicz, Mariusz and Mitchell, Edward a. D.},
doi = {10.1111/j.1502-3885.2010.00174.x},
file = {:C$\backslash$:/Users/thb1y12/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Payne, Lamentowicz, Mitchell - 2011 - The perils of taxonomic inconsistency in quantitative palaeoecology experiments with testate amoeb.pdf:pdf},
issn = {03009483},
journal = {Boreas},
number = {1},
pages = {15--27},
title = {{The perils of taxonomic inconsistency in quantitative palaeoecology: experiments with testate amoeba data}},
url = {http://doi.wiley.com/10.1111/j.1502-3885.2010.00174.x},
volume = {40},
year = {2011}
}
@article{Porinchu2003,
author = {Porinchu, David F and Macdonald, Glen M},
doi = {10.1191/0309133303pp388ra},
file = {:C$\backslash$:/Users/thb1y12/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Porinchu, Macdonald - 2003 - Progress in Physical Geography The use and application of freshwater midges (Chironomidae Insecta Diptera).pdf:pdf},
journal = {Progress in Physical Geography},
pages = {378},
title = {{Progress in Physical Geography The use and application of freshwater midges (Chironomidae: Insecta: Diptera) in geographical research}},
volume = {27},
year = {2003}
}

%% muthesis Class for LaTeX2e.
%% Last update 12th August 2013: amended evensidemargin for duplex

%%
%% Time-stamp: <July 23, 1997 11:33:00 BST [email protected]>
%%
%% This class file has been cobbled together for use of postgraduate
%% students in the Department of Computer Science at the University of
%% Manchester. Any comments or problems about its use should be made
%% via the local newsgroup man.cs.tex.
%%
%% The \school command can be used to define as a school other than
%% Mathematics, but no support is provided for users outside the
%% School of Mathematics.
%%
%% History
%%    Acquired for uk.ac.oxford.prg by Stephen Page <sdpage> on 16 Apr
%%    86 from Howard Trickey <[email protected]> , then hacked by
%%    Michael Fisher into Manchester University style.
%%
%%    Hacked from muthesis.sty by Rhod Davies ([email protected]) to
%%    match the latest ridiculous rules from the exams office (March
%%    1990) as given below.
%%
%%    Further modified by David Carlisle (DPC) September 1993.
%%
%%    Further modified by David Carlisle (DPC) September 1994.
%%      Add [PhD] option (default) and [MSc] option.
%%      Make into LaTeX2e Class file.
%%
%%    Further modified by Graham Gough at various dates
%%    Added [MPhil option.

%%    Modified William Dyke (WBD) July 1997 so that declaration is
%%    correct for use in departments other than Computer Science

%%    Modified by Chris Paul March 2006 to reflect new University 
%%    Schools and Faculty setup

%%    Modified by Chris Paul August 2013 to support duplex printed margins

%% Note that this makes no attempt to deal with multi-volume thesis -
%% if you do one that long you deserve everything you get.
%% 1) Page numbering starts on the title page and is arabic (i.e. title
%%       page is no.1), all pages are numbered (declaration, figures
%%       etc included), but the title page itself shall not show the
%%       page number!
%%
%%
%% 2) The preface will consist of the following sections in the
%%       following order!
%%       i  )    Title Page
%%       ii )    Contents page (actually we shall be fancy and have a
%%               table of contents, list of tables and list of figures.
%%               This is the correct place to put these extras)
%%       iii)    A short Abstract
%%       iv)     Declaration of honesty
%%       v)      Statement of qualifications and research
%%       vi)     Anything else you want, such as acknowledgements
%%
%%
%% 3) The ordering of the items on the title page has been changed
%%       slightly from the old muthesis style - it is now
%%               Statement - A thesis ..... Faculty of ...
%%               Year of Presentation
%%               Candidate's name
%%               Candidate's department
%%
%%
%% 4) Certain members of this university never having heard of
%%       typesetting, (i.e. the ones who will be the first against the
%%       wall when the revolution comes), the whole thing (apart from
%%       footnotes and quotations must be doublespaced. By a strang
%%       coincidence, a set of the thesis rules fell through a time
%%       warp from the future and landed on my desk. These note that
%%       single spacing is allowed in typeset thesis, with a footnote
%%       that those who were in favour of double spacing were the first
%%       against the wall when the revolution came.
%%               If everyone who submits a thesis goes and argues with
%%       them about this they may eventually get the hint, but this is
%%       unlikely. To get this we set baselinestretch to 1.5 which
%%       looks about right, and they have never noticed the difference.
%%       By all means set this to something sensible while producing
%%       draft copies, but remember DOUBLE SPACE before you hand in.
%%
%%
%% 5) The binding (left hand) margin must be no less than 40mm, other
%%       margins must be no less than 15mm, with page numbers falling
%%       within these margins. The binding margin is thus rather large,
%%       even when you take the binding (normally about 10mm) into account.
%%       Consequently you cannot reduce the other margins without
%%       making the page look unbalanced. Consequently we have a 40mm
%%       binding margin and 15 mm margin on all other sides. NOTE, this
%%       does not allow for any marginal notes. I recommend that you
%%       avoid using these, since a) there is not much space for them
%%       and they will format badly and b) they will violate the margin
%%       rules.
%%
%%
%% The rest of these notes will not be found in the written submission
%% rules, but come from converstions with the exams office.
%%
%%
%% 6)    They have not particular rules about the format of the
%%       bibliography, so long as you are consistent in your naming
%%       scheme. I would recommend the alpha style.
%%
%%
%% 7)    They do not seem to have any rules about appendices.
%%
%%
%% 8)    As before, any extra things you want to put in -
%%       acknowledgements etc, should come after the mandatory preface
%%       sections and before the first chapter.
%%
%% This style can usefully be used in conjunction with the doublespace
%% style which introduces a single spaced environment.
%%
%% It is not compatible with the drafthead style.


\ProvidesClass{muthesis}[2013/08/12 MU Thesis Class]

\DeclareOption{PhD}{\def\degreetitle{Doctor of Philosophy}}
\DeclareOption{MSc}{\def\degreetitle{Master of Science}}
\DeclareOption{MPhil}{\def\degreetitle{Master of Philosophy}}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{report}}
\def\@msc{Master of Science}

\ExecuteOptions{PhD}

\ProcessOptions


\LoadClass[a4paper]{report}

%% Manchester University PhD thesis style -- modifications to the report style
%%
\long\def\comment#1{}
\comment{

  Example of use:
    \documentclass[12pt,MSc]{muthesis}
    \begin{document}
    \title{How to Write Theses\\
            With Two Line Titles}
    \author{John Henry Candidate}
    \principaladviser{John Parker}
    \firstreader{John Green}
    \secondreader{John BigBooty\\(Another Department)}

    \beforeabstract
    \prefacesection{Abstract}
        This thesis answers all the questions you were afraid to ask ...
    \afterabstract
    \prefacesection{Acknowledgements}
        I would like to thank...
    \afterpreface

    \chapter{Introduction}
         ...
    \chapter{Conclusions}
         ...
    \appendix
    \chapter{A Long Proof}
         ...
%%%%    \addcontentsline{toc}{chapter}{Bibliography} %%% NO!
%%%% This \addcontentsline never worked anyway (it made the page
%%%% number in the table of contents one too small). It is not needed
%%%% at all with the sept 93 version. DPC.
    \bibliographystyle{alpha}
    \bibliography{mybib}


Documentation:
    It sets the margins and interline spacing and
    disallows page breaks at hyphens.

    The \beforeabstract command creates the title page, a copyright
    page (default), and a signature page (optional), the tables of
    contents, tables and figures. The signature page is not mentioned
    in the rules for submission, and by implication are not allowed.

    The user then includes the preface using the
    \prefacesection{Abstract} command.

    Next should come an \afterabstract command to insert the declaration.

    Then the user should put preface section(s), using the
    \prefacesection{section title} command. The first of these should
    be the statement of education and research, others may be
    acknowledgements etc.

    The \afterpreface command then  sets things up to start
    the main body (continuing the sequence of page numbering, but
    putting page headings etc.).

    Having one of \beforepreface or \afterpreface without the other
    may cause problems, so udon't do it.

    The following commands can control what goes in the front matter
    material:

        \title{thesis title}
        \author{author's name}
        \school{author's School}
        \faculty{author's Faculty}
        \principaladviser{the principal advisor's name}
           (or \principaladvisor, if you prefer advisor spelled with o)
        \firstreader{the first reader's name}
        \secondreader{the second reader's name}
        \submitdate{month year in which submitted to GPO}
                - date LaTeX'd if omitted
        \copyrightyear{year degree conferred (next year if submitted in Dec.)}
                - year LaTeX'd (or next year, in December) if omitted
        \copyrighttrue or \copyrightfalse
                - produce or don't produce a copyright page (true by default)
        \figurespagetrue or \figurespagefalse
                - produce or don't produce a List of Figures page
                  (true by default)
        \tablespagetrue or \tablespagefalse
                - produce or don't produce a List of Tables page
                  (true by default)
        \sigpagtrue or \sigpagfalse
                - produce or don't produce a signature page
                  (again false by default, as Manchester theses don't
                   require this. However, it's left in so that you can
                   your own `examiners page' if you like!)

        If you set all these to false, then perhaps you don't want any
        preface at all, so perhaps you hould leave out both \beforepreface
        and \afterpreface -).

This style uses interline spacing that is 1.5 times normal (about double
spaced), except in the figure and table environments where normal spacing
is used.

That can be changed by doing:
    \renewcommand{\baselinestretch}{1.6}
(or whatever you want instead of 1.6)
Unfortunately, that command probably won't take effect unless it comes
before the \begin{document} or after something like \small \normalsize.

The example above shows the 12pt substyle being used.  This seems to give
acceptable looking results, but it may be omitted to get smaller print.

}
%% We need >15mm  margins except on the binding edge, where it is >40mm
\oddsidemargin 15truemm \evensidemargin -8truemm
\marginparwidth 40pt \marginparsep 10pt
\topmargin -11.5truemm \headsep 7truemm
\textheight 245truemm \textwidth 154truemm

%% Disallow page breaks at hyphens (this will give some underfull vbox's,
%% so an alternative is to use \brokenpenalty=100 and manually search
%% for and fix such page breaks)
\brokenpenalty=10000

%% Use 1.5 times the normal baseline-to-baseline skip (approx double space)
\def\stretch{1.5}
\renewcommand{\baselinestretch}{\stretch}

%% Redefine the macro used for floats (including figures and tables)
%% so that single spacing is used.
\let\latex@xfloat=\@xfloat
\def\@xfloat #1[#2]{
        \latex@xfloat #1[#2]
        \def\baselinestretch{1}
        \@normalsize \normalsize
}

%% Redefine the macro used for footnotes to use single spacing
\long\def\@footnotetext#1{\insert\footins{\def\baselinestretch{1}\footnotesize
    \interlinepenalty\interfootnotelinepenalty
    \splittopskip\footnotesep
    \splitmaxdepth \dp\strutbox \floatingpenalty \@MM
    \hsize\columnwidth \@parboxrestore
   \edef\@currentlabel{\csname p@footnote\endcsname\@thefnmark}\@makefntext
    {\rule{\z@}{\footnotesep}\ignorespaces
      #1\strut}}}

%% \author, \title are defined in report; here are the rest of the
%% front matter defining macros
%% Note: If you really want, you can define your own macro for, say
%% \supervisor , just by copying the definitions of \principaladvisor
%%
\def\school#1{\gdef\@school{#1}}
\def\department#1{\gdef\@department{#1}}
\def\faculty#1{\gdef\@faculty{#1}}
\def\principaladviser#1{\gdef\@principaladviser{#1}}
\def\advis@r{Advisor} % default spelling---we are English!
%% Obviously, we could add a \supervisor macro
\def\principaladvisor#1{\gdef\@principaladviser{#1}\gdef\advis@r{Advisor}}
\def\firstreader#1{\gdef\@firstreader{#1}}
\def\secondreader#1{\gdef\@secondreader{#1}}
\def\submitdate#1{\gdef\@submitdate{#1}}
\def\copyrightyear#1{\gdef\@copyrightyear{#1}} % \author, \title in report
\def\@title{}
\def\@author{}
\def\@school{}
\def\@faculty{}
\def\@principaladviser{}\def\@firstreader{}\def\@secondreader{}
\def\@submitdate{\number\the\year}
%% Stanford says that December theses should have the next year as the
%% copyright year
\ifnum\month=12
    \@tempcnta=\year \advance\@tempcnta by 1
    \edef\@copyrightyear{\number\the\@tempcnta}
\else
    \def\@copyrightyear{\number\the\year}
\fi
\newif\ifcopyright \newif\iffigurespage \newif\iftablespage \newif\ifsigpage
\copyrighttrue \figurespagetrue \tablespagetrue \sigpagefalse


\ifx\degreetitle\@msc
    \def\@thesis{dissertation}
    \else
    \def\@thesis{thesis}
\fi

%% If you're doing an MSc, I'm sure you can guess which parts to change
%% below; if not then you shouldn't be doing one.
\def\titlep{%
        \thispagestyle{empty}%
        \null\vskip1in%
        \begin{center}
                \Huge\uppercase\expandafter{\@title}
        \end{center}
        \vfill
        \begin{center}
           \sc A \expandafter{\@thesis} submitted to the University of Manchester\\
           for the degree of \degreetitle\\
           in the Faculty of \expandafter{\@faculty}
        \end{center}
        \vfill
        \begin{center}
                \@submitdate
        \end{center}
        \vfill
        \begin{center}
                {\bf\@author}\\
                \ifx\@empty\@department
                \else
                Department of \expandafter{\@department}
                \fi
                
                \ifx\@empty\@school
                \else
                School of \expandafter{\@school}
                \fi
        \end{center}\vskip.5in\newpage}

\def\copyrightpage{%
\ifx\degreetitle\@msc
\prefacesection{Intellectual Property Statement}
\else
\prefacesection{Copyright Statement}
\fi

\begin{list}{\labelitemi}{\leftmargin=1em}
\item[{\bf i.}] The author of this \expandafter{\@thesis} (including any
appendices and/or schedules to this \expandafter{\@thesis}) owns certain
copyright or related rights in it (the ``Copyright'') and s/he has given
The University of Manchester certain rights to use such Copyright,
including for administrative purposes.
\item[{\bf ii.}] Copies of this \expandafter{\@thesis}, either in full or in
extracts and whether in hard or electronic copy, may be made {\bf only} in
accordance with the Copyright, Designs and Patents Act 1988 (as amended) and
regulations issued under it or, where appropriate, in accordance with
licensing agreements which the University has
\ifx\degreetitle\@msc
entered into.
\else
from time to time.
\fi
This page must form part of any such copies made.
\item[{\bf iii.}] The ownership of certain Copyright, patents, designs, trade
marks and other intellectual property (the ``Intellectual Property'') and any
reproductions of copyright works in the \expandafter{\@thesis}, for example
graphs and tables  (``Reproductions''), which may be described in this
\expandafter{\@thesis}, may not be owned by the author and may be owned by
third parties. Such Intellectual Property and Reproductions cannot and must
not be made available for use without the prior written permission of the
owner(s) of the relevant Intellectual Property and/or Reproductions.
\item[{\bf iv.}] Further information on the conditions under which disclosure,
publication and commercialisation of this \expandafter{\@thesis}, the
Copyright and any Intellectual Property and/or Reproductions described in
it may take place is available in the University IP Policy (see
http://documents.manchester.ac.uk/DocuInfo.aspx?DocID=487), in any relevant
\ifx\degreetitle\@msc
Dissertation
\else
Thesis
\fi
 restriction declarations deposited in the University Library, The University
Library's regulations (see
http://www.manchester.ac.uk/library/ab\-outus/regul\-ations) and in The 
University's 
\ifx\degreetitle\@msc
Guidance on Presentation of Dissertations.
\else
Policy on Presentation of Theses.
\fi
\end{list}
\vfill\newpage}

\long\def\signature#1{%
\begin{center}
\begin{minipage}{4in}
\parindent=0pt
I certify that I have read this thesis and that in my opinion
it is fully adequate, in scope and in quality, as a dissertation for the degree
of \degreetitle.
\par
\vspace{.5in}
\hbox to 4in{\hfil\shortstack{\vrule width 3in height 0.4pt\\#1}}
\end{minipage}
\end{center}}

\def\signaturepage{%
        \signature{\@principaladviser\\(Principal \advis@r)}
        \vfill
        \signature\@firstreader
        \vfill
        \signature\@secondreader
        \vfill
%% Again, the real format will have to be added here%
        \begin{center}
        \begin{minipage}{4in}
        Approved for the University Committee on Graduate Studies:\par
        \vspace{.5in}
        \hbox to 4in{\hfil\shortstack{\vrule width 3in height 0.4pt\\
                        Dean of Graduate Studies \& Research}}
        \end{minipage}
        \end{center}}

\def\declaration{No portion of the work referred to in the
\expandafter{\@thesis} has been submitted in support of an application for
another degree or qualification of this or any other university or other
institute of learning.}
\def\declpage{%
\prefacesection{Declaration}
        \begin{center}
        \begin{minipage}{4in}
            \parindent=0pt
            \declaration 
            \par
        \end{minipage}%
        \end{center}%
        \vfill}

\def\beforeabstract{
        \pagenumbering{arabic}
        \pagestyle{plain}
        \titlep
        \ifsigpage\signaturepage\fi
        \tableofcontents
	\vfill
	\centerline{Word count \wordcount}
        \newpage
        \iftablespage
                \addvspace{10pt}
                \listoftables
                \newpage
        \fi
        \iffigurespage
                \addvspace{10pt}
                \listoffigures
                \newpage
        \fi
        \addcontentsline{toc}{chapter}{Abstract}
        \ifx\degreetitle\@msc
             \chapter*{Abstract}
             \else
             \begin{center}\LARGE\bf The University of Manchester\end{center}
             \noindent{\bf\@author}\\
             \noindent{\bf\degreetitle}\\
             \noindent{\bf\@title}\\
             \noindent{\bf\today}\\[0.1\baselineskip]
             \def\baselinestretch{1.0}\normalsize
        \fi
        }

\def\afterabstract{
%% \newpage inserted by DPC 15/9/93
%% make the declaration come on the page after the abstract.
        \def\baselinestretch{\stretch}\normalsize
        \newpage
        \declpage
        \ifcopyright\copyrightpage\fi % moved to conform with 95 regs
        }

%% The declaration page above is the standard
%% declaration, but if you want the other sort ( where you admit
%% that parts of your thesis have been used elsewhere) then you'll
%% have to hack it yourself -- just replace the text by what you'd like
%%
\def\prefacesection#1{%
        \chapter*{#1}
        \addcontentsline{toc}{chapter}{#1}}

%% The \addvspace business below is to avoid the extra space that gets put
%% in the tables of figures and tables between chapters (it makes no sense
%% now that the numbering is continuous)
\def\afterpreface{\newpage
        \pagestyle{headings}}

\pagestyle{headings}

%% This produces the chapter title at the top of each page. It can be
%% changed in the obvious way, e.g., \pagestyle{empty} or \pagestyle{plain}
%%

%%% DPC 15/9/93 Make the bibliography generate an entry in the table
%%% of contents.

\def\thebibliography#1{\chapter*{\bibname\@mkboth
  {\uppercase{\bibname}}{\uppercase{\bibname}}}%
  \addcontentsline{toc}{chapter}{\bibname}%
  \list
  {\@biblabel{\arabic{enumiv}}}{\settowidth\labelwidth{\@biblabel{#1}}%
    \leftmargin\labelwidth
    \advance\leftmargin\labelsep
    \usecounter{enumiv}%
    \let\p@enumiv\@empty
    \def\theenumiv{\arabic{enumiv}}}%
    \def\newblock{\hskip .11em plus.33em minus.07em}%
    \sloppy\clubpenalty4000\widowpenalty4000
    \sfcode`\.=\@m}

\def\endthebibliography{%
  \def\@noitemerr{\@warning{Empty `thebibliography' environment}}%
  \endlist}

\chapter{Text and Cross-Referencing}
\section{Text}
Text can be written directly here. Sections and subsections can also be created.

\subsection{Special Characters}
Special characters can be inserted; see the crib sheets. For example, the El Ni\~no Southern Oscillation (ENSO) modulates climate across much of South America. 

\section{Cross-Referencing} \label{subsectionxrefs}
Almost any object can be cross-referenced using a unique label. For example, this is Section \ref{subsectionxrefs}. This all automatically updates so you mustn't worry about whether things point to the right place. You can do other tricks --- for example, Section \ref{subsectionxrefs} is on page \pageref{subsectionxrefs}.

\section{Inline Citations}
This document uses a package that deals with inline citations and automatically generates a bibliography. It is powerful in the way it can format the inline references; for example, it can cite a reference in parentheses \citep[\textit{e.g.}][]{Payne2011}, or without. It can cite just the author \citeauthor{Porinchu2003}, or include a figure reference \citep[\textit{e.g.}][Figure 1]{Payne2011}. 

\section{Math Mode}
\LaTeX \ allows for equations in their own environment. This can be inline, for example, $e=mc^{2}$.

\section{Quotes}
Sometimes it is nice to properly quote text, for example:

\begin{quote}						
The quick brown fox jumped over the lazy dog.					
\end{quote}

% Delete the MSc option if you are doing a PhD, or replace it with MPhil
% for a Master of Philosophy thesis
%
% The 12pt option is required by the 2001/02 thesis regulations
% Last update 15th August 2007: new Abstract format and Copyright Statement

% Replace MSc with PhD for PhD theses
% Remove the twoside option for single-sided printing
\documentclass[12pt,MSc,twoside]{muthesis}
% This file is thesis.tex
% For the history of this document, see the header to the accompanying stylesheet, geogthesis.cls
% This document lays out the body of the thesis, bookends and chapter order. This is the document you need to compile.

% This section configures the key parameters of the document, as well as expanding and modifying various typesetting functions.
\usepackage[activate={true,nocompatibility},final,
						tracking=true,factor=1100,stretch=10,
						shrink=10]{microtype}															% This makes the typesetting prettier
\usepackage[T1]{fontenc}																			
\usepackage{lmodern}
\usepackage{amsmath, amsthm, amssymb}													% These packages extend math mode functions
\usepackage{natbib}																						% This defines how references are handled (via package natbib)
\usepackage{multicol}																					% Package allows multiple columns of text - good for some lists
\usepackage{xcolor}																						% Package allows for easier colour management

% These packages help make better tables and figures
\usepackage{tabularx}																					% This package gives the option of using tabularx rather than tabular
\usepackage{longtable} 																				% Package allows spanning of tables over multiple pages
\usepackage{multirow}																					% Package used in tables to set cell width to natural text widths
\usepackage{booktabs}																					% Allows the use of \toprule, \midrule, \bottomrule insead of \hline

% These packages help with placement of floats
\usepackage{rotating}																					% This package allows for sidewaysfigure and sideways table options
\usepackage{afterpage} 																				% Allows command \afterpage{\clearpage} to allow clever page float control
\usepackage[section]{placeins} 																% Forces a page of undrawn floats after each section c.f. \FloatBarrier
\usepackage{flafter} 																					% Forces floats to only be drawn after they appear their placement in the document
%\usepackage{samepage}																				% Enables an environment that forces elements onto the same page

% These packages modify pdf properties
\usepackage{pdflscape}																				% This package can be used to make l'scape pages l'scape in pdf docs	
\usepackage{pdfpages}																					% Package allows for clever insertion of pdf pages into a document

% These packages are all to do with automatic cross-referencing
\usepackage{footnote}																					% Provides an easy way of working with footnotes
\numberwithin{equation}{chapter}															% This resets the equation number at the start of each chapter
\setcounter{secnumdepth}{5}																		% This changes the depth of section numbering
\usepackage{caption} 																					% Allows \captionsetup[figure]{list=no} to listing on/off for floats - good for appendicies
\usepackage{subfigure} 																				% Enables the use of subfigures
%\usepackage{makeidx}																					% If you want to create an index for your thesis, you have too much time on your hands
%\usepackage{showidx}																					% Use these two packages and think about a taking up a hobby
%\usepackage[none]{hyphenat}    															% This can enable or disable hyphenation on line breaks. Why would you do this?
%\hyphenation{words}																					% This defines words that cannot be hyphenated, or defines acceptable hyphenations. Much better.

% The following are useful sundries for little jobs						
%\usepackage{siunitx}																					% Automagically generate si units
%\sisetup{detect-weight, detect-display-math}									% Settings for the above
%\sisetup{detect-inline-weight=math}													% Settings for the above

% The following options are useful for drafting documents
%\usepackage{lineno} 																					% Provides line numbers on paragraphs, and references therein. Useful for transcripts
%\usepackage{draftwatermark}																	% Prints a draft watermark
%\linenumbers 																								% Makes whole document line numbers. Remember to use lineno package and \resetlinenumber[1]

% The hyperref package is used to create clickable cross-reference links.
\usepackage[hidelinks]{hyperref}

\begin{document}
% The following changes the page colour of the pdf for dyslexics.
%\pagecolor{blue!30} 																					% Changes page colour. Useful for dyslexics.
\title{Your paper}
\author{The Author's Name}
\department{The Author's Department}
% Faculty of Life Sciences people should comment the next line out
\school{The Author's School}
\faculty{The Author's Faculty}
\def\wordcount{nnnnn}

% Uncomment the line below to suppress the `List of Tables' page (optional)
%\tablespagefalse

% Uncomment the line below to suppress the `List of Figures' page (optional)
%\figurespagefalse

% Uncomment the line below to use a customised Declaration statement
%\def\declaration{All the work in this thesis has been sourced from Google.}

\beforeabstract

Write your abstract here: Remember, it must fit on this A4 page and should
describe contents of the thesis/dissertation. Here might also be a good place
to indicate what you have achieved in the thesis/dissertation and, in the
case of a PhD, what new results you have discovered. Note that for a PhD
single-spacing is used throughout the Abstract, including displayed equations
\[
e = mc^{2}
\]
as for the above example.

\afterabstract

% The next part is optional
\prefacesection{Acknowledgements}
I would like to thank...

% The next line is NOT optional and MUST appear
\afterpreface

% The following defines the chapter files and their order.
\raggedright          																					%justifies left, according to the university specifications. Comment out for fully justified.
\include{intro}
\include{textandxref}
\include{figuresandtables} 

\bibliographystyle{chicago}
\bibliography{library}

% Comment the following THREE lines if you do NOT have an Appendix
%\appendix
%\chapter{A Long Proof}
%.........

% If you need more than one appendix, then just use another \chapter command
%\chapter{Yet Another Appendix}

\end{document}