main.tex

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% OXFORD THESIS TEMPLATE

% Use this template to produce a standard thesis that meets the Oxford University requirements for DPhil submission
%
% Originally by Keith A. Gillow (gillow@maths.ox.ac.uk), 1997
% Modified by Sam Evans (sam@samuelevansresearch.org), 2007
% Modified by John McManigle (john@oxfordechoes.com), 2015
%
% This version Copyright (c) 2015-2017 John McManigle
%
% Broad permissions are granted to use, modify, and distribute this software
% as specified in the MIT License included in this distribution's LICENSE file.
%

% I've (John) tried to comment this file extensively, so read through it to see how to use the various options.  Remember
% that in LaTeX, any line starting with a % is NOT executed.  Several places below, you have a choice of which line to use
% out of multiple options (eg draft vs final, for PDF vs for binding, etc.)  When you pick one, add a % to the beginning of
% the lines you don't want.


%%%%% CHOOSE PAGE LAYOUT
% The most common choices should be below.  You can also do other things, like replacing "a4paper" with "letterpaper", etc.

% This one will format for two-sided binding (ie left and right pages have mirror margins; blank pages inserted where needed):
% \documentclass[a4paper,twoside]{ociamthesis}

% This one will format for one-sided binding (ie left margin > right margin; no extra blank pages):
\documentclass[a4paper]{ociamthesis}
% This one will format for PDF output (ie equal margins, no extra blank pages):
% \documentclass[a4paper,nobind]{ociamthesis} 

%%%%% SELECT YOUR DRAFT OPTIONS
% Three options going on here; use in any combination.  But remember to turn the first two off before
% generating a PDF to send to the printer!

% This adds a "DRAFT" footer to every normal page.  (The first page of each chapter is not a "normal" page.)
%\fancyfoot[C]{\emph{DRAFT Printed on \today}}  

% This highlights (in blue) corrections marked with (for words) \mccorrect{blah} or (for whole
% paragraphs) \begin{mccorrection} . . . \end{mccorrection}.  This can be useful for sending a PDF of
% your corrected thesis to your examiners for review.  Turn it off, and the blue disappears.
% \correctionstrue


%%%%% BIBLIOGRAPHY SETUP
% Note that your bibliography will require some tweaking depending on your department, preferred format, etc.
% The options included below are just very basic "sciencey" and "humanitiesey" options to get started.
% If you've not used LaTeX before, I recommend reading a little about biblatex/biber and getting started with it.
% If you're already a LaTeX pro and are used to natbib or something, modify as necessary.
% Either way, you'll have to choose and configure an appropriate bibliography format...

% The science-type option: numerical in-text citation with references in order of appearance.
\usepackage[style=ieee,maxcitenames=3,maxbibnames=3]{biblatex}
% \usepackage{cite}
\usepackage{physics}
\usepackage{amsmath}
\usepackage{subcaption}
\usepackage{pdfpages}
\usepackage{caption}
\usepackage[mathlines]{lineno}
\usepackage{siunitx}
\usepackage[permil]{overpic}
\usepackage{url}
% \linenumbers

\newcommand*{\bibtitle}{References}
% The humanities-type option: author-year in-text citation with an alphabetical works cited.
%\usepackage[style=authoryear, sorting=nyt, backend=biber, maxcitenames=2, useprefix, doi=false, isbn=false]{biblatex}
%\newcommand*{\bibtitle}{Works Cited}

% This makes the bibliography left-aligned (not 'justified') and slightly smaller font.
\renewcommand*{\bibfont}{\raggedright\small}

% Change this to the name of your .bib file (usually exported from a citation manager like Zotero or EndNote).
\addbibresource{references.bib}


% Uncomment this if you want equation numbers per section (2.3.12), instead of per chapter (2.18):
%\numberwithin{equation}{subsection}



%%%%% THESIS / TITLE PAGE INFORMATION
% Everybody needs to complete the following:
\title{Search for a low-energy excess of electron neutrinos in MicroBooNE}
\author{Stefano Roberto Soleti}
\college{St Catherine's College}

% Master's candidates who require the alternate title page (with candidate number and word count)
% must also un-comment and complete the following three lines:
%\masterssubmissiontrue
%\candidateno{933516}
%\wordcount{28,815}

% Uncomment the following line if your degree also includes exams (eg most masters):
\renewcommand{\submittedtext}{A thesis submitted for the degree of}
% Your full degree name.  (But remember that DPhils aren't "in" anything.  They're just DPhils.)
\degree{Doctor of Philosophy}
% Term and year of submission, or date if your board requires (eg most masters)
\degreedate{Hilary 2019}


%%%%% YOUR OWN PERSONAL MACROS
% This is a good place to dump your own LaTeX macros as they come up.

% To make text superscripts shortcuts
	
\renewcommand{\th}{\textsuperscript{th}} % ex: I won 4\th place
\newcommand{\nd}{\textsuperscript{nd}}
\renewcommand{\st}{\textsuperscript{st}}
\newcommand{\rd}{\textsuperscript{rd}}

\let\oldequation\equation
\let\oldendequation\endequation

\let\oldalign\align
\let\oldendalign\endalign

\renewenvironment{equation}
  {\linenomathNonumbers\oldequation}
  {\oldendequation\endlinenomath}


\renewenvironment{align}
  {\linenomathNonumbers\oldalign}
  {\oldendalign\endlinenomath}
%%%%% THE ACTUAL DOCUMENT STARTS HERE
\begin{document}
\newcommand\barparen[1]{\overset{(-)}{#1}}


%%%%% CHOOSE YOUR LINE SPACING HERE
% This is the official option.  Use it for your submission copy and library copy:
\setlength{\textbaselineskip}{22pt plus2pt}
% This is closer spacing (about 1.5-spaced) that you might prefer for your personal copies:
%\setlength{\textbaselineskip}{18pt plus2pt minus1pt}

% You can set the spacing here for the roman-numbered pages (acknowledgements, table of contents, etc.)
\setlength{\frontmatterbaselineskip}{17pt plus1pt minus1pt}

% Leave this line alone; it gets things started for the real document.
\setlength{\baselineskip}{\textbaselineskip}


%%%%% CHOOSE YOUR SECTION NUMBERING DEPTH HERE
% You have two choices.  First, how far down are sections numbered?  (Below that, they're named but
% don't get numbers.)  Second, what level of section appears in the table of contents?  These don't have
% to match: you can have numbered sections that don't show up in the ToC, or unnumbered sections that
% do.  Throughout, 0 = chapter; 1 = section; 2 = subsection; 3 = subsubsection, 4 = paragraph...

% The level that gets a number:
\setcounter{secnumdepth}{2}
% The level that shows up in the ToC:
\setcounter{tocdepth}{2}


%%%%% ABSTRACT SEPARATE
% This is used to create the separate, one-page abstract that you are required to hand into the Exam Schools.  You can comment it out to generate a PDF for printing or whatnot.
\begin{abstractseparate}
	\input{text/abstract} % Create an abstract.tex file in the 'text' folder for your abstract.
\end{abstractseparate}


% JEM: Pages are roman numbered from here, though page numbers are invisible until ToC.  This is in
% keeping with most typesetting conventions.
\begin{romanpages}

% Title page is created here
\maketitle

\begin{originality}
 	\input{text/originality}
\end{originality}
%%%%% DEDICATION -- If you'd like one, un-comment the following.
%\begin{dedication}
%This thesis is dedicated to\\
%someone\\
%for some special reason\\
%\end{dedication}

%%%%% ACKNOWLEDGEMENTS -- Nothing to do here except comment out if you don't want it.
\begin{acknowledgements}
 	\input{text/acknowledgements}
\end{acknowledgements}

%%%%% ABSTRACT -- Nothing to do here except comment out if you don't want it.
\begin{abstract}
	\input{text/abstract}
\end{abstract}

%%%%% MINI TABLES
% This lays the groundwork for per-chapter, mini tables of contents.  Comment the following line
% (and remove \minitoc from the chapter files) if you don't want this.  Un-comment either of the
% next two lines if you want a per-chapter list of figures or tables.
\dominitoc % include a mini table of contents
%\dominilof  % include a mini list of figures
%\dominilot  % include a mini list of tables

% This aligns the bottom of the text of each page.  It generally makes things look better.
\flushbottom

% This is where the whole-document ToC appears:
\tableofcontents

\listoffigures
	\mtcaddchapter
% \mtcaddchapter is needed when adding a non-chapter (but chapter-like) entity to avoid confusing minitoc

% Uncomment to generate a list of tables:
\listoftables
	\mtcaddchapter

%%%%% LIST OF ABBREVIATIONS
% This example includes a list of abbreviations.  Look at text/abbreviations.tex to see how that file is
% formatted.  The template can handle any kind of list though, so this might be a good place for a
% glossary, etc.
\include{text/abbreviations}

% The Roman pages, like the Roman Empire, must come to its inevitable close.
\end{romanpages}


%%%%% CHAPTERS
% Add or remove any chapters you'd like here, by file name (excluding '.tex'):
\flushbottom
\include{text/ch1-intro}
\include{text/ch2-neutrinophysics}
\include{text/ch3-anomalies}
\include{text/ch4-microboone}
\include{text/ch5-eventreco}
\include{text/ch6-analysis}
\include{text/ch6b-systematics}
\include{text/ch6c-sensitivity}
\include{text/ch7-conclusions}



%% APPENDICES %% 
% Starts lettered appendices, adds a heading in table of contents, and adds a
%    page that just says "Appendices" to signal the end of your main text.
\startappendices
% Add or remove any appendices you'd like here:
\include{text/appendix-1}


%%%%% REFERENCES

% JEM: Quote for the top of references (just like a chapter quote if you're using them).  Comment to skip.

\setlength{\baselineskip}{0pt} % JEM: Single-space References

{\renewcommand*\MakeUppercase[1]{#1}%
\printbibliography[heading=bibintoc,title={\bibtitle}]}


\end{document}