memoirthesis.tex

%\title{University of Bristol Thesis Template}
\RequirePackage[l2tabu]{nag}		% Warns for incorrect (obsolete) LaTeX usage
%
%
% File: memoirthesis.tex
% Author: Victor Brena
% Description: Contains the thesis template using memoir class,
% which is mainly based on book class but permits better control of 
% chapter styles for example. This template is an adaptation and 
% modification of Oscar's.
% 
% Memoir is a flexible class for typesetting poetry, fiction, 
% non-fiction and mathematical works as books, reports, articles or
% manuscripts. CTAN repository is found at:
% http://www.ctan.org/tex-archive/macros/latex/contrib/memoir/
%
%
% UoB guidelines for thesis presentation were found at:
% http://www.bris.ac.uk/esu/pg/pgrcop11-12topic.pdf#page=49
%
% UoB guidelines:
%
% The dissertation must be printed on A4 white paper. Paper up to A3 may be used
% for maps, plans, diagrams and illustrative material. Pages (apart from the
% preliminary pages) should normally be double-sided.
%
% Memoir class loads useful packages by default (see manual).
\documentclass[a4paper,11pt,leqno,openbib,oldfontcommands]{memoir} %add 'draft' to turn draft option on (see below)
%
%
% Adding metadata:
\let\ordinal\relax
\usepackage{datetime}
\usepackage{ifpdf}
\ifpdf
\pdfinfo{
   /Author (Author's name)
   /Title (PhD Thesis)
   /Keywords (One; Two;Three)
   /CreationDate (D:\pdfdate)
}
\fi
% When draft option is on. 
\ifdraftdoc 
	\usepackage{draftwatermark}				%Sets watermarks up.
	\SetWatermarkScale{0.3}
	\SetWatermarkText{\bf Draft: \today}
\fi
%
% Declare figure/table as a subfloat.
\newsubfloat{figure}
\newsubfloat{table}
% Better page layout for A4 paper, see memoir manual.
\settrimmedsize{297mm}{210mm}{*}
\setlength{\trimtop}{0pt} 
\setlength{\trimedge}{\stockwidth} 
\addtolength{\trimedge}{-\paperwidth} 
\settypeblocksize{634pt}{448.13pt}{*} 
\setulmargins{4cm}{*}{*} 
\setlrmargins{*}{*}{1.5} 
\setmarginnotes{17pt}{51pt}{\onelineskip} 
\setheadfoot{\onelineskip}{2\onelineskip} 
\setheaderspaces{*}{2\onelineskip}{*} 
\checkandfixthelayout
%
\frenchspacing
% Font with math support: New Century Schoolbook
% \usepackage{fouriernc}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
%
% UoB guidelines:
%
% Text should be in double or 1.5 line spacing, and font size should be
% chosen to ensure clarity and legibility for the main text and for any
% quotations and footnotes. Margins should allow for eventual hard binding.
%
% Note: This is automatically set by memoir class. Nevertheless \OnehalfSpacing 
% enables double spacing but leaves single spaced for captions for instance. 
\OnehalfSpacing 
%
% Sets numbering division level
\setsecnumdepth{subsection} 
\maxsecnumdepth{subsubsection}
%
% Chapter style (taken and slightly modified from Lars Madsen Memoir Chapter 
% Styles document
\usepackage{calc,soul,fourier} %
\makeatletter 
\newlength\dlf@normtxtw 
\setlength\dlf@normtxtw{\textwidth} 
\newsavebox{\feline@chapter} 
\newcommand\feline@chapter@marker[1][4cm]{%
	\sbox\feline@chapter{% 
		\resizebox{!}{#1}{\fboxsep=1pt%
			\colorbox{gray}{\color{white}\thechapter}% 
		}}%
		\rotatebox{90}{% 
			\resizebox{%
				\heightof{\usebox{\feline@chapter}}+\depthof{\usebox{\feline@chapter}}}% 
			{!}{\scshape\so\@chapapp}}\quad%
		\raisebox{\depthof{\usebox{\feline@chapter}}}{\usebox{\feline@chapter}}%
} 
\newcommand\feline@chm[1][4cm]{%
	\sbox\feline@chapter{\feline@chapter@marker[#1]}% 
	\makebox[0pt][c]{% aka \rlap
		\makebox[1cm][r]{\usebox\feline@chapter}%
	}}
\makechapterstyle{daleifmodif}{
	\renewcommand\chapnamefont{\normalfont\Large\scshape\raggedleft\so} 
	\renewcommand\chaptitlefont{\normalfont\Large\bfseries\scshape} 
	\renewcommand\chapternamenum{} \renewcommand\printchaptername{} 
	\renewcommand\printchapternum{\null\hfill\feline@chm[2.5cm]\par} 
	\renewcommand\afterchapternum{\par\vskip\midchapskip} 
	\renewcommand\printchaptertitle[1]{\color{gray}\chaptitlefont\raggedleft ##1\par}
} 
\makeatother 
\chapterstyle{daleifmodif}
%
% UoB guidelines:
%
% The pages should be numbered consecutively at the bottom centre of the
% page.
\makepagestyle{myvf} 
\makeoddfoot{myvf}{}{\thepage}{} 
\makeevenfoot{myvf}{}{\thepage}{} 
\makeheadrule{myvf}{\textwidth}{\normalrulethickness} 
\makeevenhead{myvf}{\small\textsc{\leftmark}}{}{} 
\makeoddhead{myvf}{}{}{\small\textsc{\rightmark}}
\pagestyle{myvf}
%
% Oscar's command (it works):
% Fills blank pages until next odd-numbered page. Used to emulate single-sided
% frontmatter. This will work for title, abstract and declaration. Though the
% contents sections will each start on an odd-numbered page they will
% spill over onto the even-numbered pages if extending beyond one page
% (hopefully, this is ok).
\newcommand{\clearemptydoublepage}{\newpage{\thispagestyle{empty}\cleardoublepage}}
%
%
% Creates indexes for Table of Contents, List of Figures, List of Tables and Index
\makeindex
% \printglossaries below creates a list of abbreviations. \gls and related
% commands are then used throughout the text, so that latex can automatically
% keep track of which abbreviations have already been defined in the text.
%
% The import command enables each chapter tex file to use relative paths when
% accessing supplementary files. For example, to include
% chapters/brewing/images/figure1.png from chapters/brewing/brewing.tex we can
% use
% \includegraphics{images/figureand the m1}
% instead of
% \includegraphics{chapters/brewing/images/figure1}
\usepackage{import}

% Add other packages needed for chapters here. For example:

\usepackage[centertags]{amsmath}			%Writes maths centred down
\usepackage{xfrac}                      % pretty fractions
\usepackage{siunitx}                    % units
\usepackage{bm}                         % bold symbols
\usepackage{amssymb}					%Calls AMS symbols

\usepackage{graphicx}					%Calls figure environment
\usepackage{longtable,rotating}			%Long tab environments including rotation. 
\usepackage{tabularx}              % for better tables
\usepackage{xltabular}
\newcolumntype{Y}{>{\centering\arraybackslash}X}

\usepackage[utf8]{inputenc}			%Needed to encode non-english characters 
									%directly for mac
\usepackage{colortbl}					%Makes coloured tables
\usepackage{float}						%Helps to place figures, tables, etc. 
\usepackage{verbatim}					%Permits pre-formated text insertion

\usepackage{latexsym}					%Extra symbols
% \usepackage[square,numbers,
% 		     sort&compress]{natbib}		%Calls bibliography commands 
\usepackage{url}						%Supports url commands
\usepackage[spanish,english]{babel}		%For languages characters and hyphenation
\usepackage{color}                    				%Creates coloured text and background

\usepackage{memhfixc}					%Must be used on memoir document 
									%class after hyperref
\usepackage{enumerate}					%For enumeration counter
\usepackage{footnote}					%For footnotes
\usepackage{microtype}					%Makes pdf look better.
\usepackage{rotfloat}					%For rotating and float environments as tables, 
									%figures, etc. 
\usepackage{alltt}						%LaTeX commands are not disabled in 
									%verbatim-like environment
\usepackage[ruled,vlined]{algorithm2e}
\usepackage{chemfig}
\usepackage{relsize}
% \usepackage{exscale} % change size of sums and products

%Reduce widows  (the last line of a paragraph at the start of a page) and orphans 
% (the first line of paragraph at the end of a page)
\widowpenalty=1000
\clubpenalty=1000

\DeclareMathOperator*{\argmax}{arg\,max}
\DeclareMathOperator*{\argmin}{arg\,min}
\DeclareSIUnit[number-unit-product = {}]\cal{\mathrm{cal}}
\DeclareSIUnit[number-unit-product = {}]\atm{\mathrm{atm}}
\DeclareSIUnit\molar{\mole\per\cubic\deci\metre}
\newcommand{\diag}[1]{\textnormal{diag} #1}                                                    %Defines diag operator
% New definition of square root:
% it renames \sqrt as \oldsqrt
\let\oldsqrt\sqrt
% it defines the new \sqrt in terms of the old one
\def\sqrt{\mathpalette\DHLhksqrt}
\def\DHLhksqrt#1#2{%
\setbox0=\hbox{$#1\oldsqrt{#2\,}$}\dimen0=\ht0
\advance\dimen0-0.2\ht0
\setbox2=\hbox{\vrule height\ht0 depth -\dimen0}%
{\box0\lower0.4pt\box2}}
%
% My caption style
\usepackage{caption}
 \captionsetup{
 format={hang},
 justification={justified},
 indention=-1.5cm,
 width={0.9\textwidth},
 labelfont ={sc},
 font = sf,
 labelsep ={colon}, %newline,
 tableposition =top,
 skip =5pt}
 
% \renewcommand{@algocf@capt@plain}{bottom}% formerly {bottom}
%
% Code 
\usepackage{listings}
\usepackage{xcolor}
\definecolor{codegreen}{rgb}{0,0.6,0}
\definecolor{codegray}{rgb}{0.5,0.5,0.5}
\definecolor{codepurple}{rgb}{0.58,0,0.82}
\definecolor{backcolour}{rgb}{0.95,0.95,0.92}
\lstdefinestyle{mystyle}{
    backgroundcolor=\color{backcolour},   
    commentstyle=\color{codegreen},
    keywordstyle=\color{magenta},
    numberstyle=\tiny\color{codegray},
    stringstyle=\color{codepurple},
    basicstyle=\ttfamily\footnotesize,
    breakatwhitespace=false,         
    breaklines=true,                 
    captionpos=b,                    
    keepspaces=true,                 
    numbers=left,                    
    numbersep=5pt,                  
    showspaces=false,                
    showstringspaces=false,
    showtabs=false,                  
    tabsize=2
}
\lstset{style=mystyle}

%
% enumeration styles
\usepackage{enumitem}
\setlist{noitemsep}

%
%An initial of the very first character of the content
\usepackage{lettrine}
\newcommand{\initial}[1]{%
	\lettrine[lines=3,lhang=0.33,nindent=0em]{
		\color{gray}
     		{\textsc{#1}}}{}}

%% BIBLIOGRAPHY STUFF
\usepackage[sorting=none,citestyle=numeric-comp, bibstyle=ieee, dashed=false]{biblatex}
% \usepackage{csquotes}

\DeclareSourcemap{
  \maps[datatype=bibtex, overwrite]{
    \map{
      \step[fieldset=isbn, null]
      \step[fieldset=issn, null]
      \step[fieldset=language, null]
    \step[fieldset=address, null]
    \step[fieldset=series, null]
    % \step[fieldset=language, null]
    }
  }
}

\usepackage[colorlinks=true,
		     allcolors=black]{hyperref}              %Creates hyperlinks in cross references

\addbibresource{thesisbiblio.bib}
\usepackage[most]{tcolorbox}
\newtcolorbox{highlighted}{colback=yellow,coltext=black,colframe=yellow,right=1pt,left=1pt,breakable}
%
%
\begin{document}
\fontfamily{lmss}\selectfont

% UoB guidlines:
%
% Preliminary pages
% 
% The five preliminary pages must be the Title Page, Abstract, Dedication
% and Acknowledgements, Author's Declaration and Table of Contents.
% These should be single-sided.
% 
% Table of contents, list of tables and illustrative material
% 
% The table of contents must list, with page numbers, all chapters,
 % sections and subsections, the list of references, bibliography, list of
% abbreviations and appendices. The list of tables and illustrations
% should follow the table of contents, listing with page numbers the
% tables, photographs, diagrams, etc., in the order in which they appear
% in the text.
% 
\frontmatter
\pagenumbering{roman}
%
\input{frontmatter/title}
\clearemptydoublepage
%
\input{frontmatter/abstract}
\clearemptydoublepage
%
\input{frontmatter/dedication}
\clearemptydoublepage
%
\input{frontmatter/declaration}
\clearemptydoublepage
%
\renewcommand{\contentsname}{Table of Contents}
\maxtocdepth{subsection}
\tableofcontents*
\addtocontents{toc}{\par\nobreak \mbox{}\hfill{\textbf{Page}}\par\nobreak}
\clearemptydoublepage
%
\listoftables
\addtocontents{lot}{\par\nobreak\textbf{{\scshape Table} \hfill Page}\par\nobreak}
\clearemptydoublepage
%
\listoffigures
\addtocontents{lof}{\par\nobreak\textbf{{\scshape Figure} \hfill Page}\par\nobreak}
\clearemptydoublepage
%
%
% The bulk of the document is delegated to these chapter files in
% subdirectories.
\mainmatter

\import{chapters/introduction/}{text.tex}
\clearemptydoublepage
\import{chapters/theory/}{text.tex}
\clearemptydoublepage
\import{chapters/water_hopping/}{text.tex}
\clearemptydoublepage
\import{chapters/msm_optimization/}{text.tex}
\clearemptydoublepage
\import{chapters/hmm_selection/}{text.tex}
\clearemptydoublepage
\import{chapters/aadh/}{text.tex}
\clearemptydoublepage
\import{chapters/conclusions/}{text.tex}

% And the appendix goes here
% \appendix
\import{chapters/appendices/}{text.tex}
\clearemptydoublepage

\printbibliography
\backmatter
\clearemptydoublepage

\end{document}






















% \usepackage{lipsum}					%Needed to create dummy text
% \usepackage{amsfonts} 					%Calls Amer. Math. Soc. (AMS) fonts

% \usepackage{stmaryrd}					%New AMS symbols
% \usepackage{amsthm}					%Calls AMS theorem environment
% \usepackage{newlfont}					%Helpful package for fonts and symbols
% \usepackage{layouts}					%Layout diagrams
% \newsubfloat{figure}                    % allows the subfigure env
% \usepackage{wasysym}					%More math symbols
% \usepackage{mathrsfs}					%Even more math symbols
% \usepackage{gensymb}
% \usepackage{upgreek }					%Calls other kind of greek alphabet
% \usepackage{etex}						%eTeXÕs extended support for counters
% \usepackage{fixltx2e}					%Eliminates some in felicities of the 
									%original LaTeX kernel
% \usepackage[version=0.96]{pgf}			%PGF/TikZ is a tandem of languages for producing vector graphics from a 
% \usepackage{tikz}						%geometric/algebraic description.
% \usetikzlibrary{arrows,shapes,snakes,
% 		       automata,backgrounds,
% 		       petri,topaths}				%To use diverse features from tikz		
%						
%
% New command definitions for my thesis
%
% \newcommand{\keywords}[1]{\par\noindent{\small{\bf Keywords:} #1}}                %Defines keywords small section
% \newcommand{\parcial}[2]{\frac{\partial#1}{\partial#2}}                             %Defines a partial operator
% \newcommand{\vectorr}[1]{\mathbf{#1}}                                                        %Defines a bold vector
% \newcommand{\vecol}[2]{\left(                                                                         %Defines a column vector
% 	\begin{array}{c} 
% 		\displaystyle#1 \\
% 		\displaystyle#2
% 	\end{array}\right)}
% \newcommand{\mados}[4]{\left(                                                       %Defines a 2x2 matrix
% 	\begin{array}{cc}
% 		\displaystyle#1 &\displaystyle #2 \\
% 		\displaystyle#3 & \displaystyle#4
% 	\end{array}\right)}
% \newcommand{\pgftextcircled}[1]{                                                %Defines encircled text
%     \setbox0=\hbox{#1}%
%     \dimen0\wd0%
%     \divide\dimen0 by 2%
%     \begin{tikzpicture}[baseline=(a.base)]%
%         \useasboundingbox (-\the\dimen0,0pt) rectangle (\the\dimen0,1pt);
%         \node[circle,draw,outer sep=0pt,inner sep=0.1ex] (a) {#1};
%     \end{tikzpicture}
% }
% \newcommand{\range}[1]{\textnormal{range }#1}                                             %Defines range operator
% \newcommand{\innerp}[2]{\left\langle#1,#2\right\rangle}                                 %Defines inner product
% \newcommand{\prom}[1]{\left\langle#1\right\rangle}                                         %Defines average operator
% \newcommand{\tra}[1]{\textnormal{tra} \: #1}                                                       %Defines trace operator
% \newcommand{\sign}[1]{\textnormal{sign\,}#1}                                                   %Defines sign operator
% \newcommand{\sech}[1]{\textnormal{sech} #1}                                                  %Defines sech

% \newcommand{\arcsech}[1]{\textnormal{arcsech} #1}                                       %Defines arcsech
% \newcommand{\arctanh}[1]{\textnormal{arctanh} #1}                                         %Defines arctanh
% %Change tombstone symbol
% \newcommand{\blackged}{\hfill$\blacksquare$}
% \newcommand{\whiteged}{\hfill$\square$}
% \newcounter{proofcount}
% \renewenvironment{proof}[1][\proofname.]{\par
%  \ifnum \theproofcount>0 \pushQED{\whiteged} \else \pushQED{\blackged} \fi%
%  \refstepcounter{proofcount}
%  \normalfont 
%  \trivlist
%  \item[\hskip\labelsep
%       \itshape
%   {\bf\em #1}]\ignorespaces
% }{%
%  \addtocounter{proofcount}{-1}
%  \popQED\endtrivlist
% }
%
%
%
% Add index
%\printindex
%   
% %
% % Theorem styles used in my thesis
% %
% \theoremstyle{plain}
% \newtheorem{theo}{Theorem}[chapter]
% \theoremstyle{plain}
% \newtheorem{prop}{Proposition}[chapter]
% \theoremstyle{plain}
% \theoremstyle{definition}
% \newtheorem{dfn}{Definition}[chapter]
% \theoremstyle{plain}
% \newtheorem{lema}{Lemma}[chapter]
% \theoremstyle{plain}
% \newtheorem{cor}{Corollary}[chapter]
% \theoremstyle{plain}
% \newtheorem{resu}{Result}[chapter]
%
% Hyphenation for some words
%
% \hyphenation{res-pec-tively}
% \hyphenation{mono-ti-ca-lly}
% \hyphenation{hypo-the-sis}
% \hyphenation{para-me-ters}
% \hyphenation{sol-va-bi-li-ty}

 
% \newcommand{\mycaption}[2][\@empty]{
% 	\captionnamefont{\scshape} 
% 	\changecaptionwidth
% 	\captionwidth{0.9\linewidth}
% 	\captiondelim{.\:} 
% 	\indentcaption{0.75cm}
% 	\captionstyle[\centering]{}
% 	\setlength{\belowcaptionskip}{10pt}
% 	\ifx \@empty#1 \caption{#2}\else \caption[#1]{#2}
% }
% %
% % My subcaption style
% \newcommand{\mysubcaption}[2][\@empty]{
% 	\subcaptionsize{\small}
% 	\hangsubcaption
% 	\subcaptionlabelfont{\rmfamily}
% 	\sidecapstyle{\raggedright}
% 	\setlength{\belowcaptionskip}{10pt}
% 	\ifx \@empty#1 \subcaption{#2}\else \subcaption[#1]{#2}
% }