haziq_thesis.sty

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%%% PACKAGES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% Structure
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% https://tex.stackexchange.com/questions/195106/page-numbers-on-the-side-of-the-page

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% Typeset and appearance
\usepackage{csquotes}  % quotes
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\usepackage[]{xcolor}  % options: usenames, dvipsnames, svgnames, table
\usepackage{soul}  % for highlighting text
\usepackage{url}
\usepackage{footmisc}  % ability to reuse footnotes 
% https://tex.stackexchange.com/questions/40072/incompatibility-between-footmisc-option-multiple-and-hyperref/62091#62091

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\usepackage{nicefrac}  % To get nice typography for units
\usepackage{units}  % and fractions
\usepackage{enumitem}  % replacing enumerate
\usepackage{xr}  % Cross-referencing between files

% Show labels in margins. See https://tex.stackexchange.com/questions/45634/printing-labels-along-with-equation-numbers
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% Coding
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\newcommand{\code}[1]{\texttt{\detokenize{#1}}}

% Bibliography
\usepackage[style=authoryear-comp, firstinits=false, giveninits=false, maxcitenames=2, uniquelist=false,
  minnames=1, maxbibnames=99, backend=biber, natbib]{biblatex}
\setlength\bibitemsep{1\itemsep}
\AtEveryCite{\color{\mycitecolour}}
\makeatletter
\AtEveryCitekey{\global\undef\cbx@lastyear}  % https://tex.stackexchange.com/questions/309697/multiple-citations-same-author-same-year-using-biblatex-list-year
\makeatother
\setcounter{biburlnumpenalty}{9000}
% https://tex.stackexchange.com/questions/134191/line-breaks-of-long-urls-in-biblatex-bibliography

% Paragraph settings
\usepackage{parskip}  
\setlength{\parindent}{15pt}  % default indentation

% Line spacing
\usepackage{setspace}\onehalfspacing % or \singlespacing, \onehalfspacing or \doublespacing

% Figures
\usepackage{float}  
\usepackage{graphicx}
%\usepackage{subfig} 
\usepackage{subcaption}  % an alternative package for sub-figures (preferred)
  \newcommand{\subfloat}[2][need a sub-caption]{\subcaptionbox{#1}{#2}}  % knitr
\usepackage{rotfloat}	
\usepackage{tikz}
\usetikzlibrary{fit,positioning,calc,decorations.pathreplacing,shapes.geometric,backgrounds}
\usepackage{forest}
\usetikzlibrary{arrows}
\usetikzlibrary{shapes.callouts}
\usetikzlibrary{patterns,hobby}
\usepackage{pgfplots}    % these are for squiggly lines
\pgfplotsset{compat=1.6}  % https://tex.stackexchange.com/questions/160237/draw-somewhat-random-function/160274
\usepackage{placeins}  % make figure stay within subsections---https://tex.stackexchange.com/questions/118662/use-placeins-for-subsections
\makeatletter
\AtBeginDocument{%
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    {\expandafter\@fb@secFB\subsection}%
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  \g@addto@macro\@afterheading{\@fb@afterHHook}%
  \gdef\@fb@afterHHook{}%
}
\makeatother

% Tables
\usepackage{longtable}
\usepackage{tabularx}
\usepackage{multirow}
%\usepackage{dcolumn}  % align columns on a decimal point
\newcommand{\Top}{\rule{0pt}{2.6ex}}  % Top strut for tables
\newcommand{\Bot}{\rule[-1.2ex]{0pt}{0pt}}  % Top strut for tables
\usepackage{booktabs}
\usepackage{colortbl}
\usepackage{lscape}  % landscape tables
\usepackage{threeparttable}
\usepackage{tablefootnote}

% Margin notes
\usepackage{marginnote}
\usepackage{mparhack}  % these two packages provides some fixes to marginnote
\usepackage{marginfix}

% TOC
\usepackage{tocloft}
\setlength{\cftfigindent}{0pt}  % indentations of fig and tab list
\setlength{\cfttabindent}{0pt}
\cftsetindents{figure}{0em}{2.7em}
\cftsetindents{table}{0em}{2.7em}
\usepackage{etoolbox}
\patchcmd{\listof}{1.5em}{0pt}{}{} % indentations of alg list
\patchcmd{\listof}{2.3em}{2.7em}{}{}
% https://tex.stackexchange.com/questions/80430/how-to-prevent-indent-on-listofalgorithms/80432

% Miscellaneous
\usepackage{lipsum} 
\usepackage{ifthen}
\usepackage{xparse}
\usepackage[linecolor=yellow, backgroundcolor=yellow!25, bordercolor=yellow, textsize=footnotesize]{todonotes}
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  \newcommand{\todonum}[2][To-do in Section \thesubsection]{\stepcounter{todocounter}\todo[caption={\thetodocounter. #1}]{\thetodocounter. #2}{}}
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\usepackage{pifont}
  \newcommand{\cmark}{\ding{51}}  % check mark
  \newcommand{\xmark}{\ding{55}}  % x mark

% Glossary, abbreviations and indices
\usepackage{imakeidx}
\usepackage[abbreviations,counter=chapter,nopostdot=false,symbols,autoseeindex=true,indexcrossrefs=true]{glossaries-extra}
%\renewcommand*{\glossarypreamble}{\emph{Numbers refer to the \textbf{chapter} where the entry was referenced.}}
\makeglossaries
\makeindex[columns=2]

% Create new macro \indx and \newabbreviationindex
\newcommand{\indx}[1]{{#1}\index{#1}}
\newcommand{\newabbreviationindex}[4]{
  \newabbreviation[#4]{#1}{#2}{#3}
  \index{#3|see{#2}}
}

% Automatically index the location of entry in the glossary
% for those entries that are in the "general" category:
%\glssetcategoryattribute{general}{indexname}{textbf}
%\glssetcategoryattribute{general}{dualindex}{true}

% Only index first use for the glossary location lists
% (doesn't affect the indexing from "dualindex" attribute):
%\glssetcategoryattribute{general}{indexonlyfirst}{true}

% Automatically index the location of entry in the glossary
% for those entries that are in the "abbreviation" category
% and use "textbf" as the encap:
%\glssetcategoryattribute{abbreviation}{indexname}{textbf}
%\glssetcategoryattribute{abbreviation}{dualindex}{true}

% Only index first use for the glossary location lists
% (doesn't affect the indexing from "dualindex" attribute):
%\glssetcategoryattribute{abbreviation}{indexonlyfirst}{true}

% Convert the first letter of the name to upper case in the 
% glossary for abbreviation entries:
%\glssetcategoryattribute{abbreviation}{glossname}{firstuc}

% Allow "format" key to override "dualindex" attribute.
\GlsXtrEnableIndexFormatOverride

% use first field instead of name field
%\renewcommand*{\glsxtrautoindexentry}[1]{\string\glsentryfirst{#1}}

% use long form for the sort value, if provided:
%\renewcommand*{\glsxtrautoindexassignsort}[2]{%
%  \ifglshaslong{#2}%
%  {\glsletentryfield{#1}{#2}{long}}%
%  {\glsletentryfield{#1}{#2}{sort}}%
%}

% Load everything before hyperref to avoid conflicts
\usepackage{hyperref}  % hyperref setup at the bottom


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% MY THESIS SPECIFIC MACROS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% For my thesis---adds a chapter heading, including to-do list and TOC (STANDALONE VERSION)

% Textbox freely placed on page. Adapted from https://tex.stackexchange.com/questions/24663/how-to-place-a-floating-text-box-at-a-specified-location-in-page-coordinates
\newcommand{\placetextbox}[3]{% \placetextbox{<horizontal pos>}{<vertical pos>}{<stuff>}
  \setbox0=\hbox{#3}% Put <stuff> in a box
\AddToShipoutPictureFG*{\put(\LenToUnit{#1\paperwidth},\LenToUnit{#2\paperheight}){\makebox[0pt][c]{\begin{tabular}{l}#3\end{tabular}}}}
}%

\newcommand{\hChapterStandalone}[2][1]{
  \ifstandalone
%  % uncomment for final version  
%    \pagenumbering{roman}
%    \begingroup
%    \let\clearpage\relax  % Don't allow page break
%    {\hypersetup{allcolors=.} %pdfborder=0 0 0
%      \listoftodos[\vspace{-3.03cm}To-do list]        \vspace{-1em}
%      \tableofcontents
%    }
%    \endgroup
    
    \setcounter{chapter}{#1-1}
    \chapter{#2}
    \placetextbox{0.521}{0.8585}{
      {\small Haziq Jamil} \\[-0.4em]
      {\it\footnotesize Department of Statistics} \\[-0.45em]
      {\it\footnotesize London School of Economics and Political Science} \\[-0.45em]
      {\footnotesize PhD thesis: `Regression modelling using priors depending on Fisher information covariance kernels'} \\[-0.45em]
      {\footnotesize 29 October 2018 (\code{v1.2@dae7107})}
    }
  \fi
%  \pagenumbering{arabic}
}

% Adds Bibliography to TOC
\newcommand{\hPrintBibliography}{
  \cleardoublepage
  \phantomsection
  \ifstandalone
    \renewcommand{\thepage}{}
  \else
    \addcontentsline{toc}{chapter}{Bibliography}
  \fi
  \begingroup
    \singlespacing
    \printbibliography
  \endgroup
}

% Change arXiv style
\makeatletter
\DeclareFieldFormat{eprint:arxiv}{%
  \textsc{arXiv}\addcolon\space
  \ifhyperref
    {\href{https://arxiv.org/\abx@arxivpath/#1}{%
       \nolinkurl{#1}%
       \iffieldundef{eprintclass}
         {}
         {\addspace\texttt{\mkbibbrackets{\thefield{eprintclass}}}}}}
    {\nolinkurl{#1}%
     \iffieldundef{eprintclass}
       {}
       {\addspace\texttt{\mkbibbrackets{\thefield{eprintclass}}}}}}
\makeatother


% List of figures, tables, symbols, and abbreviations
\newcommand{\hLists}{
%  \addcontentsline{toc}{chapter}{Lists}
  
  \newpage
  \cleardoublepage
  \renewcommand{\listfigurename}{Figures}
  \listoffigures
  \addcontentsline{toc}{chapter}{Figures}
  
  \newpage
  \cleardoublepage
  \renewcommand{\listtablename}{Tables}  
  \listoftables
  \addcontentsline{toc}{chapter}{Tables}
  
  \newpage
  \cleardoublepage
  \renewcommand{\listtheoremname}{Theorems}  
  \listoftheorems[ignoreall,onlynamed={theorem,lemma,corollary,proposition},numwidth=2.7em]
  \addcontentsline{toc}{chapter}{Theorems}
  
  \newpage
  \cleardoublepage
  \renewcommand{\listtheoremname}{Definitions}
  \listoftheorems[ignoreall,show={definition}, numwidth=2.7em]
  \addcontentsline{toc}{chapter}{Definitions}   
  
  \newpage
  \cleardoublepage
  \renewcommand{\listalgorithmname}{Algorithms}
%  {\let\cleardoublepage\clearpage\listofalgorithms}
  \listofalgorithms
  \addcontentsline{toc}{chapter}{Algorithms}
        
  \begingroup
    \cleardoublepage
    \singlespacing
    \hnomenclature
    \addcontentsline{toc}{chapter}{Nomenclature}   
    
    \cleardoublepage
    \printabbreviations[title={Abbreviations},style=long,nogroupskip, nonumberlist,nopostdot]
    \glsaddall[types=abbreviations]
  \endgroup
}

% Manual input of nomenclature, depending on individual tex files or main thesis
\newcommand{\hnomenclature}{
  \hypersetup{
  colorlinks=true,
  linkcolor=\mycitecolour,
  citecolor=\mycitecolour,
  urlcolor=lsepur
}
  \ifstandalone
    \input{../../nomenclature}
  \else 
    \input{nomenclature}
  \fi
}

% Adds the closing stuff (STANDALONE VERSION)
\newcommand{\hClosingStuffStandalone}{
  \ifstandalone
    \hPrintBibliography
%    {\hypersetup{allcolors=.} %pdfborder=0 0 0  
%      \hLists
%      \begingroup
%        \singlespacing
%        \printindex
%      \endgroup
%    }
  \fi
}

% Adds TOC and lists (MAIN VERSION)
\newcommand{\hTOCandLists}{
  {\hypersetup{allcolors=.} %pdfborder=0 0 0
%    \listoftodos[To-do list]  % uncomment for final version
    \tableofcontents
    \hLists
  }
}

% Adds the closing stuff/print index (MAIN VERSION)
\newcommand{\hPrintIndex}{%
  {\hypersetup{allcolors=.}
    \begingroup
      \singlespacing
      \printindex
    \endgroup
  }
}

% Cleverref needs to be loaded last
\usepackage{nameref}
\usepackage[capitalise,noabbrev,nameinlink]{cleveref}
\Crefname{misc}{Miscellanea}{Miscellanea}
\Crefname{supchap}{Supplementary Chapter}{Supplementary Chapter}
\Crefname{equation}{}{}
\hypersetup{
  colorlinks=true,
  linkcolor=\mycitecolour,
  citecolor=\mycitecolour,
  urlcolor=lsepur
}
\newcommand{\mypageref}[1]{{{\color{\mycitecolour}p.} \pageref{#1}}}
\newcommand{\mypagereffull}[1]{{{\color{\mycitecolour}page} \pageref{#1}}}

% Page intentionally left blank
\makeatletter
\def\cleardoublepage{\clearpage\if@twoside%
    \ifodd\c@page\else
    \vspace*{\fill}
%    \vspace{3cm}
    \hfill
%    \begin{center}
%    \emph{This page intentionally left blank.}
%    \end{center}
%    \vspace{\fill}
    \thispagestyle{plainnomark}
    \newpage
    \if@twocolumn\hbox{}\newpage\fi\fi\fi
}
\makeatother
% https://tex.stackexchange.com/questions/290802/page-intentionally-left-blank-with-twoside-openright/308522

%\usepackage[fontsize=10.5]{scrextend}  % place here due to conflict

% Coloured parantheses
\newcommand{\colp}[1]{{\color{\mycitecolour}(#1)}}

\makeatletter
\DeclareFieldFormat{eprint:arxiv}{%
  \textsc{arXiv}\addcolon\space
  \ifhyperref
    {\href{https://arxiv.org/\abx@arxivpath/#1}{%
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         {}
         {\addspace\texttt{\mkbibbrackets{\thefield{eprintclass}}}}}}
    {\nolinkurl{#1}%
     \iffieldundef{eprintclass}
       {}
       {\addspace\texttt{\mkbibbrackets{\thefield{eprintclass}}}}}}
\makeatother

\usepackage[nodayofweek]{datetime}