main.tex

%%% LaTeX template
%%% Dae Houlihan

%%%%%%%%%%%%%%%%%%%%%%%
%%% Document setup
%%%%%%%%%%%%%%%%%%%%%%%

\documentclass[12pt,letterpaper]{article}

\usepackage[american]{babel}

\usepackage{cmap} % provides character map tables, which make PDF files generated by pdfLATEX both searchable and copy-able in acrobat reader and other compliant PDF viewers

%%% for pdflatex %%% see https://tex.stackexchange.com/questions/44694/fontenc-vs-inputenc
\usepackage[T1]{fontenc} % use 8-bit T1 fonts; oriented to output, that is, what fonts to use for printing characters
\usepackage[utf8]{inputenc} % allow utf-8 input; allows the user to input accented characters directly from the keyboard
%%% The two packages are not connected, though it is best to call fontenc first and then inputenc %%%

%%% If you use \usepackage[T1]{fontenc} with Computer Modern, it uses bitmap fonts which end up pixelated. Latin Modern doesn't suffer from this problem %%%
\usepackage{lmodern}

%%% Set page size and margins %%%
\usepackage[letterpaper,top=2cm,bottom=2cm,left=3cm,right=3cm,marginparwidth=1.75cm]{geometry} %% add 'showframe' to geometry package for debugging

\usepackage[font={small}]{caption} % format captions font

%%%%%%%%%%%%%%%%%%%%%%%
%%% BibLaTeX with biber backend
%%%%%%%%%%%%%%%%%%%%%%%

\usepackage[
	backend=biber,
	style=apa,
	natbib=true,
	url=true,
	doi=true,
	eprint=true,
%	uniquename=false,
%	giveninits=false,
%	uniquelist=false,
]{biblatex}
\addbibresource{bibliography.bib}
%%% have in-parentheses citation notes separated by ; rather than , %%%
%\setcitestyle{citesep={;}}
\renewcommand*{\postnotedelim}{\addsemicolon\space}


%%%%%%%%%%%%%%%%%%%%%%%
%%% Packages
%%%%%%%%%%%%%%%%%%%%%%%

\usepackage{url} % simple URL typesetting
\usepackage{booktabs} % professional-quality tables
%\usepackage{multirow}
%\usepackage{tabularray}
%\usepackage[table]{xcolor}
\usepackage{graphicx}
\usepackage{mathtools}
\usepackage{amsfonts} % blackboard math symbols
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{csquotes}
\usepackage{nicefrac} % compact symbols for 1/2, etc.
\usepackage{pifont} % special characters like dings
\usepackage{bm,microtype} % italic bold math % microtypography % for some reason microtype turns off Texifier live
\usepackage{xspace} % for variable formatting

\usepackage{placeins} % control float placement with \FloatBarrier
\usepackage{comment} % \begin{comment}\end{comment} environment

\usepackage{authblk} % for author affiliations

\usepackage[raggedright]{titlesec} %%% don't hyphenate titles

%\usepackage{lgrind} % prepares various programming language source code for pretty-printing


%%%%%%%%%%%%%%%%%%%%%%%
%%% Variable formatting
%%%%%%%%%%%%%%%%%%%%%%%

%%%%%%%%%
%%% Hyphenation
%%%%%%%%%

\hyphenation{Golden-Balls}

%%%%%%%%%
%%% Acronyms
%%%%%%%%%

\newcommand*{\DefaultAcronymStyle}[1]{#1}
\newcommand*{\Acronym}[2][\DefaultAcronymStyle]{\expandafter\def\csname #2\endcsname{#1{#2}\xspace}}

\Acronym{ToM}
\Acronym[\textsc]{BToM}

%%%%%%%%%
%%% Greek variants
%%%%%%%%%

\newcommand*{\swap}[2]{\let\temp#1 \let#1#2 \let#2\temp \let\temp\relax}
\swap{\epsilon}{\varepsilon}
%\swap{\theta}{\vartheta}
\swap{\phi}{\varphi}

%%%%%%%%%
%%% Text commands
%%% (N.B \newcommand can contain \par, \newcommand* cannot)
%%%%%%%%%

\xspaceaddexceptions{]\}} %%% prevents extra spaces when command is closed with ] or }

\newcommand*{\ie}{i.e.\xspace}
\newcommand*{\eg}{e.g.\xspace}
\newcommand*{\Ie}{I.e.\xspace}
\newcommand*{\Eg}{E.g.\xspace}

\newcommand*{\cmark}{\ding{51}}%
\newcommand*{\xmark}{\ding{55}}%

\newcommand*{\somemarkup}{\texttt{SomeMarkup}\xspace}
\newcommand*{\somemodel}{\textsc{SomeModel}\xspace}

%%%%%%%%%
%%% Math commands
%%%%%%%%%

\DeclarePairedDelimiter{\abs}{\lvert}{\rvert}
\DeclarePairedDelimiter{\ceil}{\lceil}{\rceil}
\DeclarePairedDelimiter{\floor}{\lfloor}{\rfloor}
\DeclarePairedDelimiter{\paren}{\lparen}{\rparen}
\DeclarePairedDelimiter{\brak}{[}{]}
\DeclarePairedDelimiter{\setbrak}{\left\{}{\right\}}
\DeclarePairedDelimiter{\tuple}{\langle}{\rangle}
\def\pp#1{\paren*{#1}}

%\renewcommand*{\vec}[1]{{\bm{#1}}}
\let\vec\relax
\newcommand*{\vec}[1]{\bm{#1}}
\newcommand*{\mat}[1]{{\bm{\mathrm{#1}}}}
\newcommand*{\mvec}[1]{\begin{pmatrix}#1\end{pmatrix}}

\DeclareMathOperator{\pr}{P}
\DeclareMathOperator{\giv}{\mid}
\DeclareMathOperator{\givmiddle}{\;\middle\vert\;}
\DeclareMathOperator{\param}{\,\!\mathbin{;}\,}

\DeclareMathOperator*{\E}{\mathbf{E}} %%% star takes subscripts below
\DeclareMathOperator{\Ee}{\mathbf{E}}

\DeclareMathOperator{\Like}{\mathcal{L}}
\DeclareMathOperator{\Lagr}{\ell}

\DeclareMathOperator{\Corr}{Corr}
\DeclareMathOperator{\Cov}{Cov}

\DeclareMathOperator*{\argmax}{argmax}


%%%%%%%%%%%%%%%%%%%%%%%
%%% Draft Markup
%%%%%%%%%%%%%%%%%%%%%%%

%%% DRAFT %%%
\usepackage[dvipsnames]{xcolor}
\definecolor{ccpink}{rgb}{0.858, 0.188, 0.478}
\definecolor{ccmulberry}{RGB}{168, 62, 158}
\definecolor{ccburentorange}{RGB}{193, 92, 0}
\definecolor{ccdgreen}{RGB}{0, 133, 19}
\definecolor{ccbrown}{RGB}{135, 32, 1}
\definecolor{lightgrey}{rgb}{0.95, 0.95, 0.95}
\newcommand{\hide}[1]{\ignorespaces}
\newcommand{\wip}[1]{{\color{red}#1}}
\newcommand{\reword}[1]{{\color{ccbrown}#1}}
\newcommand{\dae}[1]{{\color{ccmulberry}#1}}

%%% FINAL %%%
%\newcommand{\reword}[1]{#1}
%\newcommand{\hide}[1]{\ignorespaces}
%\newcommand{\dae}[1]{\ignorespaces}


%%%%%%%%%%%%%%%%%%%%%%%
%%% Regulate auto-hyphenation
%%%%%%%%%%%%%%%%%%%%%%%

\tolerance=9999 %% allows as much whitespace as possible.
%\emerencystretch=10pt %% allows some extra whitespace per line.
\hyphenpenalty=10000 %% disables hyphens completely.
\exhyphenpenalty=100 %% allows using hyphens which were already present.

%%% or %%%

%\usepackage[none]{hyphenat} % Uncomment this block to turn off hyphenation.

%%%%%%%%%%%%%%%%%%%%%%%
%%% PDF-A Standard
%%%%%%%%%%%%%%%%%%%%%%%

%%% 
%%% PDF-A (overleaf example: https://www.overleaf.com/latex/templates/creating-pdf-slash-a-and-pdf-slash-x-files-with-the-pdfx-package/bbbycnbyqhnm)
%%% Check metadata with >> pdfinfo main.pdf
%%% Disable hyperref package to use pdfx package
%%% Conflicts with package tabularray
%%%

%\usepackage[a-3u]{pdfx} %%% for PDF/A-3u
%\hypersetup{
%	hidelinks,
%	breaklinks=true,
%}
%
%\begin{filecontents*}[overwrite]{\jobname.xmpdata}
%\Title{LaTeX Template}
%\Author{Sean Dae Houlihan}
%\Language{en-US}
%\Subject{The abstract or short description.}
%\Keywords{keyword1\sep keyword2\sep keyword3}
%\end{filecontents*}

%%%%%%%%%%%%%%%%%%%%%%%
%%% Internal links
%%%%%%%%%%%%%%%%%%%%%%%

\usepackage[colorlinks=true, allcolors=blue]{hyperref} % hyperlinks - best loaded at end of preamble
\hypersetup{
	hidelinks,
	breaklinks=true,
	pdftitle={LaTeX Template},
	pdfauthor={Sean Dae Houlihan},
	pdflang={en-US},
	pdfsubject={The abstract or short description.},
	pdfkeywords={keyword1, keyword2, keyword3},
	pdfstartview=
}
\usepackage{subfiles} % subfiles - best loaded last in the preamble

%%%%%%%%%%%%%%%%%%%%%%%
%%% Header
%%%%%%%%%%%%%%%%%%%%%%%

\title{LaTeX template, with BibLaTeX and biber backend}
\author[a,b]{Sean Dae Houlihan}
\affil[a]{Department of Psychological and Brain Sciences, Dartmouth College}
\affil[b]{Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology}
\setcounter{Maxaffil}{0}
\renewcommand\Affilfont{\small}
\date{}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%% DOCUMENT
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\begin{document}
\maketitle

\begin{abstract}
\noindent 
This thesis develops a framework for computationally recapitulating human emotion understanding. I argue that expression cues and contextual information mutually constrain inference over an intuitive theory of mind. Emotion concepts reflect computations in the space of inferred appraisals, and inferred appraisals function as latent causal explanations that link expressions, actions, preferences, beliefs, costs, and world states across time. 
\end{abstract}


%%% relax \clearpage to prevent page breaks between subfiles, bibliography %%%

\begingroup
\let\clearpage\relax
\include{writing/intro}
\endgroup

\begingroup
\let\clearpage\relax
\printbibliography
\endgroup

\clearpage

\pagenumbering{arabic} %%% resets `page` counter to 1
\renewcommand*{\thepage}{S\arabic{page}}
\appendix

\setcounter{section}{0}
\makeatletter 
\renewcommand{\thesection}{S\@arabic\c@section}
\makeatother

\setcounter{figure}{0}
\makeatletter 
\renewcommand{\thefigure}{S\@arabic\c@figure}
\makeatother

\setcounter{table}{0}
\makeatletter 
\renewcommand{\thetable}{S\@arabic\c@table}
\makeatother

\include{writing/supplement}


\end{document}