%%% ------------ OVERVIEW OF THIS TEMPLATE ------------ %%%
% This is a Capra Lab Manuscript template! It was developed by the Capra
% Lab and converted to a LaTex document by Evonne McArthur 2/2022 and last
% edited 2/2022.
% To use this template, you should probably read the whole compiled document
% because it contains lots of great tips. Once you are ready to go, you
% should delete the tips in each section (\abstractTips \introTips \resultsTips
% \captionTips \methodsTips \discussionTips and \generalTips). Then you should
% delete the REMOVEME_tips.tex file and the call to that file in this document
% (\input{REMOVEME_tips}). Then add your own content to the relevant subfiles.
% Figures should be uploaded to the ./main_figs and ./supplement/suppl_figs
% folders. Tables should be uploaded to ./supplement/suppl_tabs. When you work
% with main text figures, you should create a "code name" for them. You will
% follow the format in 4maintextFigs.tex to add a function that will generate
% the figure. When you want that figure to appear in the manuscript call that
% function (e.g. \codename).
% Note that this document contains info about how to customize these things:
% fontsize, font (to Arial), line spacing, line numbers, left vs. justified
% aligned, number or author-date citations, natbib vs bibLaTeX citations,
% sideways tables and figures, figure references and more!
% See these resources for more LaTeX tips:
%https://en.m.wikibooks.org/wiki/LaTeX
%https://tobi.oetiker.ch/lshort/lshort.pdf
%https://gangw.cs.illinois.edu/latex.pdf
%https://web.mit.edu/rsi/www/pdfs/new-latex.pdf
%http://hoffman.physics.harvard.edu/Hoffman-example-paper.pdf
%%% ------------ READ IN PACKAGES & SETUP ------------ %%%
% Basics, font size, page setup, link format, line spacing/numbering
\documentclass[11pt]{article} % font size
\usepackage[english]{babel}
\usepackage[a4paper,margin=1in]{geometry} % page setup
\usepackage{authblk} % author affiliations
\usepackage[colorlinks=true, linkcolor=black, citecolor=black, urlcolor=blue, filecolor=blue,breaklinks=true]{hyperref} % Hyperlinks, needed for biblatex, other option: allcolors=blue
\setcounter{secnumdepth}{0} % disable section numbering, generates a few warnings but these should not effect the document
\usepackage{setspace} % linespacing
\usepackage{lineno} % line numbering
\renewcommand\linenumberfont{\normalfont\scriptsize\fontspec{Arial}\color{black}}
\usepackage{csquotes} % Recommended for biblatex, must load after lineno or will get a warning
\usepackage{ragged2e}% for left aligning
\setlength{\RaggedRightParindent}{\parindent} % for paragraph indent with left aligning
\usepackage{array} % used to soft wrap text in Table S3
% Write math as font
\usepackage[no-math]{fontspec}
\setmainfont{Arial}
\usepackage[defaultmathsizes]{mathastext}
\usepackage{amsmath}
% Figure references and bolding them https://tex.stackexchange.com/questions/87903/bold-cross-references
\usepackage[capitalise, noabbrev, nameinlink]{cleveref}
\usepackage[labelsep=period]{caption} % change separator to period instead of colon
\crefdefaultlabelformat{#2#1#3}
\Crefname{figure}{Figure}{Figures}
\Crefname{table}{Table}{Tables}
\Crefname{section}{\textbf{Section}}{\textbf{Sections}}
\newcommand{\crefrangeconjunction}{--} % change conjunction b/w figures
\newcommand{\crefpairconjunction}{, }
\newcommand{\creflastconjunction}{, }
\newcommand{\crefmiddleconjunction}{, }
% Figures, Tables and captions
\usepackage{graphicx}
\graphicspath{{./main_figs/}{./supplement/suppl_figs/}} % paths for figs
\DeclareGraphicsExtensions{.pdf,.jpeg,.JPG,.png,.PNG, .eps, .tiff}
\usepackage{subcaption} % for subcaptions (panels), and add parentheses
\DeclareCaptionLabelFormat{bold}{{(#2)}} % bold subpanel letter in caption
\captionsetup{subrefformat=bold} % bold subpanel letter in caption
\renewcommand{\thesubfigure}{\Alph{subfigure}} % Make subpanel numbering capitalized
\newcommand{\labelphantom}[1]{% To make subpanel references easier from https://tex.stackexchange.com/a/255790/121424
\parbox{0pt}{\phantomsubcaption\label{#1}}%
}
\usepackage{pgffor} % for function to make figures with subpanels
\usepackage{alphalph} % for function to make figures with subpanels
\usepackage[labelfont=bf, textfont=bf, singlelinecheck=off, textfont=footnotesize]{caption} % boldness of captions
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{rotating}
% Read in helper functions
\input{helperFunctions}
% Can remove, are for the tips
\usepackage[dvipsnames]{xcolor} % can remove, for coloring the tips
\usepackage{changepage} % can remove, for width on the tips
\usepackage{enumitem} % can remove, for width on the tips
% soft wrap URLs and use same font as document
\usepackage{xurl}
\urlstyle{same}
%%% ------------ REFERENCES FORMAT ------------ %%%
\usepackage[backend=biber, citestyle=numeric-comp, bibstyle=authoryear, sorting=none, natbib=true, url=false, minbibnames=10, maxbibnames=10, uniquename=false, uniquelist=false, giveninits=true]{biblatex}
% add numbers to authoryear bibstyle in References
\defbibenvironment{bibliography}
{\list
{\printtext[labelnumberwidth]{%
\printfield{labelprefix}%
\printfield{labelnumber}}}
{\setlength{\labelwidth}{\labelnumberwidth}%
\setlength{\leftmargin}{\labelwidth}%
\setlength{\labelsep}{\biblabelsep}%
\addtolength{\leftmargin}{\labelsep}%
\setlength{\itemsep}{\bibitemsep}%
\setlength{\parsep}{\bibparsep}}%
\renewcommand*{\makelabel}[1]{##1}}
{\endlist}
{\item}
% add a period to each numbered reference
\DeclareFieldFormat{labelnumberwidth}{#1.}
% last names first
\DeclareNameAlias{author}{family-given}
% clear the month, issue number, and ISSN from references
\AtEveryBibitem{\clearfield{month}}
\AtEveryBibitem{\clearfield{number}}
\AtEveryBibitem{\clearfield{issn}}
% remove quotes from article title
\DeclareFieldFormat[article]{title}{#1}
% deitalicize journal title
\DeclareFieldFormat{journaltitle}{#1\isdot}
% axe "In:" before journal name
\renewbibmacro{in:}{}
% italicize volume number
\renewbibmacro*{volume+number+eid}{%
\printfield{volume}%
}
\DeclareFieldFormat[article]{volume}{\mkbibitalic{#1}}
% format DOI
\DeclareFieldFormat{doi}{\url{https://doi.org/#1}}
% removes "pp" from pages
\DefineBibliographyStrings{english}{%
page = {},
pages = {},
}
% add a space between entries
\setlength\bibitemsep{\baselineskip}
% add bibliography resource
\addbibresource{example.bib}
%%% ------------ FONT COLOR FORMAT ------------ %%%
\usepackage{xcolor}
\usepackage{caption}
% Define a custom colors using the hexadecimal code
\definecolor{sectioncolor}{HTML}{9c4847}
\definecolor{black}{HTML}{000000}
\definecolor{linkcolor}{HTML}{008ebe}
% Set custom colors
\usepackage{titlesec}
\titleformat{\section}
{\color{sectioncolor}\normalfont\Large\bfseries}
{\thesection}{1em}{}
\titleformat{\subsection}
{\color{sectioncolor}\normalfont\large\bfseries}
{\thesubsection}{1em}{}
% Redefine the figures title color
\DeclareCaptionFont{figuretitlecolor}{\color{sectioncolor}}
\DeclareCaptionFont{figurecaptioncolor}{\color{black}}
\captionsetup[figure]{labelfont=bf, textfont=figurecaptioncolor, font=figuretitlecolor}
% Redefine the tables title color
\DeclareCaptionFont{tabletitlecolor}{\color{sectioncolor}}
\DeclareCaptionFont{tablecaptioncolor}{\color{black}\footnotesize}
\captionsetup[table]{labelfont=bf, textfont=tablecaptioncolor, font=tabletitlecolor}
\hypersetup{
colorlinks=true,
linkcolor=linkcolor,
urlcolor=linkcolor,
citecolor=linkcolor
}
%%% ------------ TITLE PAGE FORMATTING ------------ %%%
% left align title, authors, and affiliations
\makeatletter
\renewcommand\maketitle{\par
\begingroup
\flushleft
\Large{\@title}\par
\endgroup
\vspace{0.5em}
\begin{flushleft}
\@author
\end{flushleft}
}
\makeatother
% left align abstract title and justify abstract body
\renewenvironment{abstract}{
\begin{flushleft}
\textbf{\abstractname}
\end{flushleft}
\vspace{-1.5em}
\par
\noindent\justify
\parfillskip=0pt
}{
\par
}
%%% ------------ DOCUMENT ORGANIZATION ------------ %%%
\input{1titlepage}
\begin{document}
\setstretch{1.15} %\onehalfspace
\linenumbers
\input{REMOVEME_tips}
\maketitle
\makeAbstract
\clearpage
\input{2intro}
\input{3results}
\input{5discussion}
\input{6methods}
\begin{singlespace}
\printbibliography
\end{singlespace}
\clearpage
%\section*{Supplementary Information}
\setcounter{page}{1} % Set page at 1
\input{supplement/0suppl_text}
\clearpage
\input{supplement/1suppl_figs}
\input{supplement/2suppl_tabs}
\end{document}
