%%% ------------ 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 3/2022.
% Find details and an MS word version here:
% https://github.com/CapraLab/lab-manuscript-template
% 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 \methodsDataTips, \methodsAnalysisTips \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[utf8]{inputenc}
\usepackage[english]{babel}
\usepackage[a4paper,margin=1in]{geometry} % page setup, margins
\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
\usepackage{setspace} % for linespacing
\usepackage{lineno} % line numbering (change with \linespacing below)
\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
% Figure references and bolding them https://tex.stackexchange.com/questions/87903/bold-cross-references
\usepackage[capitalise, noabbrev, nameinlink]{cleveref}
\crefdefaultlabelformat{#2\textbf{#1}#3} % To bold figure refs
\Crefname{figure}{\textbf{Figure}}{\textbf{Figures}} % To bold figure refs
\Crefname{section}{\textbf{Section}}{\textbf{Sections}} % To bold section refs
\Crefname{table}{\textbf{Table}}{\textbf{Tables}} % To bold table refs
\newcommand{\crefrangeconjunction}{--} % change conjunction b/w figures
\newcommand{\crefpairconjunction}{, } % change conjunction b/w figures
\newcommand{\creflastconjunction}{, } % change conjunction b/w figures
\newcommand{\crefmiddleconjunction}{, } % change conjunction b/w figures
% 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}{\textbf{(#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}
%\usepackage{tabularx}
%\usepackage{makecell}
% Read in helper functions
\input{helperFunctions}
% Change Fonts
%\usepackage{fontspec} % To use arial font but you must change your compiler to XeLaTeX (upper left corner Menu > compilier)
%\setmainfont{Arial} % To use arial font but you must change your compiler to XeLaTeX (upper left corner Menu > compilier)
% 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
%%% ------------ REFERENCES FORMAT ------------ %%%
% Note: Change the print bibliography command if switching between BibLaTex and Natbib
% See this for a great comparison: https://tex.stackexchange.com/questions/25701/bibtex-vs-biber-and-biblatex-vs-natbib
%% BibLaTeX format %% (newer/better but not all journals accept)
% Numbered:
%\usepackage[sorting=none, backend=biber, style=numeric-comp,maxbibnames=10,minbibnames=3, maxcitenames= 2,giveninits=true, natbib=true, url=false,hyperref=true]{biblatex}
% Author Year:
\usepackage[backend=biber,style=authoryear-comp,sorting=nyt,natbib=true, url=false]{biblatex}
\addbibresource{library.bib} % add bibliography resource
%% Natbib format %% (more basic)
% Numbered:
% \usepackage[square,numbers]{natbib}
% \bibliographystyle{unsrtnat}
% Author Year:
%\usepackage{natbib}
%\bibliographystyle{unsrtnat}
%%% ------------ DOCUMENT ORGANIZATION ------------ %%%
\input{1titlepage}
\begin{document}
%\RaggedRight % If you want left-aligned (ie ragged right text) rather than justified
\setstretch{1.15} %\onehalfspace
\linenumbers
\input{REMOVEME_tips} % For the tips, eventually remove!
\maketitle
\makeAbstract
\clearpage
\input{2intro}
\clearpage % can remove if you don't want a new page
\input{3results}
\clearpage % can remove if you don't want a new page
\input{5discussion}
\clearpage % can remove if you don't want a new page
\input{6methods}
\begin{singlespace}
\printbibliography % for biblatex
%\bibliography{library} % for natbib
\end{singlespace}
\clearpage
\section*{Supplementary Information}
\setcounter{page}{1} % Set page at 1
\input{supplement/0suppl_text}
\input{supplement/1suppl_figs}
\input{supplement/2suppl_tabs}
\end{document}
