template.tex

\documentclass[9pt,twocolumn,twoside,$if(lineno)$lineno$endif$]{pnas-new}

% Use the lineno option to display guide line numbers if required.
% Note that the use of elements such as single-column equations
% may affect the guide line number alignment.


\usepackage[T1]{fontenc}
\usepackage[utf8]{inputenc}
$if(highlighting-macros)$
% Pandoc syntax highlighting
$highlighting-macros$
$endif$

% tightlist command for lists without linebreak
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}

$if(tables)$
% From pandoc table feature
\usepackage{longtable,booktabs,array}
$if(pandoc3821)$\newcounter{none} % for unnumbered tables
$endif$
$if(multirow)$
\usepackage{multirow}
$endif$
\usepackage{calc} % for calculating minipage widths
% Correct order of tables after \paragraph or \subparagraph
\usepackage{etoolbox}
\makeatletter
\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
\makeatother
% Allow footnotes in longtable head/foot
\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
\makesavenoteenv{longtable}
$endif$

% Add imagehandling
$-- Only needed for pandoc 3.2.1 and above requiring graphics for new command.
$if(graphics)$$if(pandoc321)$
% Custom command from Pandoc 3.2.1 to scale images if necessary
\usepackage{graphicx}
\makeatletter
\newsavebox\pandoc@box
\newcommand*\pandocbounded[1]{% scales image to fit in text height/width
  \sbox\pandoc@box{#1}%
  \Gscale@div\@tempa{\textheight}{\dimexpr\ht\pandoc@box+\dp\pandoc@box\relax}%
  \Gscale@div\@tempb{\linewidth}{\wd\pandoc@box}%
  \ifdim\@tempb\p@<\@tempa\p@\let\@tempa\@tempb\fi% select the smaller of both
  \ifdim\@tempa\p@<\p@\scalebox{\@tempa}{\usebox\pandoc@box}%
  \else\usebox{\pandoc@box}%
  \fi%
}
\makeatother
$endif$$endif$

$if(csl-refs)$
% Pandoc citation processing
$if(pandoc318)$
%From Pandoc 3.1.8
% definitions for citeproc citations
\NewDocumentCommand\citeproctext{}{}
\NewDocumentCommand\citeproc{mm}{%
  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
\makeatletter
 % allow citations to break across lines
 \let\@cite@ofmt\@firstofone
 % avoid brackets around text for \cite:
 \def\@biblabel#1{}
 \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
\makeatother
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
 {\begin{list}{}{%
  \setlength{\itemindent}{0pt}
  \setlength{\leftmargin}{0pt}
  \setlength{\parsep}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1
   \setlength{\leftmargin}{\cslhangindent}
   \setlength{\itemindent}{-1\cslhangindent}
  \fi
  % set entry spacing
  \setlength{\itemsep}{#2\baselineskip}}}
 {\end{list}}
$else$$if(pandoc317)$
% definitions for citeproc citations
\NewDocumentCommand\citeproctext{}{}
\NewDocumentCommand\citeproc{mm}{%
  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
% avoid brackets around text for \cite:
\makeatletter
 \def\@biblabel#1{}
 \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
\makeatother
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacing}
\setlength{\cslentryspacing}{0em}
\usepackage{enumitem}
\newlist{CSLReferences}{itemize}{1}
\setlist[CSLReferences]{label={},
  leftmargin=\cslhangindent,
  itemindent=-1\cslhangindent,
  parsep=\parskip,
  itemsep=\cslentryspacing}
$else$
\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newlength{\csllabelwidth}
\setlength{\csllabelwidth}{3em}
\newlength{\cslentryspacingunit} % times entry-spacing
\setlength{\cslentryspacingunit}{\parskip}
% for Pandoc 2.8 to 2.10.1
\newenvironment{cslreferences}%
  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
  {\par}
% For Pandoc 2.11+
\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
 {% don't indent paragraphs
  \setlength{\parindent}{0pt}
  % turn on hanging indent if param 1 is 1
  \ifodd #1
  \let\oldpar\par
  \def\par{\hangindent=\cslhangindent\oldpar}
  \fi
  % set entry spacing
  \setlength{\parskip}{#2\cslentryspacingunit}
 }%
 {}
$endif$$endif$
\usepackage{calc}
\newcommand{\CSLBlock}[1]{#1\hfill\break}
\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
$endif$

$for(header-includes)$
$header-includes$
$endfor$

$if(pnas_type)$
\templatetype{$pnas_type$}  % Choose template
$else$
\templatetype{pnasresearcharticle}
$endif$

\title{$title$}

$for(author)$
\author[$author.affiliation$]{$author.name$}
$endfor$

$for(address)$
  \affil[$address.code$]{$address.address$}
$endfor$


% Please give the surname of the lead author for the running footer
\leadauthor{$lead_author_surname$}

% Please add here a significance statement to explain the relevance of your work
\significancestatement{$significance$}


\authorcontributions{$author_contributions$}

$if(conflict_of_interest)$
\authordeclaration{$conflict_of_interest$}
$endif$

$if(equal_authors)$
\equalauthors{\textsuperscript{$equal_authors.code$} $equal_authors.text$}
$endif$

\correspondingauthor{\textsuperscript{$corresponding_author.code$} $corresponding_author.text$}

% Keywords are not mandatory, but authors are strongly encouraged to provide them. If provided, please include two to five keywords, separated by the pipe symbol, e.g:
$if(keywords)$ \keywords{ $for(keywords)$ $keywords$ $sep$| $endfor$ } $endif$

\begin{abstract}
$abstract$
\end{abstract}

\dates{This manuscript was compiled on \today}
\doi{\url{www.pnas.org/cgi/doi/10.1073/pnas.XXXXXXXXXX}}

\begin{document}

% Optional adjustment to line up main text (after abstract) of first page with line numbers, when using both lineno and twocolumn options.
% You should only change this length when you've finalised the article contents.
\verticaladjustment{-2pt}

$for(include-before)$
$include-before$

$endfor$


\maketitle
\thispagestyle{firststyle}
\ifthenelse{\boolean{shortarticle}}{\ifthenelse{\boolean{singlecolumn}}{\abscontentformatted}{\abscontent}}{}

% If your first paragraph (i.e. with the \dropcap) contains a list environment (quote, quotation, theorem, definition, enumerate, itemize...), the line after the list may have some extra indentation. If this is the case, add \parshape=0 to the end of the list environment.

\acknow{$acknowledgements$}

$body$

$for(include-after)$
$include-after$
$endfor$


% Bibliography
% \bibliography{pnas-sample}

\end{document}