\documentclass[a4paper]{report}
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{RJournal}
\usepackage{amsmath,amssymb,array}
\usepackage{booktabs}

$if(highlighting-macros)$
% 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}
$if(multirow)$
\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}
$endif$

% Always define CSL refs as bib entries are contained in separate doc
% Pandoc citation processing
\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}
 }%
 {}
\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}


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

\begin{document}

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

$endfor$

%% do not edit, for illustration only
\sectionhead{$journal.section$}
\volume{$volume$}
\volnumber{$issue$}
\year{$issueyear$}
\month{$issuemonth$}
$if(journal.firstpage)$
\setcounter{page}{$journal.firstpage$}
$endif$

\begin{article}
  \input{$filename$}
\end{article}

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

$endfor$

\end{document}
