rticles/inst/rmarkdown/templates/peerj_article/skeleton/wlpeerj.cls

%
% An unofficial LaTeX class for PeerJ articles.
%
% Created by Overleaf (writeLaTeX).
%
% Based on the SelfArx document class.
%
\NeedsTeXFormat{LaTeX2e}
\ProvidesClass{wlpeerj}[18/08/2016, v1.2]
\RequirePackage[utf8]{inputenc}
\RequirePackage[english]{babel}

\RequirePackage{ifthen}
\RequirePackage{calc}
\AtEndOfClass{\RequirePackage{microtype}}
\newif\if@peerjlineno
\DeclareOption{lineno}{\@peerjlinenotrue}
\DeclareOption*{\PassOptionsToClass{\CurrentOption}{article}}
\ProcessOptions*
\LoadClass{article}
\RequirePackage{times}      % Loads the Times-Roman Fonts
\RequirePackage{mathptmx}   % Loads the Times-Roman Math Fonts
\RequirePackage{lineno}     % For numbering the lines if lineno option is given
\if@peerjlineno\linenumbers\fi

\RequirePackage{ifpdf}

\RequirePackage{amsmath,amsfonts,amssymb}
\RequirePackage{graphicx,xcolor}
\RequirePackage{booktabs}
\RequirePackage{authblk}

\RequirePackage[left=5cm,%
                right=2cm,%
                top=2.25cm,%
                bottom=2.25cm,%
                headheight=12pt,%
                letterpaper]{geometry}%

\RequirePackage[labelfont={bf,sf},%
                labelsep=period,%
                justification=raggedright]{caption}

% \RequirePackage{natbib}
% \bibliographystyle{apalike}

%
% writeLaTeX logo
%
\newcommand\wllogo{%
\renewcommand*\rmdefault{ugq}\normalfont\upshape{}write%
\renewcommand*\rmdefault{cmr}\normalfont\upshape{\bf\LaTeX}}

%
% headers and footers
%
\RequirePackage{fancyhdr}  % custom headers/footers
\RequirePackage{lastpage}  % Number of pages in the document
\pagestyle{fancy}          % Enables the custom headers/footers
% Headers
\lhead{}%
\chead{}%
\rhead{}%
% Footers
\lfoot{}%
\cfoot{}%
\rfoot{\small\sffamily\bfseries\thepage/\pageref{LastPage}}%
\renewcommand{\headrulewidth}{0pt}% % No header rule
\renewcommand{\footrulewidth}{0pt}% % No footer rule

%
% section/subsection/paragraph set-up
%
\RequirePackage[explicit]{titlesec}
\titleformat{\section}
  {\color{color1}\large\sffamily\bfseries}
  {\thesection}
  {0.5em}
  {\MakeUppercase{#1}}
  []
\titleformat{name=\section,numberless}
  {\color{color1}\large\sffamily\bfseries}
  {}
  {0em}
  {\MakeUppercase{#1}}
  []
\titleformat{\subsection}
  {\sffamily\bfseries}
  {\thesubsection}
  {0.5em}
  {#1}
  []
\titleformat{\subsubsection}
  {\sffamily\small\bfseries\itshape}
  {\thesubsubsection}
  {0.5em}
  {#1}
  []
\titleformat{\paragraph}[runin]
  {\sffamily\small\bfseries}
  {}
  {0em}
  {#1}
\titlespacing*{\section}{0pc}{3ex \@plus4pt \@minus3pt}{5pt}
\titlespacing*{\subsection}{0pc}{2.5ex \@plus3pt \@minus2pt}{0pt}
\titlespacing*{\subsubsection}{0pc}{2ex \@plus2.5pt \@minus1.5pt}{0pt}
\titlespacing*{\paragraph}{0pc}{1.5ex \@plus2pt \@minus1pt}{10pt}

%
% tableofcontents set-up
%
\usepackage{titletoc}
\contentsmargin{0cm}
\titlecontents{section}[\tocsep]
  {\addvspace{4pt}\small\bfseries\sffamily}
  {\contentslabel[\thecontentslabel]{\tocsep}}
  {}
  {\hfill\thecontentspage}
  []
\titlecontents{subsection}[\tocsep]
  {\addvspace{2pt}\small\sffamily}
  {\contentslabel[\thecontentslabel]{\tocsep}}
  {}
  {\ \titlerule*[.5pc]{.}\ \thecontentspage}
  []
\titlecontents*{subsubsection}[\tocsep]
  {\footnotesize\sffamily}
  {}
  {}
  {}
  [\ \textbullet\ ]

\RequirePackage{enumitem}
%\setlist{nolistsep} % Uncomment to remove spacing between items in lists (enumerate, itemize)

% Remove brackets from numbering in List of References
\renewcommand{\@biblabel}[1]{\bfseries\color{color1}\textsuperscript{[#1]}}

%
% article meta data
%% LLT 18 Aug 2016: no more!
% \newcommand{\keywords}[1]{\def\@keywords{#1}}
%% LLT 18 Aug 2016: but need corresponding author
\newcommand{\corrauthor}[3][]{%
  \def\thecorrauthor{%
  Corresponding author:\par #2$^{#1}$\par
  \medskip
  Email address: #3\par}
}

\def\xabstract{abstract}
\long\def\abstract#1\end#2{\def\two{#2}\ifx\two\xabstract
\long\gdef\theabstract{\ignorespaces#1}
\def\go{\end{abstract}}\else
\typeout{^^J^^J PLEASE DO NOT USE ANY \string\begin\space \string\end^^J
COMMANDS WITHIN ABSTRACT^^J^^J}#1\end{#2}
\gdef\theabstract{\vskip12pt BADLY FORMED ABSTRACT: PLEASE DO
NOT USE {\tt\string\begin...\string\end} COMMANDS WITHIN
THE ABSTRACT\vskip12pt}\let\go\relax\fi
\go}

%
% custom title page
%
\renewcommand{\@maketitle}{%
{%
\thispagestyle{empty}%
\vskip-36pt%
{\raggedright\sffamily\bfseries\fontsize{20}{25}\selectfont \@title\par}%
\vskip10pt
{\raggedright\sffamily\fontsize{12}{16}\selectfont  \@author\par}
\vskip1em%
% LLT 18 Aug 2016: needs corresponding author now
\ifdefined\thecorrauthor
  {\raggedright\sffamily\thecorrauthor\par}
\fi
\vskip18pt
{%
\noindent
{\parbox{\dimexpr\linewidth-2\fboxsep\relax}{\color{color1}\large\sffamily\textbf{ABSTRACT}}}
}%
\vskip10pt\nolinenumbers
{%
\noindent
\colorbox{color2}{%
\parbox{\dimexpr\linewidth-2\fboxsep\relax}{%
\sffamily\small\vskip1ex\if@peerjlineno\internallinenumbers\fi\theabstract
}%
}%
%% LLT 18 Aug 2016: no more keywords
% \vskip18pt%
% \noindent
% \parbox{\dimexpr\linewidth-2\fboxsep\relax}{%
% \if@peerjlineno\internallinenumbers\fi%
% {\color{color1}\keywordname\hspace*{1em}} \@keywords%
% }%
}%
\vskip25pt%
}%
}%
%-----------------------------------------------
\setlength{\columnsep}{0.55cm} % Distance between the two columns of text
\setlength{\fboxrule}{0.75pt} % Width of the border around the abstract

\definecolor{color1}{RGB}{0,0,0} % Color of section headings
\definecolor{color2}{RGB}{250,232,207} % Color of the box behind the abstract
\newcommand{\keywordname}{Keywords:} % Defines the keywords heading name

\renewcommand\Authfont{\fontsize{12}{14}\usefont{OT1}{phv}{b}{n}}
\renewcommand\Affilfont{\fontsize{10}{12}\usefont{OT1}{phv}{b}{n}}

\newlength{\tocsep}
\setlength\tocsep{1.5pc} % Sets the indentation of the sections in the table of contents
\setcounter{tocdepth}{3} % Show only three levels in the table of contents section: sections, subsections and subsubsections

\usepackage{lipsum} % Required to insert dummy text
%-----------------------------------------------
\let\oldbibliography\thebibliography
\renewcommand{\thebibliography}[1]{%
\addcontentsline{toc}{section}{\hspace*{-\tocsep}\refname}%
\oldbibliography{#1}%
\setlength\itemsep{0pt}%
}