DCNorris' Peerj Latex template

peerj.tex

\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(papersize)$$papersize$paper,$endif$$for(classoption)$$classoption$$sep$,$endfor$]{$documentclass$}
$if(fontfamily)$
\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
$else$
\usepackage{lmodern}
$endif$

% Originally coded by Matt Ralston, Jan 14 2021
% Alex Ball's tutorial LaTeX code for making a bibLaTeX oxyear style (biblatex-oxref)
% Bibliography.
% I used the following document, hosted on the CTAN servers of math.utah.edu
% to create the bibliography using Alex's style guide.
% Thank you, sincerely, Alex for the awesome library.
% http://ctan.math.utah.edu/ctan/tex-archive/macros/latex/contrib/biblatex-contrib/biblatex-oxref/oxref.pdf
% $if(biblatex)$
% $if(biblio-title)$
% 
% \RequireBibliographyStyle{oxref}
% \ExecuteBibliographOptions{giveninits,labeldateparts,sorting=nyt,pagetracker,mergedate,maxcitenames=2}
% 
% \RequireCitationStyle{authoryear-comp}
% \ExecuteBibliographOptions{uniquename=init}
% $endif$
% $endif$
\usepackage{biorxiv} % github.com/alexsbaldwin/biorxiv-inspired-latex-style
\usepackage{lineno}


\newlength{\cslhangindent}
\setlength{\cslhangindent}{1.5em}
\newenvironment{CSLReferences}%
{\setlength{\parindent}{0pt}%
\everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces}%
{\par}

$if(linestretch)$
\usepackage{setspace}
\setstretch{$linestretch$}
$endif$
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
  \usepackage[utf8]{inputenc}
$if(euro)$
  \usepackage{eurosym}
$endif$
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
$for(fontfamilies)$
  \newfontfamily{$fontfamilies.name$}[$fontfamilies.options$]{$fontfamilies.font$}
$endfor$
$if(euro)$
  \newcommand{\euro}{€}
$endif$
$if(mainfont)$
    \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
$endif$
$if(sansfont)$
    \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
$endif$
$if(monofont)$
    \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$for(monofontoptions)$$monofontoptions$$sep$,$endfor$$endif$]{$monofont$}
$endif$
$if(mathfont)$
    \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
$endif$
$if(CJKmainfont)$
    \usepackage{xeCJK}
    \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
$endif$
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(geometry)$
\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
$endif$
\usepackage[unicode=true]{hyperref}
$if(colorlinks)$
\PassOptionsToPackage{usenames,dvipsnames}{color} % color is loaded by hyperref
$endif$
\hypersetup{
$if(title-meta)$
            pdftitle={$title-meta$},
$endif$
$if(author-meta)$
            pdfauthor={$author-meta$},
$endif$
$if(keywords)$
            pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
$endif$
$if(colorlinks)$
            colorlinks=true,
            linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
            citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
            urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
$else$
            pdfborder={0 0 0},
$endif$
            breaklinks=true}
\urlstyle{same}  % don't use monospace font for urls
$if(lang)$
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[shorthands=off,$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
$if(babel-newcommands)$
  $babel-newcommands$
$endif$
\else
  \usepackage{polyglossia}
  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
$endfor$
\fi
$endif$


% Import biblatex
$if(biblatex)$
\usepackage[$if(biblio-style)$style=$biblio-style$,$endif$$for(biblatexoptions)$$biblatexoptions$$sep$,$endfor$]{biblatex}
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
% Fix footnotes in tables (requires footnote package)
\IfFileExists{footnote.sty}{\usepackage{footnote}\makesavenoteenv{long table}}{}
$endif$
$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
$endif$
$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
$if(indent)$
$else$
\IfFileExists{parskip.sty}{%
\usepackage{parskip}
}{% else
\setlength{\parindent}{0pt}
\setlength{\parskip}{6pt plus 2pt minus 1pt}
}
$endif$
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
$if(numbersections)$
\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(subparagraph)$
$else$
% Redefines (sub)paragraphs to behave more like sections
\ifx\paragraph\undefined\else
\let\oldparagraph\paragraph
\renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
\fi
\ifx\subparagraph\undefined\else
\let\oldsubparagraph\subparagraph
\renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
\fi
$endif$
$if(dir)$
\ifxetex
  % load bidi as late as possible as it modifies e.g. graphicx
  $if(latex-dir-rtl)$
  \usepackage[RTLdocument]{bidi}
  $else$
  \usepackage{bidi}
  $endif$
\fi
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \TeXXeTstate=1
  \newcommand{\RL}[1]{\beginR #1\endR}
  \newcommand{\LR}[1]{\beginL #1\endL}
  \newenvironment{RTL}{\beginR}{\endR}
  \newenvironment{LTR}{\beginL}{\endL}
\fi
$endif$

% set default figure placement to htbp
\makeatletter
\def\fps@figure{htbp}
\makeatother

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

$if(title)$
\title{$title$}
$else$
\typeout{A TITLE MUST BE PROVIDED}\QUIT
$endif$

$if(author)$
  $for(author)$%
    \author[$author.no$]{$author.name$}
    \affil[$author.no$]{$author.affil$}
    $if(author.email)$%
      \corrauthor[$author.no$]{$author.name$}{$author.email$}
    $endif$
    $if(author.thanks)$%
      \thanks{$author.thanks$}
    $endif$
  $endfor$
$else$
\typeout{AT LEAST ONE AUTHOR MUST BE LISTED}\QUIT
$endif$


$if(abstract)$
\begin{abstract}
$abstract$
\end{abstract}
$endif$





$if(keywords)$
\subsection*{Keywords}\label{keywords}
$for(keywords)$$keywords$$sep$, $endfor$
$endif$

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

$endfor$
$if(toc)$
{
$if(colorlinks)$
\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$black$endif$}
$endif$
\setcounter{tocdepth}{$toc-depth$}
\tableofcontents
}
$endif$
$if(lot)$
\listoftables
$endif$
$if(lof)$
\listoffigures
$endif$
\rfoot{\small\sffamily\bfseries\thepage/\pageref{endmain}}



\begin{document}

\linenumbers
\flushbottom
\thispagestyle{empty}
\maketitle
% $if(bibliography)$
% \newcommand{\pjbibliography}{\small\bibliographystyle{unsrtnat}%
% \bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}%
% \label{endmain}%
% }
% $endif$



$body$



$if(biblatex)$
\printbibliography$if(biblio-title)$[title=$biblio-title$]$endif$

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

$endfor$
\end{document}

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}
                

%
% 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}%
}