settings.tex

\usepackage[top=0.85in,left=2.75in,footskip=0.75in]{geometry}

% amsmath and amssymb packages, useful for mathematical formulas and symbols
\usepackage{amsmath,amssymb}

% Use adjustwidth environment to exceed column width (see example table in text)
\usepackage{changepage}

% Use Unicode characters when possible
\usepackage[utf8x]{inputenc}

% textcomp package and marvosym package for additional characters
\usepackage{textcomp,marvosym}

% cite package, to clean up citations in the main text. Do not remove.
\usepackage{cite}

% Use nameref to cite supporting information files (see Supporting Information section for more info)
\usepackage{nameref,hyperref}

% line numbers
\usepackage[right]{lineno}

% ligatures disabled
\usepackage{microtype}
\DisableLigatures[f]{encoding = *, family = * }

% color can be used to apply background shading to table cells only
\usepackage[table]{xcolor}

% array package and thick rules for tables
\usepackage{array}

% enumerate package lets us use letters instead of numbers
\usepackage{enumerate}

% create "+" rule type for thick vertical lines
\newcolumntype{+}{!{\vrule width 2pt}}

% create \thickcline for thick horizontal lines of variable length
\newlength\savedwidth
\newcommand\thickcline[1]{%
  \noalign{\global\savedwidth\arrayrulewidth\global\arrayrulewidth 2pt}%
  \cline{#1}%
  \noalign{\vskip\arrayrulewidth}%
  \noalign{\global\arrayrulewidth\savedwidth}%
}

% \thickhline command for thick horizontal lines that span the table
\newcommand\thickhline{\noalign{\global\savedwidth\arrayrulewidth\global\arrayrulewidth 2pt}%
\hline
\noalign{\global\arrayrulewidth\savedwidth}}

\usepackage{color}

% Remove comment for double spacing
%\usepackage{setspace}
%\doublespacing

% Text layout
\raggedright
\setlength{\parindent}{0.5cm}
\textwidth 5.25in
\textheight 8.75in

% Bold the 'Figure #' in the caption and separate it from the title/caption with a period
% Captions will be left justified
\usepackage[aboveskip=1pt,labelfont=bf,labelsep=period,justification=raggedright,singlelinecheck=off]{caption}
\renewcommand{\figurename}{Fig}

% Use the PLoS provided BiBTeX style
\bibliographystyle{plos2015}

% Remove brackets from numbering in List of References
\makeatletter
\renewcommand{\@biblabel}[1]{\quad#1.}
\makeatother

% Leave date blank
\date{}

% Header and Footer with logo
\usepackage{lastpage,fancyhdr,graphicx}
\usepackage{epstopdf}
\pagestyle{myheadings}
\pagestyle{fancy}
\fancyhf{}
\setlength{\headheight}{27.023pt}
\lhead{\includegraphics[width=2.0in]{PLOS-submission.eps}}
\rfoot{\thepage/\pageref{LastPage}}
\renewcommand{\footrule}{\hrule height 2pt \vspace{2mm}}
\fancyheadoffset[L]{2.25in}
\fancyfootoffset[L]{2.25in}
\lfoot{\sf PLOS}