preamble.tex

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% DO NOT EDIT THIS FILE UNLESS YOU KNOW WHAT YOU ARE DOING!!! %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Useful packages
\usepackage[]{authblk}
\usepackage{graphicx}
\usepackage{color}
\usepackage{longtable}
\usepackage{hanging}
\usepackage{indentfirst}
\usepackage{setspace}
\usepackage{enumitem}
\usepackage{verbatim}
\usepackage{upgreek}
\usepackage{framed}
\usepackage{textcomp}
\usepackage{url}
\usepackage{soul}
\usepackage{amsmath,amsfonts,amssymb,mathrsfs}
\usepackage{fancyhdr}
\usepackage[compact]{titlesec}
\usepackage[T1]{fontenc}
\usepackage{lmodern}
\usepackage[utf8]{inputenc}
\usepackage[]{listings}
%\usepackage{fontspec}
\usepackage{placeins}
\usepackage{epstopdf}
\usepackage[export]{adjustbox}
\usepackage{tikz}
\usepackage[breaklinks]{hyperref}
\usepackage[all]{hypcap}


% References
\usepackage[backend=bibtex,hyperref=true,citestyle=authoryear,bibstyle=authortitle,firstinits=true,terseinits=true,doi=false,url=false,eprint=false,maxbibnames=10,maxcitenames=2]{biblatex}
\input{biblatex_macros}

% Page margins
\setlength{\evensidemargin}{0in}
\setlength{\headheight}{0in}
\setlength{\headsep}{0in}
\setlength{\oddsidemargin}{-0.25in}
\setlength{\paperheight}{11in}
\setlength{\paperwidth}{8.5in}
\setlength{\tabcolsep}{0in}
\setlength{\textheight}{9in}
\setlength{\textwidth}{7in}
\setlength{\topmargin}{0in}
\setlength{\topskip}{0in}
\setlength{\voffset}{0in}
\parskip = 0.15in
\pagestyle{plain}
\setlength{\parindent}{0cm}

% No white space between list items
\setlist{nolistsep}

% Hyperlink setup
\hypersetup{colorlinks=true,linkcolor=linkscol,citecolor=citescol,urlcolor=urlscol}

% Settings for code blocks
\lstset{backgroundcolor=\color[rgb]{0.972,0.972,0.972},
    tabsize=4,
    rulecolor=,
        basicstyle=\scriptsize,
        upquote=true,
        aboveskip={1.5\baselineskip},
        columns=fixed,
        showstringspaces=false,
        extendedchars=true,
        breaklines=true,
        prebreak = \raisebox{0ex}[0ex][0ex]{\ensuremath{\hookleftarrow}},
        frame=single,
        showtabs=false,
        showspaces=false,
        showstringspaces=false,
        identifierstyle=\ttfamily,
        keywordstyle=\color[rgb]{0,0,1},
        commentstyle=\color[rgb]{0.133,0.545,0.133},
        stringstyle=\color[rgb]{0.627,0.126,0.941}
}

% Colour definitions
\definecolor{citescol}{RGB}{194,101,1}
\definecolor{urlscol}{RGB}{0,150,206}
\definecolor{linkscol}{RGB}{149,0,207}
\definecolor{mycol}{RGB}{25,23,191}
\definecolor{outputcol}{RGB}{34,139,34}
\definecolor{tcol}{RGB}{165,0,14}







% TODO: The rest of the file needs to be cleaned up!
%       Past this point I am not sure what is necessary or not - Louis


\DeclareMathAlphabet{\msfsl}{T1}{cmr}{m}{it}
\DeclareMathAlphabet{\msyf}{OMX}{pcr}{m}{it}
\newcommand{\alf}{\upalpha}
\newcommand{\hilight}[1]{\colorbox{yellow}{#1}}

\newcommand{\levelone}[1]{
\bigskip
\noindent{\LARGE{\textsc{#1}}}
\vspace {0.05in}
}

\newcommand{\leveltwo}[1]{
\bigskip
\noindent{\Large{\textit{#1}}}
\vspace {-1mm}
}

\newcommand{\descriptionhead}[1]{
\noindent{\textcolor{mycol}{\textbf{\textit{#1}}}}\\ \vspace{-7mm}
}

\newcommand{\dhead}[1]{
\noindent{\textbf{\textit{#1 --}}}
}

\newcommand{\exs}[1]{
\vspace{-4mm}
\begin{itemize}
\item #1 \\ \vspace{-8mm}
\end{itemize}
}


\newcommand{\nbo}[1]{{\color{red}{#1}}}


\newcommand{\stepbullet}{\noindent \textbullet \ }
\newcommand{\mi}[1]{\textbf{\textit{#1}}}


\newcommand{\levelthree}[1]{\textit{#1 --}}


%\bibliographystyle{apalike}
%\bibpunct[; ]{(}{)}{;}{a}{,}{;}


\usepackage[breaklinks]{hyperref}
\usepackage[all]{hypcap}
\hypersetup{colorlinks=true,linkcolor=linkscol,citecolor=citescol,urlcolor=urlscol}

% Some macros for software packages
\newcommand{\R}{\texttt{R} }
\newcommand{\TESS}{\texttt{TESS}}
\newcommand{\PBD}{\texttt{PBD}}
\newcommand{\DDD}{\texttt{DDD}}
\newcommand{\Laser}{\texttt{laser}}
\newcommand{\TreePar}{\texttt{TreePar}}
\newcommand{\diversitree}{\texttt{diversitree}}
\newcommand{\RevBayes}{\texttt{RevBayes}}
\newcommand{\Rev}{\texttt{Rev}}
\newcommand{\MrBayes}{\texttt{MrBayes}}
\newcommand{\BEAST}{\texttt{BEAST}}
\newcommand{\PhyloBayes}{\texttt{PhyloBayes}}
\newcommand{\PAML}{\texttt{PAML}}

\let\otheriint\iint
\let\iint\relax
\usepackage{ wasysym }







\definecolor{shadecolor}{RGB}{194,225,255}

\setlength{\tabcolsep}{5pt}
\setlength{\topmargin}{-0.4in}
\setlength{\headheight}{14.5pt}
\pagestyle{fancy}

\newcommand{\taha}[1]{{\textcolor{red}{[TAH comment: #1]}}} % TAH comment

\titlespacing{\section}{0pt}{*0}{*0}
\titlespacing{\subsection}{0pt}{*0}{*0}
\titlespacing{\subsubsection}{0pt}{*0}{*0}

\titleformat{\section}
  {\normalfont\Large\bfseries\color{mycol}}
  {\thesection}{1em}{}

\titleformat{\subsection}
  {\normalfont\large\bfseries\color{mycol}}
  {\thesubsection}{1em}{}

\titleformat{\subsubsection}
  {\normalfont\bfseries\color{mycol}}
  {\thesubsubsection}{1em}{}

% command for MrBayes command-line step
\newcommand{\cl}[1]{{\texttt{\textbf{#1}}}}
\newcommand{\colx}[1]{{\textcolor{tcol}{#1}}}
\newcommand{\mbcl}[1]{\exs{\cl{MrBayes > {#1}}}}

\newcommand{\rbprmt}{RevBayes > } 
\newcommand{\rbcl}[1]{\exs{\cl{\rbprmt{#1}}}}
\newcommand{\rbout}[1]{\exs{\cl{\textcolor{outputcol}{#1}}}}
\newcommand{\rbdn}{{\Large \symbol{126}}} % This makes a copy/pasteable tilde
\newcommand{\rbclml}[1]{\exs{\cl{\ \ \ \ \ \ \ \ \ \ \ {#1}}}}

% text box settings
% requires compiling w/ XeLaTeX
%\newfontfamily\listingsfont[Scale=1.0]{Courier New}
%\lstset{basicstyle=\listingsfont, columns=texcl}
%\defaultfontfeatures{Mapping=tex-text}


\makeatletter
\lst@CCPutMacro\lst@ProcessOther {"2D}{\lst@ttfamily{-{}}{-{}}}
\@empty\z@\@empty
\makeatother



\setlength{\topmargin}{-0.4in}
\setlength{\headheight}{14.5pt}
\pagestyle{fancy}



\definecolor{lg}{gray}{0.75}
\def\gcirc{{%
    \setbox0\hbox{$\fullmoon$}%
    \rlap{\hbox to \wd0{\hss{$\textcolor{lg}{\newmoon}$}\hss}}\box0
}}

% passthrough command for Pandoc combined with \lst
\newcommand{\passthrough}[1]{#1}