template for writing an article in RStudio that combines text + R code and compiles into .tex and .pdf via LaTeX

rnw article template

%-------------------------------------------------------------------------------
% Title
% Code written by AUTHOR, email
% Date
% Other notes
%-------------------------------------------------------------------------------

\documentclass[authoryear,11pt]{elsarticle} % requires elsarticle package

\usepackage[T1]{fontenc}
\usepackage{enumerate}
\usepackage{graphics}
\usepackage{graphicx}
\usepackage[shortlabels]{enumitem}
\setlist[itemize]{noitemsep, topsep=0pt}
\usepackage{lmodern}
\usepackage{threeparttable}
\usepackage{booktabs}
\usepackage{dcolumn}
\usepackage[group-separator={,}]{siunitx}
\usepackage{float}
\usepackage{url}
\usepackage[english]{babel}
\usepackage{multirow}
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e}
\usepackage[dark,bottom,none]{draftcopy}
\usepackage[colorlinks=true,
            urlcolor=blue, % external links
            citecolor=blue, % citations
            filecolor=blue, % local files
            linkcolor=blue,
            ]{hyperref} 
%\usepackage{endfloat}
%\usepackage[super, sort, numbers]{natbib}
%\usepackage[round]{natbib}
\def\citeapos#1{\citeauthor{#1}'s (\citeyear{#1})}
\usepackage{rotating}
\usepackage{parskip}
\usepackage[margin=1in]{geometry}
\usepackage{caption}
\newcommand*{\h}{\hspace{5pt}}% for indentation
\newcommand*{\hh}{\h\h}% double indentation
\usepackage[toc,page]{appendix}
\usepackage{array}
\usepackage{parskip}
\usepackage{fancyhdr}
\pagestyle{fancy}
\lhead{}
\chead{}
\fancyfoot[C]{}
\rhead{Header \thepage} % change
\renewcommand{\headrulewidth}{0pt}
% \usepackage{Sweavel} % only helpful for including code chunks
\usepackage{inconsolata}
\usepackage{listings}
\lstset{breaklines=true} % break long lines

% get rid of footer included in elsarticle
\makeatletter
\def\ps@pprintTitle{%
 \let\@oddhead\@empty
 \let\@evenhead\@empty
 \def\@oddfoot{}%
 \let\@evenfoot\@oddfoot}
\makeatother

\begin{document}
\bibliographystyle{apalike}

\begin{frontmatter}
\title{This is my title}
\author[add1]{Author1\corref{cor1}}
\ead{mail@email.com}
\author[add2]{Author2\corref}
\ead{mail@email.com}
\author[add3]{Author3\corref}
\ead{mail@email.com}

\cortext[cor1]{Note about correspondence}
\address[add1]{Affilition, address}
\address[add2]{Affilition, address}
\address[add3]{Affilition, address}

\begin{abstract}
This is my abstract
\end{abstract}

\begin{keyword}
my, key, words
\end{keyword}

\end{frontmatter}

\newpage
\section*{Acknowledgements} % include * removes from numbering
Say something nice.
\newpage

% \newpage % uncomment to add a table of contents
% \tableofcontents
% \newpage

\section{Introduction}

Main text and R code chunks go here

<<setup, include=FALSE>>==
# set chunk options
  # if the .rnw file is in a folder 1-level inside the root folder
  # R thinks the working directory is inside
  # so set root.dir up one level
  opts_knit$set(root.dir = '../') 
  # same issue for figures
  opts_chunk$set(echo=FALSE, fig.path='../output/figures/', 
                 cache=TRUE, tidy=FALSE, dev='pdf', echo=FALSE, message=FALSE, 
                 include=FALSE)
@

\newpage
\section{References}
\bibliography{refs} % refs.bib needs to go in same directory as .swf file 

% \begin{appendices} % uncomment to add appendices
% \end{appendices}

\end{document}