RMarkdown to PDF with pandoc (using Makefile)

README.md

Previous version: https://gist.github.com/reinholdsson/7426608/566d8104363cd2fef2d6dd50e90aceab377b4a45

How to build pdf

make build
make clean

Future

Perhaps to combine with: https://bitbucket.org/reinholdsson/knitr-whisker-template

or use something like:

<%= source("modules/graph1.r") %>

It could even be nice to be able to use both alternatives! Not only for figures or tables, but also for including chapters or sections.

build.r

# On Mac OS install X11 support, e.g. XQuartz-2.7.5.dmg
library(pander)

# Evaluation options
evalsOptions("graph.output", "pdf")
evalsOptions('graph.unify', T)  # OBS!
evalsOptions("cache", F)

# Plot options
panderOptions("graph.background", "white")
panderOptions("graph.grid", F)
panderOptions("graph.grid.minor", F)
panderOptions("graph.legend.position", "bottom")

template <- "tufte-handout.template"
brew <- "report.brew"
tex <- "temp.tex"

# brew -> tex
Pandoc.brew(
  file = brew,
  output = tex,
  convert = 'tex',
  options = paste0('--template=', template),
  open = F
)

# Replace figure to marginfigure
system(paste("sed -i -e 's/figure}.*/marginfigure}/'", tex))

# tex -> pdf
system(paste("pdflatex", tex))

Makefile

build:
	Rscript build.r

clean:
	rm -rf *.tex *.tex-e *.bbl *.blg *.aux *.out *.log *.spl plots/ cache/ *.gz\(busy\) *.gz *.pdf

report.brew

% Thomas Reinholdsson
% Minimal report example

# Title

This is an R Markdown document. Markdown is a simple formatting syntax for authoring web pages (click the **Help** toolbar button for more details on using R Markdown).

When you click the **Knit HTML** button a web page will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

Pander option:
<%= panderOptions("graph.background") %>

<%= plot(cars) %>

You can also embed plots, for example:

<%=
if (require(ggplot2, quietly = TRUE)) {
  ggplot(diamonds, aes(clarity, fill=cut)) + geom_bar()
}
%>

tufte-handout.template

% tufte-handout.tex - DESC
% Iago Mosqueira - JRC. 2013
%

\documentclass{tufte-handout}

% pdf graphs
\usepackage{epstopdf}
\usepackage{grffile}

% tables
\usepackage{longtable}

% ams
\usepackage{amssymb,amsmath}

% Set up the images/graphics package
\usepackage{graphicx}
\setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio}
\graphicspath{{graphics/}}

% natbib
\usepackage{natbib}
\bibliographystyle{plainnat}

% biblatex
$if(biblatex)$
\usepackage{biblatex}
$if(biblio-files)$
\bibliography{$biblio-files$}
$endif$
$endif$

% booktabs
\usepackage{booktabs}

% url
\usepackage{url}

% hyperref
\usepackage{hyperref}

% units.
\usepackage{units}

% fancyvrb
\usepackage{fancyvrb}
\fvset{fontsize=\normalsize}
\DefineShortVerb[commandchars=\\\{\}]{\|}
\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}


% multiplecol
\usepackage{multicol}

% lipsum
\usepackage{lipsum}

% These commands are used to pretty-print LaTeX commands
\newcommand{\doccmd}[1]{\texttt{\textbackslash#1}}% command name -- adds backslash automatically
\newcommand{\docopt}[1]{\ensuremath{\langle}\textrm{\textit{#1}}\ensuremath{\rangle}}% optional command argument
\newcommand{\docarg}[1]{\textrm{\textit{#1}}}% (required) command argument
\newenvironment{docspec}{\begin{quote}\noindent}{\end{quote}}% command specification environment
\newcommand{\docenv}[1]{\textsf{#1}}% environment name
\newcommand{\docpkg}[1]{\texttt{#1}}% package name
\newcommand{\doccls}[1]{\texttt{#1}}% document class name
\newcommand{\docclsopt}[1]{\texttt{#1}}% document class option name

% Shaded
\newenvironment{Shaded}{}{}
\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{\textbf{{#1}}}}
\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.56,0.13,0.00}{{#1}}}
\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.25,0.63,0.44}{{#1}}}
\newcommand{\CharTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\StringTok}[1]{\textcolor[rgb]{0.25,0.44,0.63}{{#1}}}
\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.38,0.63,0.69}{\textit{{#1}}}}
\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.00,0.44,0.13}{{#1}}}
\newcommand{\AlertTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.02,0.16,0.49}{{#1}}}
\newcommand{\RegionMarkerTok}[1]{{#1}}
\newcommand{\ErrorTok}[1]{\textcolor[rgb]{1.00,0.00,0.00}{\textbf{{#1}}}}
\newcommand{\NormalTok}[1]{{#1}}

$if(title)$
\title{$title$}
$endif$
$if(author)$
\author{$for(author)$$author$$sep$ \and $endfor$}
$endif$
$if(date)$
\date{$date$}
$endif$

\begin{document}
$if(title)$
\maketitle
$endif$

$body$

$if(natbib)$
$if(biblio-files)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\bibliography{$biblio-files$}
\bibliographystyle{plainnat}

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

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

$endfor$
\end{document}