RMarkdown to PDF with pandoc (using Makefile)

README.md

First, run make to create the PDF:

make

To remove all temporary files, run:

make clean

See also: ggplotFL vignette.

To get it to work on MacOS, I have changed sed -i to sed -i -e.

Makefile

TEMPLATE=tufte-handout.template
PDFS:=$(patsubst %.Rmd,%.pdf,$(wildcard *.Rmd))

all: $(PDFS)

clean:
	rm -rf *.tex *.bbl *.blg *.aux *.out *.log *.spl *.md figure/ cache/

cleanall: clean
	rm $(PDFS)

%.pdf: %.tex
	pdflatex $*.tex

%.tex: %.md
	pandoc -o $*.tex --template=$(TEMPLATE) $*.md
	sed -i -e 's/figure}.*/marginfigure}/' $*.tex

%.md: %.Rmd
	R -e "library(knitr)" \
	  -e "knit('$*.Rmd')"

test.Rmd

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:

```{r}
summary(cars)
```

You can also embed plots, for example:

```{r fig.width=7, fig.height=6}
plot(cars)
```

tufte-handout.template

% tufte-handout.tex - DESC
% Iago Mosqueira - JRC. 2013
%
\documentclass{tufte-handout}

% 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}