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    <h3>Updated Answer (10 Feb 2013)</h3> <p><strong>rmarkdown package</strong>: There is now an <a href="https://github.com/rstudio/rmarkdown" rel="noreferrer"><code>rmarkdown</code> package available on github</a> that interfaces with Pandoc. It includes a <code>render</code> function. The documentation makes it pretty clear how to convert rmarkdown to pdf among a range of other formats. This includes including output formats in the rmarkdown file or running supplying an output format to the rend function. E.g.,</p> <pre><code>render("input.Rmd", "pdf_document") </code></pre> <p><strong>Command-line:</strong> When I run <code>render</code> from the command-line (e.g., using a makefile), I sometimes have issues with pandoc not being found. Presumably, it is not on the search path. The following answer explains <a href="https://stackoverflow.com/a/29710643/180892">how to add pandoc to the R environment</a>.</p> <p>So for example, on my computer running OSX, where I have a copy of pandoc through RStudio, I can use the following:</p> <pre><code>Rscript -e "Sys.setenv(RSTUDIO_PANDOC='/Applications/RStudio.app/Contents/MacOS/pandoc');library(rmarkdown); library(utils); render('input.Rmd', 'pdf_document')" </code></pre> <hr> <h3>Old Answer (circa 2012)</h3> <p>So, a number of people have suggested that Pandoc is the way to go. See notes below about the importance of having an up-to-date version of Pandoc.</p> <h3>Using Pandoc</h3> <p>I used the following command to convert R Markdown to HTML (i.e., <a href="https://stackoverflow.com/a/10969107/180892">a variant of this makefile</a>), where <code>RMDFILE</code> is the name of the R Markdown file without the <code>.rmd</code> component (it also assumes that the extension is <code>.rmd</code> and not <code>.Rmd</code>). </p> <pre><code>RMDFILE=example-r-markdown Rscript -e "require(knitr); require(markdown); knit('$RMDFILE.rmd', '$RMDFILE.md'); markdownToHTML('$RMDFILE.md', '$RMDFILE.html', options=c('use_xhml'))" </code></pre> <p>and then this command to convert to pdf</p> <pre><code>Pandoc -s example-r-markdown.html -o example-r-markdown.pdf </code></pre> <p><hr /> A few notes about this:</p> <ul> <li>I removed the reference in the example file which exports plots to imgur to host images.</li> <li>I removed a reference to an image that was hosted on imgur. Figures appear to need to be local.</li> <li>The options in the <code>markdownToHTML</code> function meant that image references are to files and not to data stored in the HTML file (i.e., I removed <code>'base64_images'</code> from the option list).</li> <li>The resulting output looked like <a href="http://cloud.github.com/downloads/jeromyanglim/assorted-files/example-r-markdown.pdf" rel="noreferrer">this</a>. It has clearly made a very LaTeX style document in contrast to what I get if I print the HTML file to pdf from a browser.</li> </ul> <h3>Getting up-to-date version of Pandoc</h3> <p>As mentioned by @daroczig, it's important to have an up-to-date version of Pandoc in order to output pdfs. On Ubuntu as of 15th June 2012, I was stuck with version 1.8.1 of Pandoc in the package manager, but it seems from the <a href="http://johnmacfarlane.net/pandoc/releases.html" rel="noreferrer">change log</a> that for pdf support you need at least version 1.9+ of Pandoc.</p> <p>Thus, I installed <code>caball-install</code>. And then ran:</p> <pre><code>cabal update cabal install pandoc </code></pre> <p>Pandoc was installed in <code>~/.cabal/bin/pandoc</code> Thus, when I ran <code>pandoc</code> it was still seeing the old version. See here for <a href="https://askubuntu.com/a/33443/2521">adding to the path</a>.</p>
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    1. POHow to convert R Markdown to PDF?
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    1. COThanks for this answer. I just want to comment that my experience was that giving the .md file to *pandoc*, rather than the .html file, gave a better output. So it's worth to experiment.
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    2. COThis is the closest I've come to a good process as well. Is there any way of changing the figure text from "plot chunk of ..." to something else?
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