When you knit your.Rmd file to pdf, the plot you produce should look like the one below. Not so pretty, eh? Don’t worry - we will learn more about plotting in a later tutorial! Where is the File? In the steps above, we downloaded a file. However, where did that file go on your computer? Let’s find it before we go any further. Select and upload your file containing markdown markup and we'll convert it to a PDF for you in an instant.
I've previously asked about the. What is a good way to convert R Markdown files to PDF documents? A good solution would preserve as much as possible of the content (e.g., images, equations, html tables, etc.).
The solution needs to be able to be run from the command-line. A good solution would also be cross-platform, and ideally minimise dependencies to make it easier to share makefiles and so forth. Specifically, there are a lot of options: • Whether to convert RMD to MD to HTML to PDF; or RMD to MD to PDF; or RMD to PDF • If using the markdown package in R, which options to specify • Whether to use pandoc, a package built into R, or something else Here's an example that presumably provides a reasonable test of any proposed solution. It was used as the basis for. Updated Answer (10 Feb 2013) rmarkdown package: There is now an that interfaces with Pandoc. It includes a render 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., render('input.Rmd', 'pdf_document') Command-line: When I run render 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. Firefox browser for mac 10.4.11. The following answer explains.
So for example, on my computer running OSX, where I have a copy of pandoc through RStudio, I can use the following: Rscript -e 'Sys.setenv(RSTUDIO_PANDOC='/Applications/RStudio.app/Contents/MacOS/pandoc');library(rmarkdown); library(utils); render('input.Rmd', 'pdf_document')' Old Answer (circa 2012) 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. Using Pandoc I used the following command to convert R Markdown to HTML (i.e., ), where RMDFILE is the name of the R Markdown file without the.rmd component (it also assumes that the extension is.rmd and not.Rmd). RMDFILE=example-r-markdown Rscript -e 'require(knitr); require(markdown); knit('$RMDFILE.rmd', '$RMDFILE.md'); markdownToHTML('$RMDFILE.md', '$RMDFILE.html', options=c('use_xhml'))' and then this command to convert to pdf Pandoc -s example-r-markdown.html -o example-r-markdown.pdf A few notes about this: • I removed the reference in the example file which exports plots to imgur to host images. • I removed a reference to an image that was hosted on imgur.
Figures appear to need to be local. • The options in the markdownToHTML function meant that image references are to files and not to data stored in the HTML file (i.e., I removed 'base64_images' from the option list). • The resulting output looked like. 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. Getting up-to-date version of Pandoc 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 that for pdf support you need at least version 1.9+ of Pandoc.
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Thus, I installed caball-install. And then ran: cabal update cabal install pandoc Pandoc was installed in ~/.cabal/bin/pandoc Thus, when I ran pandoc it was still seeing the old version. See here for. I think you really need, which great software was designed and built just for this task:) Besides pdf, you could convert your md file to e.g. Docx or odt among others.
Well, might be challanging on Linux (as you would need the entire haskell-platform˙to build from the sources), but really easy on Windows/Mac with only a few megabytes of download. If you have the brewed/knitted markdown file you can just call pandoc in e.g bash or with the system function within R. A POC demo of that latter is implemented in the ( which you must be terribly bored of as I try to point your attention there at every opportunity).
For an option that looks more like what you get when you print from a browser, provides one option. On Ubuntu sudo apt-get install wkhtmltopdf And then the same command as for the pandoc example to get to the HTML: RMDFILE=example-r-markdown Rscript -e 'require(knitr); require(markdown); knit('$RMDFILE.rmd', '$RMDFILE.md'); markdownToHTML('$RMDFILE.md', '$RMDFILE.html', options=c('use_xhml'))' and then wkhtmltopdf example-r-markdown.html example-r-markdown.pdf The resulting file looked like. It did not seem to handle the MathJax (), and the page breaks are ugly. However, in some cases, such a style might be preferred over a more LaTeX style presentation.