How to convert R Markdown to PDF

Question

I ve previously asked about the commands for converting R Markdown to HTML    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 rmd file that presumably provides a reasonable test of any proposed solution  It was used as the basis for this blog post

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Follow these simple  steps    1  In the Rmarkdown script run Knit Ctrl Shift K   2  Then after the html markdown is opened click Open in Browser top left side  and     the html is opened in your web browser 3  Then use Ctrl P and save as PDF

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If you don t want to install anything you can output html  Then open the html file - it should open in a browser window  then right click to print  In the print window  select  save as pdf  in the bottom right hand corner if you re on a Mac  Voila

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Updated Answer  10 Feb 2013   rmarkdown package   There is now an rmarkdown package available on github 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  The following answer explains how to add pandoc to the R environment   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   a variant of this makefile   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 this  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 change log that for pdf support you need at least version 1 9  of Pandoc   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 adding to the path

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I think you really need pandoc  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  installing an up-to-date version of Pandoc 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  andoc convert function of my little package  which you must be terribly bored of as I try to point your attention there at every opportunity

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For an option that looks more like what you get when you print from a browser  wkhtmltopdf 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 this  It did not seem to handle the MathJax  this issue is discussed here   and the page breaks are ugly  However  in some cases  such a style might be preferred over a more LaTeX style presentation

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Only two steps    Install the latest release  pandoc  from here   https   github com jgm pandoc releases Call the function pandoc in the library knitr   library knitr  pandoc  input md   format    latex      Thus  you can convert your  input md  into  input pdf

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Right now  August 2014  You could use RStudio for converting R Markdown to PDF   Basically  RStudio use pandoc to convert Rmd to PDF    You could change metadata to    Add table of contents  Change figure options Change syntax highlighting style Add LaTeX options And many more       For more details - http   rmarkdown rstudio com pdf document format html

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I found using R studio the easiest way  but if wanting to control from the command line  then a simple R script can do the trick using rmarkdown render command  as mentioned above    Full script details here     usr bin env R    Render R markdown to PDF    Invoke with     gt  R -q -f make R --args my report Rmd    load packages require rmarkdown     require a parameter naming file to render if  length args     0        stop  Error  missing file operand   call    TRUE    else         read report to render from command line     for  rmd in commandArgs trailingOnly   TRUE               render Rmd to PDF         if   grepl     Rmd    rmd   amp  amp  file exists rmd                 render rmd  pdf document              else               print paste  Ignoring     rmd

[r-markdown] How to convert R Markdown to PDF?

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