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.

I believe pandoc should be the best way to go. It does not make much sense to me to build it into R, and I do not think it is possible either (it is written in Haskell). I have some very early work here: https://github.com/yihui/knitr-book (see two shell scripts `knit` and `mdconvert.sh`). It may be hard to come up a general approach since LaTeX is too flexible; you can use all kinds of templates for pandoc. — Yihui Xie, Jun 14 '12 at 03:32
What is 'R Markdown*? http://www.rstudio.com/ide/docs/r_markdown — Colonel Panic, Mar 12 '13 at 17:02
http://www.markdowntopdf.com/ this site is pretty good, actually. However, there is no latex support — padawan, Mar 16 '15 at 09:28

score 72 · Answer 1 · edited May 23 '17 at 10:31

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.

Thanks 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. — yoavram, Nov 19 '12 at 23:58
This 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? — svenski, Jan 28 '13 at 17:25
`pandoc` is in version 1.12 even in my now outdated Ubuntu 13.04. — krlmlr, Feb 07 '14 at 10:52

daroczig · Answer 2 · 2012-11-29T16:59:14.750

23

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 Ṗandoc.convert function of my little package (which you must be terribly bored of as I try to point your attention there at every opportunity).

edited Nov 29 '12 at 16:59

answered Jun 14 '12 at 19:55

daroczig

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+1 The function looks good; Do you have a recommended one-liner pandoc command for converting R Markdown to PDF? – Jeromy Anglim Jun 15 '12 at 00:00
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Adding `--toc` would be useful on the command line (resulting in a nics table of content based on your headings) and also customizing the LaTeX template for your needs (like adding there `\listoffigures` and/or `\listoftables` etc.) could result in wonderful documents. – daroczig Jun 15 '12 at 18:39
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What challenging about `apt-get install pandoc` ? – sumid Nov 23 '12 at 05:51
@sumid you might have missed the **up-to-date** part (well, if you are not using testing). – daroczig Nov 23 '12 at 08:34
Yeah you're right - twice. I missed it and I'm also using testing ;-) Then I perceive as easier temporary allowing testing in `sources.list` and doing `apt-get install -t testing pandoc` then installing `haskell-platform` and compilation. (Usually I do this with experimental. I hope is works the same way in testing.) – sumid Nov 24 '12 at 06:38
As `pandoc` depends on some core or quite standard packages too (like `glibc6`, `texlive` etc.), it can be a real pain to install/update the package from `testing`. I mean I have ended up with some systems with installed packages from `stable` and also from `testing` before, and I did not like to do a dist-update at all on those machines :) That's possible, but I rather compile `pandoc` in my `$HOME`. Either way: it can get complicated from a POV :( – daroczig Nov 24 '12 at 20:10
@daroczig, your "Pandoc.convert function of my little package" link is broken. – GSee Nov 29 '12 at 15:44
Thanks @GSee for pointing my attention here, just update the link. – daroczig Nov 29 '12 at 16:59

score 15 · Answer 3 · answered Aug 05 '14 at 18:21

15

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 enter image description here

answered Aug 05 '14 at 18:21

Jot eN

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'knit PDF' option is not available in the Ubuntu 14.04, pandoc v1.17.1. Is there any settings needs to be done? – Prradep Jul 08 '16 at 11:45
What version of RStudio do you have? Did you create a new rmarkdown file? – Jot eN Jul 08 '16 at 12:03
Rstudio - v 0.98.507 – Prradep Jul 08 '16 at 12:06
Let us [continue this discussion in chat](http://chat.stackoverflow.com/rooms/116818/discussion-between-prradep-and-jot-en). – Prradep Jul 08 '16 at 15:01
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@Prradep What was the result of the conversation? – nealmcb Feb 10 '17 at 01:30

Jeromy Anglim · Answer 4 · 2012-07-05T00:46:33.843

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.

I am unable to run the last command in RStudio. I have tried `system("wkhtmltopdf temp.html temp.pdf")` Any idea how to fix that — Urvah Shabbir, Jun 24 '17 at 23:58

score 9 · Answer 5 · edited Nov 18 '16 at 08:28

9

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".

edited Nov 18 '16 at 08:28

Athafoud

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answered Jun 21 '14 at 22:16

Wei

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score 4 · Answer 6 · answered Aug 12 '16 at 05:22

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:
# > 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) && file.exists(rmd)) {
            render(rmd, pdf_document())
        } else {
            print(paste("Ignoring: ", rmd))
        }
    }
}

score 0 · Answer 7 · answered Jul 18 '17 at 05:17

0

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!

answered Jul 18 '17 at 05:17

Mariah Akinbi

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score 0 · Answer 8 · answered Nov 22 '17 at 09:14

0

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 .

answered Nov 22 '17 at 09:14

Ankit Kamboj

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How to convert R Markdown to PDF?

8 Answers8

Updated Answer (10 Feb 2013)

Old Answer (circa 2012)

Using Pandoc

Getting up-to-date version of Pandoc

Linked