Using Gitbook with R Markdown

April 18, 2014

(This article was first published on Blog - R, and kindly contributed to R-bloggers)

Gitbook has been getting some (deserved) attention. For those who haven’t seen it, Gitbook is a system to create really beautiful interactive web (or PDF and ebook) books. For me, the timing of discovering this framework could not be better as I am preparing documentation for propensity score analysis for an upcoming workshop I am giving. Of course, I want to use it to write about R and would prefer to use R markdown instead of just plain markdown. I have written a number of R functions to combine the functionality of knitr and Gitbook. The source code is on Gist or can be sourced directly using the devtools package.

> devtools::source_gist(11049319)

The first step is to create a new Gitbook. The newGitbook will create a new directory and create four files.

  • .bookignore – This file is formatted like any .gitignore file, but is specifically for Gitbook. That is, list files here that you want Gitbook to ignore, but want Git to manage. This defaults to include .Rmd, .md, .R, and .Rproj files as well as the log directory (this will be discussed below).
  • .gitignore – This defaults to include the _book directory. This is the default location for the built book and it is likely you do not want to include it in your master branch. As we will see below, this directory will be published to the gh-pages branch.
  • – Introduction to your Gitbook.
  • – Defines the structure (i.e. table of contents) of your Gitbook.

You can get more information about how Gitbook is organized at their webiste

> newGitbook('~/Dropbox/Projects/testbook')
Creating /Users/jbryer/Dropbox/Projects/testbook
Writing .bookignore...
Writing .gitignore...
You can now open and Once you are done 
editting, initGitbook() will create the file and folder 
structure for your new Gitbook.

I should note that the newGitbook will change the working directory to the location of your new Gitbook.

> getwd()
[1] "/Users/jbryer/Dropbox/Projects/testbook"

And we can see the four files it created.

Jasons-MacBook-Air:testbook jbryer$ ls -la
total 32
drwxr-xr-x    6 jbryer  staff   204 Apr 18 10:52 .
drwxr-xr-x  110 jbryer  staff  3740 Apr 18 10:52 ..
-rw-r--r--    1 jbryer  staff    35 Apr 18 10:52 .bookignore
-rw-r--r--    1 jbryer  staff    49 Apr 18 10:52 .gitignore
-rw-r--r--    1 jbryer  staff    75 Apr 18 10:52
-rw-r--r--    1 jbryer  staff   231 Apr 18 10:52

At this stage you can open and change the outline of your book. Once you are done, the initGitbook function will create the files and folders for your book. Unlike the Gitbook command line, this function will change the file extensions of all your files to .Rmd (excluding and even though you specify .md in the links in that file. The buildRmd function discussed below will convert those .Rmd files to .md.

> initGitbook()


The buildRmd function will convert all .Rmd files in your project to .md using the knitr package. It should be noted that this function will create a file, .rmdbuild.Rda, in your working directory. This is an R data file that saves the status of the last build. This allows this function to only build R markdown files that have changed since the last build and therefore, increase the execution time. By default, all the knitr messages will be printed to the console. If you specify log.dir parameter, then all the output will be saved to log files in that given directory (one log file per Rmd file). There is also a clean parameter that will build all R markdown files regardless of their modification timestamp.

> buildRmd()

The buildGitbook function is simply a wrapper to the Gitbook command line and will generate your book from the markdown sources. As of this writing, there is a bug in Gitbook where the image URLS are incorrect. This function will fix the URLs. There is also another issue that links to the Introduction point to / and not /index.html. These will also be fixed.

> buildGitbook()

The openGitbook will open your built book using your system’s default web browser.

> openGitbook()

Lastly, the publishGitbook will publish your built Gitbook to the gh-pages branch of the specified Github repository. Special thanks to Ramnath Vaidyanathan who provided the shell script to do this. Take a look at the link as you can optionally save this as a Git hook to publish atomically after checking in code to the master branch.

> publishGitbook(repo='jbryer/testbook')

Please leave comments below or suggestions to make this better. I would also be interested if there is interest in rolling this up into an R package.

Here is the source code:

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