Rmd to IPython Notebook and HTML

I had blogged earlier about a proof-of-concept for how to convert an R Markdown Notebook into an IPython Notebook. The idea was to allow R users to author reproducible documents in R Markdown, but be able to seamlessly convert into HTML or an IPython Notebook, which allows greater interactivity.

This is an update to the same post that makes use of the native R kernel for the IPython Notebook, being developed by @takluyver.

As noted earlier, the bulk of the work here is done by notedown, a python module that helps create IPython notebooks from markdown. The approach I have taken here is to convert the RMarkdown file into a Markdown file using a custom knitr script, and then using notedown to render it as an IPython notebook.

If you want to test this out, you will first need to install notedown

$ pip install notedown

The next step is to convert the Rmd source into html and ipynb. For the sake of convenience, I have added a Makefile that will do it all. Just run make all and it will create example.html using knit2html and example.ipynb using knitr and notedown. So you get two birds with one stone!

Now, to open the ipython notebook, you will need to install the native R kernel. Installation instructions can be found here. Once you have installed all dependencies, you can open the notebook from the command line using:

ipython notebook --KernelManager.kernel_cmd="['R', '-e', 'IRkernel::main(\'{connection_file}\')']"

The notebook will not contain any output, since I set eval = F while converting it. You will need to select Cell > Run All from the toolbar to automatically execute all cells and embed output. I am presuming there might be a mechanism in the IPython Notebook architecture to trigger this execution from the command line.