I wrote earlier about using Rakefiles with Pandoc. Now that I’m engaged in writing a series of posts on historical history dissertations, I have another problem that Rake can solve. Each of the blog posts for the series is written in R Markdown, which lets me mix R code and writing together in a kind of literate programming or research notebook. Then the fabulous knitr package by Yihui Xie runs the code to create a combination of writing and output in a Markdown file.
Let’s assume that you have a set of R Markdown files in your project directory, and that you want to knit them without loading any
.Rprofile files so that your research is reproducible. You can do this by with a Rakefile like this:
I have some additional options for this kind of project Rakefile, which you can see here. Mostly they run data munging scripts and define cleaning tasks.