make + rmarkdown

by: Austin G. Davis-Richardson harekrishna@gmail.com

Example of using knitR + Make + RMarkdown for minimally replicable scientific computing. Use this as a skeleton for new R projects.

Instructions

1. Data goes in data/ (I usually use symlinks or git modules and track this in a separate repository).
2. Rmarkdown files go in notebooks. I've been trying to treat them like a lab notebook and write one per day.
3. Type make (this renders all Rmarkdown files to HTML).

You should see something like:

$ make
notebooks/1-hello-world.Rmd -> notebooks/1-hello-world.html
echo "library(knitr); knit(\"notebooks/1-hello-world.Rmd\", \"notebooks/1-hello-world.html\")" | R --slave --vanilla --no-save


processing file: notebooks/1-hello-world.Rmd
  |.................................................................| 100%
  ordinary text without R code


output file: notebooks/1-hello-world.html

[1] "notebooks/1-hello-world.html"

Or, using Docker:

$ docker build --tag myrproject

$ docker run myrproject

TODO

• Add Packrat for dependency management/vendoring.