Lately, I’ve been using Rmarkdown + Make to perform statistical analysis and generate reports.

I saw Shaun Jackman’s slideshow “Open, reproducible science using Make, RMarkdown and Pandoc” and thought it was lacking a key example: how do you use Make to generate reports from RMarkdown files? So I put together a little recipe for doing just that. It is a basic project directory structure and a tiny Makefile that automatically renders Rmarkdown files to HTML.

In the example repo, there is a Makefile which defines a couple of rules for converting .md files into .pdf and .html files:

%.html: %.Rmd
	@Rscript -e "rmarkdown::render('$<')"

%.pdf: %.Rmd
	@Rscript -e "rmarkdown::render('$<')"

After adding this to your Makefile you can type make my-analysis.pdf to render

To automatically convert all .md files to .pdf, add the following lines which will create a target .pdf file for all of the .Rmd files in the current working directory:

# define targets
SOURCES=$(shell find notebooks -name *.Rmd)

default: $(TARGETS)

# type `make clean` to delete all of the target PDFs
	rm -rf $(TARGETS)