I still use a Makefile for R markdown, but that's largely because I don't use only R for any analysis. There's normally some amount of calculation or pre-proces

I still use a Makefile for R markdown, but that's largely because I don't use only R for any analysis. There's normally some amount of calculation or pre-processing that happens before I flip into R. Makefiles are particularly good at describing the relationships between datafiles when you mix different tools.