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One thing they (intentionally) left out was including a Makefile. This is one of the "Good Enough" practices that I also include. It doesn't matter if it is a Makefile or another master script or tool. What is important is that you have a manifest for how each derived data file was generated. And it should be able to be executed w/o arguments to have the entire analysis run from the raw/primary data.

This has saved me many times in the past.

They do mention this, though it's somewhat buried in #4 on page 8 and in their paragraph saying they left out "Build Tools". They do suggest having a "controller script" (or set of shell scripts) to run all the complete analysis.

Unless you use R markdown, in which case there is no need for a separate script or makefile.

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.

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