metrumresearchgroup / expo1-nonmem-foce

An example population pharmacokinetic (pop PK) NONMEM analysis using a MetrumRG Ecosystem (MeRGE) workflow.

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location for yspec YAML files

andreashandel opened this issue · comments

@kylebaron told me he prefers/recommends yspec YAML files to be inside the /data/derived folder. That's how I've seen it in projects. The example has it on a separate /data/spec folder.

Probably useful to decide if the recommended workflow is to have in /data/derived, then update example, or decide that going forward it should be in /data/spec. Doing it both ways without explanation is confusing (at least to me - twice already so far 😁).

FWIW ... it's not that data/derived is my preference, but there's less user intervention required if you just have it all in data/derived. Obviously we can handle spreading the files around, but seems like we should avoid it to simplify stuff.

The key limitation is that define.pdf must hyperlink to the .xpt files and the only way we could do that is to have define.pdf in data/derived, the same folder as the .xpt file. So if we put the yaml file there too, we don't need to worry about directory paths anymore. That's where this all comes from.

This is good discussion. Do we want to keep this issue open or should we just close it and have it for reference if needed?

@kylebaron do we want to consider moving where we have the spec stored in this example project? I'm not totally clear on the pros and cons, but it seems like there are some definite pros to having it in data/derived/ (notably, the directory path issue you mention above).