A prototype - Githubissues

CDCgov / cfa-viral-lineage-model

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A prototype #6

Closed thanasibakis closed 2 months ago

thanasibakis commented 2 months ago

I've implemented a prototype of the pipeline from data pre-processing, to modeling of lineage proportions, to post-processing. I also have a simulation study implemented.

Some short-term wishlist items (these could likely be separate PRs):

The simulation study results could look better as we generalize out of the 2 divisions, 2 lineages setting
poetry
Thinking harder about priors

swo commented 2 months ago

@thanasibakis CFA practice is that the author (ie you, not the reviewers) do the squash & merge

thanasibakis commented 2 months ago

Not to sneak commits in post-review, but I don't know how my simulation study sample size configuration was lost at some point. Results are looking much nicer now that I have that back :)

(Changes are very minor)

afmagee42 commented 2 months ago

This is definitely not something to pile into this PR (it's entirely separable and can be handled after merging), but some basic documentation would be good.

For example, after some poking around I can see that one should run python load_metadata.py before I try to run the simulations, and it would be good for the README to mention this.

thanasibakis commented 2 months ago

Totally. I think that would be good for me to do when I package things up with poetry (which is up next for this codebase)