plotting functions for coverage and survival

[davidsantiagoquevedo]

• Functions to plot survival
• Functions to calculate and plot vaccine coverages
• Current coverage: 60%

[pratikunterwegs]

Thanks @davidsantiagoquevedo - I'll take a look at this next week and get back to you by Weds? Meanwhile perhaps you could already fix the linting.

[davidsantiagoquevedo]

Hi @pratikunterwegs. Thanks! By Wednesday is perfect. I'll check the lining. We also have today a collaborative session at PUJ for the test coverage. Currently 60%

[pratikunterwegs]

Thanks - I'm taking a look now, and I can take another look tomorrow in case you've added more tests for the plots. Snapshot tests should do the trick.

[davidsantiagoquevedo]

Hello @pratikunterwegs, we fixed the errors on the checks generated by the tests. Could you please take a look at this PR when you have time?
Thanks!

[pratikunterwegs]

Hi @davidsantiagoquevedo sure, I could take a look by the end of the week if that's alright?

[davidsantiagoquevedo]

Hello @pratikunterwegs . Yes, by the end of the week is fine. Thank you!

[pratikunterwegs]

Nice stuff @davidsantiagoquevedo - looks good to me overall. I had only a few comments which I've made on the code.

One recommendation though would be to refactor plot_coverage() --- this function wraps coh_coverage(). I would instead let the two be chain-able, so that the output of coh_coverage() can be passed to plot_coverage(). You would need to add some input checks on data to ensure it has the expected columns.

coh_coverage(<ARGS>) |> plot_coverage()

This reduces the nestedness of the code overall, and if there are other methods (i.e., study methods) from which coverage can be calculated, these could also be handled by plot_coverage() in future.

some_method_coverage(<ARGS>) |> plot_coverage()