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Como-DTC-Collaboration / como-models

Pedagogical materials for learning COVID-19 transmission dynamics modelling
https://Como-DTC-Collaboration.github.io/como-models/
MIT License
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Births, natural deaths and waning natural immunity #53

Closed ben18785 closed 2 years ago

ben18785 commented 2 years ago

Adds a model and vignette that allows: births, natural deaths and waning natural immunity (i.e. protection from reinfection due to a previous infection). The vignette shows how epidemic waves occur and gives an order of magnitude estimate for the case counts that would be reached at endemic equilibrium for COVID-19.

Addresses #14.

solveigvandervegt commented 2 years ago

Looks really good! I fixed some typos and grammar issues, hope that's ok. The only thing that I have some reservations about is the computation of beta. I know it comes from the other vignette but since you already mention that in the text, I would be tempted to just set the values here and not derive it again. It's quite a confusing computation out of context and if people want to know why these values are used, they know where to look.

solveigvandervegt commented 2 years ago

Oh also, the last situation in the references list is missing an author?

solveigvandervegt commented 2 years ago

And is it correct that there are no tests for this class? I cannot see them in the test that folder

ben18785 commented 2 years ago

Thanks @solveigvandervegt -- you're spot on re: tests. I'll add some now. I'll also address your other comments.

ben18785 commented 2 years ago

Thanks @solveigvandervegt I've added tests. Re: R_0, I actually quite favour having it in there (as a more pedagogical aspect of the vignette). I've added a little more text that explains both the relevance of the calculation (for the vignette itself) and the calculation. Anyhow, see what you think!

solveigvandervegt commented 2 years ago

Hey Ben, yeah sorry you are totally right re: R0 and beta, I read it wrong. I think my point is actually about how gamma and mu are computed. The zeta and ifr come a bit out of nowhere, though I know this is addressed in the other vignette. Sorry for the poorly written comment before!

ben18785 commented 2 years ago

Cool no worries -- I've now added an explicit reference to the other vignette. I actually think that this will partly be addressed by #67 so perhaps we can leave this as is for now and address later?

solveigvandervegt commented 2 years ago

Yeah sure, sounds good!