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epiverse-trace / howto

https://epiverse-trace.github.io/howto/
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How to use epidemics-classes with {odin} models #60

Closed pratikunterwegs closed 3 months ago

pratikunterwegs commented 5 months ago

This draft PR aims to fix #54 and is a work in progress. It builds off the update-renv branch and needs to be rebased on main before merging. This is a trial and may or may not be merged depending on whether {epidemics} features can be used with {odin} models.

pratikunterwegs commented 5 months ago

Unsure why checks are failing as the scripts have been updated to use epiparameter::epidist_db().

pratikunterwegs commented 5 months ago

Workflow failing as {rlang} v1.1.4 binaries may not yet be ready - will rerun later in the week to check.

adamkucharski commented 4 months ago

Was exploring the odin model more and noticed that interventions seem to have different effect in odin and original epidemics implementation (despite the two outputs matching in the absence of interventions once model was SEIR - see this branch).

If R0=1.5, then reducing contacts across ages by 33% should cause the epidemic to roughly level off (because R = 1.5*(1-0.33) = 1). Or just under 33% given some immunity has already accumulated. This is what happens with the {odin} implementation. However, in the {epidemics} README implementation, the epidemic seems to level off when the contact reduction is around 15%, suggesting that the effect of interventions may be inflated somewhere in the model code. Will also flag as potential issue on {epidemics}.

adamkucharski commented 4 months ago

Note the above issue has been resolved as a diffference in assumptions about how interventions acting on contacts (i.e. acting on both contacts to and from). The further-odin-development branch now has an {odin} implementation that matches the {epidemics} README, so might be worth merging that with this PR

avallecam commented 3 months ago

this is ready to merge 🚀

We'll continue the review in an upcoming PR from further-odin-development branch. These include: