How to use epidemics-classes with {odin} models

[pratikunterwegs]

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]

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

[pratikunterwegs]

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

[avallecam]

One review comment related to #43, which is now solved:

• We just added an setup chunk to template and all entries.
• We added the rationale behind this in the Code style section in the CONTRIBUTING guidelines

[adamkucharski]

Thanks for putting this together. This is a useful addition showing how epidemics objects can fit together within odin methods, and open that ecosystem in the process.

I've also made a suggestion for how a vector input of age-specific reduction can make it feasible to incorporate the school closure intervention object already defined in {epidemics} README.

[adamkucharski]

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]

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]

this is ready to merge 🚀

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

• combine isolated chunks to only one code chunk ready to make this ready to copy and paste for user
• add the warning and message FALSE to this chunk
• add question mark to entry name
• add options(odin.verbose = FALSE) to setup chunk