In bbolker/McMasterPandemic: Pandemic Model

A place to keep notes on expandify implementation (ageify, vaxify) assumptions and future work (instead of relying on disparate FIXMEs).

Assumptions

Wherever distribute_counts or smart_round is used, it fills preferentially from right to left (e.g. in expand_state_age, counts from a specified state will be preferentially distributed from older age groups to younger)

By default, everyone starts in the unvaccinated compartment, regardless of epi status or point in the epidemic.
I think we can get around this by specifying make_state(x = vec) manually?
We know the number of doses per day administered to each subgroup (e.g. age category) of the population.
Currently assuming there is only one dose, but could expand to two doses
would need to update how vax efficacy gets handled in make_beta()
would need to update how rates get assigned for movement between vax strata (currently only have people move (from non-symptomatic states) vax_cat[1] -> vax_cat[2] (vaccine allocation step) and susceptibles from vax_cat[2] -> vax_cat[3] (vaccine response step))
Currently assuming there is no difference in the disease course for vaccinated individuals that get infected (this happens since we're not assuming 100% vaccine efficacy).
We only vaccinate non-symptomatic classes ($S$, $E$, $I_a$, $I_p$, $R$) because of symptom screening at vax sites & the fact that hospitalized individuals aren't being vaccinated while they're receiving treatment.
Currently, we split the number of doses per day evenly over the population, regardless of age.

Make condense_vax() work for ageified case (without losing age groups).
Age-specific doses per day: check that mk_vaxrates() works for ageified parameters (specifically the doses_per_day/params[["N"]] calculation, since this is a vector divided by a vector).
make_ratemat(): update epi rates in vaxdose strata to reflect reduced disease severity of breakthrough infections (increase asymptomatic proportion and turn off flows to severe illness, i.e. hospitalization, and death)
make_vaxrates(): use an age-specific vector of vax_doses_per_day in computing age-specific vaccination rates (rates from state_age_unvax to state_age_vaxwait)