A library of published compartmental epidemic models, and classes to represent demographic structure, non-pharmaceutical interventions, and vaccination regimes, to compose epidemic scenarios.
This issue logs feedback from @ffinger on the diphtheria model model_diphtheria() based on Finger et al. 2019, and potential next steps for package development - thanks @ffinger! If there's anything I've missed or that you'd like to add just put it in the comments.
General
The model would also be suitable for diseases targeted by routine vaccination such as measles or pertusis
Not suitable for diseases with different transmission dynamics such as Ebola or cholera
Demographic stratification of contacts
There is not always good evidence for whethr or how contacts vary by demographic group in a camp setting, but the option to model this would be good to have
[ ] Dev: Add social contacts functionality to the model, with a default assumption of homogeneous social contacts across demographic groups
Vaccination
Reactive vaccination campaigns are often conducted in response to diphtheria outbreaks
[ ] Dev: The model should support the {epidemics} vaccination functionality via <vaccination> objects
Reactive diphtheria vaccination campaigns may be conducted periodically every ±6 months, and may comprise of 1 - 3 doses, depending on dose availability;
[ ] Dev: Consider whether the intended use case covers a long-term simulation which would require implementing a repeated vaccination functionality (see also #227);
[ ] Dev: Consider whether more than one vaccination compartment/stratum needs to be implemented (as in Vacamole);
Vaccination may only prevent symptomatic disease but may not prevent transmission
[ ] Dev: Consider whether the model needs more compartments ($Is, I{as}$ for symptomatic and asymptomatic), and how these can be linked to the hospitalisation compartment;
Population movements
Modelling movements between camps in a metapopulation model may not be necessary for a scenario model, and it may be more appropriate to implement separate models for each camp;
Population influxes into camps (see the population_change functionality) may differ in their vaccine coverage profiles, but there may not be good estimates for this
[ ] Dev: It is currently sufficient to assume that all individuals in an influx enter the susceptible compartment
This issue logs feedback from @ffinger on the diphtheria model
model_diphtheria()
based on Finger et al. 2019, and potential next steps for package development - thanks @ffinger! If there's anything I've missed or that you'd like to add just put it in the comments.General
Demographic stratification of contacts
Vaccination
<vaccination>
objectsPopulation movements
population_change
functionality) may differ in their vaccine coverage profiles, but there may not be good estimates for this