Compute incidence and total number of, e.g., infected

[mknaranja]

In order to reliably activate dynamics NPIs or to compute the total number of infected individuals, we should follow more than just the different "Infected" compartments. With different durations for stays in compartments of, e.g., "Infected" and "Infected Vaccinated" this becomes even more important.

[xsaschako]

Needs more information for abm, what exactly do you mean? Out of date or coverred by other improvments? Then please close or remove from abm.