The hidden model is a two virus model with crossover and the possibility of vaccination against virus 1.

After: Zarnitsyna VI, Bulusheva I, Handel A, Longini IM, Halloran ME, Antia R (2018). Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaks. PLoS ONE 13(6): e0199674. https://doi.org/10.1371/journal.pone.0199674

Rt values for the multiple infected states were calculated as the ratio of the fluxes into the infected state divided by the flux out of the same state.

Rt_max is the maximum Rt, at a given time point,
across the set of infected states, ignoring the very
large value that low occupancy states have at the
beginning of the simulated season.

Score is the sum, over all rounds, of
0.8*RMSEHosp + 0.2*RMSERt

Score is the sum, over all rounds, of
0.8*RMSEHosp + 0.2*RMSERt