EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
Fig 2
Example ReMASTER epidemic simulation and resulting data used for the EpiFusion program (specifically, according to the “Baseline Scenario” described in the section “Scenario Testing”).
(a) True number of people infectedover time, from which (b) weekly reported case incidence counts and a (c) phylogenetic tree of simulated samples were derived based on given sampling rates. Plots of the other simulated datasets are provided in S2–S4 Figs.