A computationally tractable birth-death model that combines phylogenetic and epidemiological data
Fig 4
The tips of the transmission tree are subsampled to reflect the observation process. (A) The full transmission tree of the simulated epidemic where green tips have been observed either as sequenced or unsequenced samples. (B) Bar chart showing the number of unobserved infections, the number of observed and potentially sequenced infections and the prevalence at the end of the simulation. (C) Time series of the number of cases after aggregation: the sequenced samples are aggregated into daily counts and the unsequenced occurrences are aggregated into weekly counts. Fig 5 shows the marginal posterior distributions using either the raw or aggregated data above.