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Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
Figure 5
Effect of different information used in the 
parameter inference.
For setting 
and 
(
), we estimated the 
parameter from the birth-death trees (A) and the coalescent trees (B) using four methods. First, using the coalescent posterior estimates of the growth rate 
and the true 
, we obtained 
(red bars). Second, we used the birth-death posterior estimates of 
(trees analysed under uniform priors for 
, 
, and 
), and the true 
in the post-processing (blue bars), similar to the procedure used for the coalescent. Third, we also analyzed the trees by fixing the prior on the death rate 
to the true value, 
(green bars) or by fixing the prior on the sampling probability 
to the true value, 
(purple bars) during the MCMC analysis. Note that y-axis now displays 95% HPD of the 
parameter, and within each figure, the trees (simulations) are ordered (x-axis) by the median estimate of growth rate 
parameter estimated by the coalescent on the birth-death trees.
doi: https://doi.org/10.1371/journal.pcbi.1003913.g005