Figure legends
Figure 1: Effective reproductive number (R e) as a
function of time (years). Each considered epoch was approximately five
years. Shaded area indicates the 95% highest probability density. First
row are parameter estimates under the Bayesian Sampled Ancestor
Birth-Death Skyline model, second raw under the Bayesian Birth-Death
Skyline model. On the left-hand side, with common δ and sampling
proportion parameter across all epochs, while on the right-hand side
with a variable sampling proportion parameter.
Figure 2: Violin plots of sampling proportion parameter (s) estimates
for different time intervals (x-axis) under the Bayesian Sampled
Ancestor Birth-Death Skyline (left) and the Bayesian Birth-Death Skyline
(right) models. Dots indicate the medians.
Figure 3: Bayesian Skyline Plot of virus demographic changes (y-axis in
log scale) over time. Shaded area indicates the 95% highest probability
density.