Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

doi:10.1371/journal.pcbi.1003913

Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models

Figure 2

Influence of branch length extension in various parts of the tree on the growth rate parameter estimation.

For setting and (), we modified all 100 birth-death trees (A) and all 100 coalescent trees (B) by branch extension. The unchanged tree is denoted as “orig” on x-axis. We added 48 units of time, roughly corresponding to the full length of the longest trees, to the branches. We extended the branches that were present in the tree at 10% of the tree (going from the root), at 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% (see x-axis from left to right). We then re-estimated the growth rate parameter for each such tree. Unlike in previous plot, here we display a summary in form of the median values of the start and the end of the 95% HPD intervals, and the median of the medians of the posterior estimates for all 100 trees per setting.

doi: https://doi.org/10.1371/journal.pcbi.1003913.g002