Table 1.
Phylodynamic model | Parameter | Value | Evolutionary model | Clock model |
---|---|---|---|---|
Birth–death skyline model with serial sampling (BD) | Effective reproductive number (Re) | Estimated; 3, 4, 6 intervals (3 × Re, 4 × Re, 6 × Re) with LN prior with various parameterizations | HKY+Γ | Relaxed clock |
Become uninfectious rate (δ) |
|
Strict clock | ||
Sampling probability (P) | Estimated; with prior Beta(1, 700) | |||
Coalescent Bayesian skyline plot (Coal) | Effective population size (Ne) |
|
HKY+Γ | Relaxed clock Strict clock |
The abbreviations used in Figs 3 and 4 and Supplementary Figs S3 and S4 refer to this scheme. For example, BD: 3×Re∼LN(0, 1), refers to the birth–death skyline model with serial sampling which allows for three intervals for Re, each with LN(0, 1) distributed prior, and the become uninfectious rate δ = 18.25.