EpiInf is a BEAST 2 package that uses particle MCMC to perform phylodynamic inference under both linear and nonlinear birth-death models, with a particular emphasis on models relevant to epidemiology. In addition to inferring model parameters and transmission trees, EpiInf directly samples epidemic prevalence and incidence trajectories. The algorithm implemented by EpiInf is described in this preprint.
The documentation for EpiInf currently consists of:
Please complete the tutorial before attempting to analyze your own data.