BEAST 2 version
The phylodynamics package contains classes for inferring epidemic parameters (such as the basic reproduction number R0) from genetic sequence data using the Bayesian software package BEAST 2. It can be installed through the package manager
Example XML files for birth-death-sampling SIR (BDSIR) and coalescent SIR analyses using both simulated trees and real data can be found on GitHub: https://github.com/denisekuehnert/phylodynamics/tree/master/examples. This includes analyses for which the data is either serially-sampled or contemporaneous.