This package provides a statistical platform for reconstructing transmission trees ('who infects whom') in densely sampled disease outbreaks. It reimplements, as a particular case, the model of 'outbreaker' (see references). 'outbreaker2' extends and replaces 'outbreaker'.

Details

The emphasis of 'outbreaker2' is on modularity, which enables customisation of priors, likelihoods and even movements of parameters and augmented data by the user. This the dedicated vignette on this topic vignette("outbreaker2_custom").

The main functions of the package are: