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'.
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:
outbreaker: main function to run analyses
outbreaker_data: function to process input data
create_config: function to create default and customise
configuration settings
custom_priors: function to specify customised prior
functions
custom_likelihoods: function to specify customised likelihoods
functions
custom_moves: function to create default and customise movement
functions