outbreaker_package {outbreaker2}

outbreaker2: a platform for disease outbreak reconstruction

Description

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:

• 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

Author(s)

Thibaut Jombart [e-mail]