Estimate and understand individual-level variation in transmission. Implements density and cumulative compound Poisson discrete distribution functions ('Kremer et al.' (2021) tools:::Rd_expr_doi("10.1038/s41598-021-93578-x")), as well as functions to calculate infectious disease outbreak statistics given epidemiological parameters on individual-level transmission; including the probability of an outbreak becoming an epidemic/extinct ('Kucharski et al.' (2020) tools:::Rd_expr_doi("10.1016/S1473-3099(20)30144-4")), or the cluster size statistics, e.g. what proportion of cases cause X% of transmission ('Lloyd-Smith et al.' (2005) tools:::Rd_expr_doi("10.1038/nature04153")).
Maintainer: Joshua W. Lambert joshua.lambert@lshtm.ac.uk (ORCID) [copyright holder]
Authors:
Adam Kucharski adam.kucharski@lshtm.ac.uk (ORCID) [copyright holder]
Dillon C. Adam dcadam@hku.hk (ORCID)
Other contributors:
Sebastian Funk sebastian.funk@lshtm.ac.uk (ORCID) (.chain_sim uses code from bpmodels::chain_sim) [contributor, copyright holder]
Pratik Gupte pratik.gupte@lshtm.ac.uk (ORCID) [reviewer]
Hugo Gruson hugo@data.org (ORCID) [reviewer]
James M. Azam james.azam@lshtm.ac.uk (ORCID) [reviewer, contributor]
Chris Hartgerink chris@data.org (ORCID) [reviewer]