consTTree

record

Proportion of the MCMC output to be discarded as burnin

burnin

Minimum probability for inclusion of a partition in the consensus

minimum

debug

Build a consensus transmission tree from a MCMC output

Inference of transmission tree from a dated phylogeny.
Includes methods to simulate and analyse outbreaks.
The methodology is described in
Didelot et al. (2014) <doi:10.1093/molbev/msu121>,
Didelot et al. (2017) <doi:10.1093/molbev/msw275>.

consTTree: Build a consensus transmission tree from a MCMC output

Description

Usage

Arguments

Value