Description Usage Arguments Value Author(s) References Examples
Identify the maximum clade credibility tree from a phybreak
-object containing posterior samples.
1 2 |
x |
An object of class |
samplesize |
The number of posterior samples that is used, taken from the tail. |
support |
Whether to return the support (= posterior probability) for each infector as a |
phylo.class |
Whether to return an object of class |
A data.frame
with per item (=node) its parent and support per clade, and optionally summary node times.
The first n nodes are the samples, the last n-1 nodes are the internal nodes.
Don Klinkenberg don@xs4all.nl
Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.
1 2 3 4 5 6 7 8 | #First build a phybreak-object containing samples.
simulation <- sim_phybreak(obsize = 5)
MCMCstate <- phybreak(dataset = simulation)
MCMCstate <- burnin_phybreak(MCMCstate, ncycles = 20)
MCMCstate <- sample_phybreak(MCMCstate, nsample = 50, thin = 2)
phylotree(MCMCstate)
plot(phylotree(MCMCstate, phylo.class = TRUE))
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