phybreak (version 0.2.0)

plotPhylo: Plotting a phybreak object phylogenetic tree.

Description

Plots a phybreak-object as phylogenetic tree with coloured branches indicating hosts. The default is to plot the current state, but any posterior sample can be chosen, as well as various consensus trees.

Usage

plotPhylo(x, plot.which = c("sample", "mpc", "mtcc", "mcc"), samplenr = 0,
  ...)

Arguments

x

An object of class phybreak.

plot.which

Either "sample" to plot the current state or a selected posterior sample, "mpc" or "mtcc" to plot a consensus transmission tree (see transtree) or "mcc" to plot the maximum clade credibility tree (see phylotree).

samplenr

If plot.which = "sample", this indicates which posterior tree should be plotted: samplenr = 0 to plot the current state.

...

Additional options for plotSimmap.

References

Klinkenberg et al. (2017) Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks. PLoS Comput Biol, 13(5): e1005495.

Examples

# NOT RUN {
#First build a phybreak-object containing samples.
simulation <- sim.phybreak(obsize = 5)
MCMCstate <- phybreak(data = simulation$sequences, times = simulation$sample.times)
MCMCstate <- burnin.phybreak(MCMCstate, ncycles = 20)
MCMCstate <- sample.phybreak(MCMCstate, nsample = 50, thin = 2)

plot(MCMCstate, plot.which = "mpc")
# }