Description Usage Arguments Author(s) References Examples
View source: R/plot-phybreak.R
Plots a phybreak
-object twice: (1) as transmission tree and (2) as phylogenetic tree, using the default graphical parameters
of plotTrans
and plotPhylo
. The default
is to plot the current state, but any posterior sample can be chosen, as well as various consensus trees. Consensus tree "edmonds"
plots only a transmission tree, consensus tree "mcc" only a phylogenetic tree.
1 2 3 |
x |
An object of class |
plot.which |
Either |
samplenr |
If |
... |
Some methods for this generic require additional arguments. None are used in this method. |
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 | #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")
|
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