S3 methods to summarize the results of one or more stochastic maps.
# S3 method for multiSimmap
density(x, ...)
# S3 method for changesMap
plot(x, ...)For method="changes"
density.multiSimmap returns an object of class "changesMap".
For method="densityMap"
density.multiSimmap returns an object of class "densityMap".
plot.changesMap generates a plot.
object of class "multiSimmap" (see make.simmap), or, in the case plot.changesMap, an object of class "changesMap" produced via a call to density.multiSimmap.
optional arguments. For density.multiSimmap these consist of bw (bandwidth) & method ("changes", "densityMap", or "timings").
Liam Revell liam.revell@umb.edu
density.multiSimmap method="changes" (the default) results in a posterior distribution of the number & types of changes on the tree.
If the package coda has been installed, then the function HPD.interval is used to compute a 95% high probability density interval for the number of changes of each type on the tree. Otherwise, the central 95% of the posterior sample is returned as an estimate of the 95% HPD interval for each change type.
The method also computes the full posterior density for each change type using a bandwidth specified by the user.
method="densityMap" computes a standard "densityMap" object, and thus only permits binary characters.
plot.changesMap plots the posterior density returned by density.multiSimmap for method= "changes".
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.