This function summarizes the result 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
In 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-percent high probability density interval for the number of changes of each type on the tree. Otherwise, the central 95-percent of the posterior sample is returned as an estimate of the 95-percent 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. Finally method="changes" has not yet been implemented.
plot.changesMap plots the posterior density returned by density.multiSimmap for method= "changes".
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.