Computes a posterior distribution for the number and types of changes on the tree
This function summarizes the result of one or more stochastic maps.
## S3 method for class 'multiSimmap' density(x, ...) ## S3 method for class 'changesMap' plot(x, ...)
x |
object of class |
... |
optional arguments. For |
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".
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.
Liam Revell liam.revell@umb.edu
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
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