density.multiSimmap {phytools}

Computes a posterior distribution for the number and types of changes on the tree

Description

S3 methods to summarize the results of one or more stochastic maps.

Usage

## S3 method for class 'multiSimmap'
density(x, ...)
## S3 method for class 'changesMap'
plot(x, ...)

Arguments

x

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").

Details

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".

Value

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.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.