density.multiSimmap | R Documentation |
S3 methods to summarize the results 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 |
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"
.
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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
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