describe.simmap {phytools}

Summarizes a stochastic mapped tree or set of trees

Description

Summarizes the result of one or more stochastic maps.

Usage

describe.simmap(tree, ...)
## S3 method for class 'simmap'
summary(object, ...)
## S3 method for class 'multiSimmap'
summary(object, ...)
## S3 method for class 'describe.simmap'
plot(x, ...)

Arguments

tree

a single tree or a set of trees as an object of class "simmap" or "multiSimmap", respectively.

object

object of class "simmap" or "multiSimmap".

x

for S3 plot method, an object of class "describe.simmap".

...

optional arguments which include: plot, a logical value indicating whether or not to plot the posterior probabilities at nodes (default is plot=FALSE); check.equal, a logical value indicating whether or not to check if all trees are equal using all.equal.phylo (default is check.equal=FALSE); and message, a logical indicating whether or not to print an informative message to the screen (default is message=TRUE).

Value

An object of class "describe.simmap" with the following elements:

count

a matrix containing the number and types of transitions for each tree, if tree is an object of class "multiSimmap".

times

a matrix containing the times spend in each state on each tree.

ace

the posterior probabilities of each node being in each state, if tree is an object of class "multiSimmap".

legend

a vector containing the plot legend, if plot=TRUE.

if class(tree)="simmap" then the function simply returns the results of countSimmap combined with the states at each node of the tree and a matrix containing the total and relative times spent in each state on the tree.

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.