describe.simmap {phytools}R Documentation

Summarizes a stochastic mapped tree or set of trees

Description

This function summarizes the result of one or more stochastic maps.

Usage

describe.simmap(tree, ...)

Arguments

tree

a single tree or a set of trees with a mapped discrete character (e.g, see make.simmap or read.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

A list with the following elements is returned (invisibly if message=TRUE):

count

a matrix containing the number and types of transitions for each tree, if class(tree)="multiPhylo".

times

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

ace

the posterior probabilities of each node being in each state, if class(tree)="multiPhylo".

legend

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

if class(tree)="phylo" 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 liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

[Package phytools version 0.4-60 Index]