phytools (version 0.2-40)

describe.simmap: 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

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.