describe.simmap: Summarizes a stochastic mapped tree or set of trees In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

 describe.simmap R Documentation

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 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.

phytools documentation built on Nov. 10, 2023, 1:08 a.m.