Fits the Yule Model to a Phylogenetic Tree

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Description

This function fits by maximum likelihood a Yule model, i.e., a birth-only model to the branching times computed from a phylogenetic tree.

Usage

1
yule(phy, use.root.edge = FALSE)

Arguments

phy

an object of class "phylo".

use.root.edge

a logical specifying whether to consider the root edge in the calculations.

Details

The tree must be fully dichotomous.

The maximum likelihood estimate of the speciation rate is obtained by the ratio of the number of speciation events on the cumulative number of species through time; these two quantities are obtained with the number of nodes in the tree, and the sum of the branch lengths, respectively.

If there is a ‘root.edge’ element in the phylogenetic tree, and use.root.edge = TRUE, then it is assumed that it has a biological meaning and is counted as a branch length, and the root is counted as a speciation event; otherwise the number of speciation events is the number of nodes - 1.

The standard-error of lambda is computed with the second derivative of the log-likelihood function.

Value

An object of class "yule" which is a list with the following components:

lambda

the maximum likelihood estimate of the speciation (birth) rate.

se

the standard-error of lambda.

loglik

the log-likelihood at its maximum.

Author(s)

Emmanuel Paradis

See Also

branching.times, diversi.gof, diversi.time, ltt.plot, birthdeath, bd.ext, yule.cov

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