Fits the Yule Model to a Phylogenetic Tree
This function fits by maximum likelihood a Yule model, i.e. a birth-only model to the branching times computed from a phylogenetic tree.
yule(phy, use.root.edge = FALSE)
- an object of class
- a logical specifying whether to consider the root edge in the calculations.
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.
- 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.