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
yule(phy)
Arguments
phy
an object of class "phylo".
Value
An object of class "yule" which is a list with the following
components:
lambdathe maximum likelihood estimate of the speciation
(birth) rate.
sethe standard-error of lambda.
loglikthe log-likelihood at its maximum.
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, 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.