https://github.com/cran/ape
Tip revision: 10898aebdf6661a0b81ba21bf24969336b544a60 authored by Emmanuel Paradis on 21 December 2021, 08:20:05 UTC
version 5.6
version 5.6
Tip revision: 10898ae
yule.Rd
\name{yule}
\alias{yule}
\title{Fits the Yule Model to a Phylogenetic Tree}
\usage{
yule(phy, use.root.edge = FALSE)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{use.root.edge}{a logical specifying whether to consider the root
edge in the calculations.}
}
\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.
}
\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
\code{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:
\item{lambda}{the maximum likelihood estimate of the speciation
(birth) rate.}
\item{se}{the standard-error of lambda.}
\item{loglik}{the log-likelihood at its maximum.}
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{branching.times}}, \code{\link{diversi.gof}},
\code{\link{diversi.time}}, \code{\link{ltt.plot}},
\code{\link{birthdeath}}, \code{\link{bd.ext}}, \code{\link{yule.cov}}
}
\keyword{models}