https://github.com/cran/ape
Tip revision: 7efe9fcea2f713c0510c1c5279cd575e66e5e0cd authored by Emmanuel Paradis on 19 June 2007, 00:00:00 UTC
version 1.10-1
version 1.10-1
Tip revision: 7efe9fc
yule.Rd
\name{yule}
\alias{yule}
\title{Fits Yule Model to a Phylogenetic Tree}
\usage{
yule(phy)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
}
\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, 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 \email{Emmanuel.Paradis@mpl.ird.fr}}
\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}