https://github.com/cran/ape
Tip revision: c41bd2896eb9820dc00b9ba27eb8ae518464f0a8 authored by Emmanuel Paradis on 27 March 2007, 00:00:00 UTC
version 1.9-4
version 1.9-4
Tip revision: c41bd28
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}