3 \title{Fits Yule Model to a Phylogenetic Tree}
5 yule(phy, use.root.edge = FALSE)
8 \item{phy}{an object of class \code{"phylo"}.}
9 \item{use.root.edge}{a logical specifying whether to consider the root
10 edge in the calculations.}
13 This function fits by maximum likelihood a Yule model, i.e. a
14 birth-only model to the branching times computed from a phylogenetic
18 The tree must be fully dichotomous.
20 The maximum likelihood estimate of the speciation rate is obtained by
21 the ratio of the number of speciation events on the cumulative number
22 of species through time; these two quantities are obtained with the
23 number of nodes in the tree, and the sum of the branch lengths,
26 If there is a `root.edge' element in the phylogenetic tree, and
27 \code{use.root.edge = TRUE}, then it is assumed that it has a
28 biological meaning and is counted as a branch length, and the root is
29 counted as a speciation event; otherwise the number of speciation
30 events is the number of nodes - 1.
32 The standard-error of lambda is computed with the second derivative of
33 the log-likelihood function.
36 An object of class "yule" which is a list with the following
38 \item{lambda}{the maximum likelihood estimate of the speciation
40 \item{se}{the standard-error of lambda.}
41 \item{loglik}{the log-likelihood at its maximum.}
43 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
45 \code{\link{branching.times}}, \code{\link{diversi.gof}},
46 \code{\link{diversi.time}}, \code{\link{ltt.plot}},
47 \code{\link{birthdeath}}, \code{\link{bd.ext}}, \code{\link{yule.cov}}