3 \title{Extended Version of the Birth-Death Models to Estimate Speciation
9 \item{phy}{an object of class \code{"phylo"}.}
10 \item{S}{a numeric vector giving the number of species for each tip.}
13 This function fits by maximum likelihood a birth-death model to the
14 combined phylogenetic and taxonomic data of a given clade. The
15 phylogenetic data are given by a tree, and the taxonomic data by the
16 number of species for the its tips.
19 A re-parametrization of the birth-death model studied by Kendall
20 (1948) so that the likelihood has to be maximized over \emph{d/b} and
21 \emph{b - d}, where \emph{b} is the birth rate, and \emph{d} the death
24 The standard-errors of the estimated parameters are computed using a
25 normal approximation of the maximum likelihood estimates.
27 If the argument \code{S} has names, then they are matched to the tip
28 labels of \code{phy}. The user must be careful here since the function
29 requires that both series of names perfectly match, so this operation
30 may fail if there is a typing or syntax error. If both series of names
31 do not match, the values \code{S} are taken to be in the same order
32 than the tip labels of \code{phy}, and a warning message is issued.
34 Note that the function does not check that the tree is effectively
35 ultrametric, so if it is not, the returned result may not be meaningful.
38 Paradis, E. (2003) Analysis of diversification: combining phylogenetic
39 and taxonomic data. \emph{Proceedings of the Royal Society of
40 London. Series B. Biological Sciences}, \bold{270}, 2499--2505.
42 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
44 \code{\link{birthdeath}}, \code{\link{branching.times}},
45 \code{\link{diversi.gof}}, \code{\link{diversi.time}},
46 \code{\link{ltt.plot}}, \code{\link{yule}}, \code{\link{yule.cov}}
49 ### An example from Paradis (2003) using the avian orders:
51 ### Number of species in each order from Sibley and Monroe (1990):
52 S <- c(10, 47, 69, 214, 161, 17, 355, 51, 56, 10, 39, 152,
53 6, 143, 358, 103, 319, 23, 291, 313, 196, 1027, 5712)
54 bd.ext(bird.orders, S)