3 \title{Extended Version of the Birth-Death Models to Estimate Speciation
6 bd.ext(phy, S, conditional = TRUE)
9 \item{phy}{an object of class \code{"phylo"}.}
10 \item{S}{a numeric vector giving the number of species for each tip.}
11 \item{conditional}{whether probabilities should be conditioned on no
12 extinction (mainly to compare results with previous analyses; see
16 This function fits by maximum likelihood a birth-death model to the
17 combined phylogenetic and taxonomic data of a given clade. The
18 phylogenetic data are given by a tree, and the taxonomic data by the
19 number of species for the its tips.
22 A re-parametrization of the birth-death model studied by Kendall
23 (1948) so that the likelihood has to be maximized over \emph{d/b} and
24 \emph{b - d}, where \emph{b} is the birth rate, and \emph{d} the death
27 The standard-errors of the estimated parameters are computed using a
28 normal approximation of the maximum likelihood estimates.
30 If the argument \code{S} has names, then they are matched to the tip
31 labels of \code{phy}. The user must be careful here since the function
32 requires that both series of names perfectly match, so this operation
33 may fail if there is a typing or syntax error. If both series of names
34 do not match, the values \code{S} are taken to be in the same order
35 than the tip labels of \code{phy}, and a warning message is issued.
37 Note that the function does not check that the tree is effectively
38 ultrametric, so if it is not, the returned result may not be
41 If \code{conditional = TRUE}, the probabilities of the taxonomic data
42 are calculated conditioned on no extinction (Rabosky et al. 2007). In
43 previous versions of the present function (until ape 2.6-1),
44 unconditional probabilities were used resulting in underestimated
45 extinction rate. Though it does not make much sense to use
46 \code{conditional = FALSE}, this option is provided to compare results
47 from previous analyses: if the species richnesses are relatively low,
48 both versions will give similar results (see examples).
51 Paradis, E. (2003) Analysis of diversification: combining phylogenetic
52 and taxonomic data. \emph{Proceedings of the Royal Society of
53 London. Series B. Biological Sciences}, \bold{270}, 2499--2505.
55 Rabosky, D. L., Donnellan, S. C., Talaba, A. L. and Lovette,
56 I. J. (2007) Exceptional among-lineage variation in diversification
57 rates during the radiation of Australia's most diverse vertebrate
58 clade. \emph{Proceedings of the Royal Society of London. Series
59 B. Biological Sciences}, \bold{274}, 2915--2923.
61 \author{Emmanuel Paradis}
63 \code{\link{birthdeath}}, \code{\link{branching.times}},
64 \code{\link{diversi.gof}}, \code{\link{diversi.time}},
65 \code{\link{ltt.plot}}, \code{\link{yule}}, \code{\link{yule.cov}},
69 ### An example from Paradis (2003) using the avian orders:
71 ### Number of species in each order from Sibley and Monroe (1990):
72 S <- c(10, 47, 69, 214, 161, 17, 355, 51, 56, 10, 39, 152,
73 6, 143, 358, 103, 319, 23, 291, 313, 196, 1027, 5712)
74 bd.ext(bird.orders, S)
75 bd.ext(bird.orders, S, FALSE) # same than older versions