\title{Extended Version of the Birth-Death Models to Estimate Speciation
and Extinction Rates}
\usage{
-bd.ext(phy, S)
+bd.ext(phy, S, conditional = TRUE)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{S}{a numeric vector giving the number of species for each tip.}
+ \item{conditional}{whether probabilities should be conditioned on no
+ extinction (mainly to compare results with previous analyses; see
+ details).}
}
\description{
This function fits by maximum likelihood a birth-death model to the
than the tip labels of \code{phy}, and a warning message is issued.
Note that the function does not check that the tree is effectively
- ultrametric, so if it is not, the returned result may not be meaningful.
+ ultrametric, so if it is not, the returned result may not be
+ meaningful.
+
+ If \code{conditional = TRUE}, the probabilities of the taxonomic data
+ are calculated conditioned on no extinction (Rabosky et al. 2007). In
+ previous versions of the present function (until ape 2.6-1),
+ unconditional probabilities were used resulting in underestimated
+ extinction rate. Though it does not make much sense to use
+ \code{conditional = FALSE}, this option is provided to compare results
+ from previous analyses: if the species richnesses are relatively low,
+ both versions will give similar results (see examples).
}
\references{
Paradis, E. (2003) Analysis of diversification: combining phylogenetic
and taxonomic data. \emph{Proceedings of the Royal Society of
London. Series B. Biological Sciences}, \bold{270}, 2499--2505.
+
+ Rabosky, D. L., Donnellan, S. C., Talaba, A. L. and Lovette,
+ I. J. (2007) Exceptional among-lineage variation in diversification
+ rates during the radiation of Australia's most diverse vertebrate
+ clade. \emph{Proceedings of the Royal Society of London. Series
+ B. Biological Sciences}, \bold{274}, 2915--2923.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{birthdeath}}, \code{\link{branching.times}},
\code{\link{diversi.gof}}, \code{\link{diversi.time}},
- \code{\link{ltt.plot}}, \code{\link{yule}}, \code{\link{yule.cov}}
+ \code{\link{ltt.plot}}, \code{\link{yule}}, \code{\link{yule.cov}},
+ \code{\link{bd.time}}
}
\examples{
### An example from Paradis (2003) using the avian orders:
S <- c(10, 47, 69, 214, 161, 17, 355, 51, 56, 10, 39, 152,
6, 143, 358, 103, 319, 23, 291, 313, 196, 1027, 5712)
bd.ext(bird.orders, S)
+bd.ext(bird.orders, S, FALSE) # same than older versions
}
\keyword{models}