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\name{compute.brtime}
\alias{compute.brtime}
\title{Compute and Set Branching Times}
\description{
This function computes the branch lengths of a tree giving its
branching times (aka node ages or heights).
}
\usage{
compute.brtime(phy, method = "coalescent", force.positive = NULL)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{method}{either \code{"coalescent"} (the default), or a numeric
vector giving the branching times.}
\item{force.positive}{a logical value (see details).}
}
\details{
By default, a set of random branching times is generated from a simple
coalescent, and the option \code{force.positive} is set to \code{TRUE}
so that no branch length is negative.
If a numeric vector is passed to \code{method}, it is taken as the
branching times of the nodes with respect to their numbers (i.e., the
first element of \code{method} is the branching time of the node
numbered \eqn{n + 1} [= the root], the second element of the node
numbered \eqn{n + 2}, and so on), so \code{force.positive} is set to
\code{FALSE}. This may result in negative branch lengths. To avoid
this, one should use \code{force.positive = TRUE} in which case the
branching times are eventually reordered.
}
\value{
An object of class \code{"phylo"} with branch lengths and ultrametric.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{compute.brlen}}, \code{\link{branching.times}}
}
\examples{
tr <- rtree(10)
layout(matrix(1:4, 2))
plot(compute.brtime(tr)); axisPhylo()
plot(compute.brtime(tr, force.positive = FALSE)); axisPhylo()
plot(compute.brtime(tr, 1:9)); axisPhylo() # a bit nonsense
plot(compute.brtime(tr, 1:9, TRUE)); axisPhylo()
layout(1)
}
\keyword{manip}
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