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\name{force.ultrametric}
\alias{force.ultrametric}
\title{Forces a phylogenetic tree to be ultrametric}
\usage{
force.ultrametric(tree, method=c("nnls","extend"))
}
\arguments{
\item{tree}{an object of class \code{"phylo"}.}
\item{method}{the method to use to force the tree to be ultrametric. Options are \code{"nnls"} (which uses the phangorn function \code{\link{nnls.tree}} internally), or \code{"extend"}.}
}
\description{
This function forces an object of class \code{"phylo"} to be ultrametric. This is achieved either by using \code{\link{nnls.tree}} from the phangorn package to compute the set of edge lengths that result in a minimized sum-of-squares distance between the patristic distance of the output and input trees (\code{method="nnls"}); or by simply extending all the external edges of the tree to match the external edge with the greatest total height (\code{method="extend"}). Note that neither of these should be treated as formal statistical methods for inferring an ultrametric tree. Rather, this method can be deployed when a genuinely ultrametric tree read from file fails \code{\link{is.ultrametric}} for reasons of numerical precision.
}
\value{
An ultrametric tree in an object of class \code{"phylo"}.
}
\seealso{
\code{\link{is.ultrametric}}, \code{\link{nnls.tree}}
}
\references{
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). \emph{Methods Ecol. Evol.}, \bold{3}, 217-223.
}
\author{Liam Revell \email{liam.revell@umb.edu}}
\keyword{statistics}
\keyword{utilities}
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