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\name{chronoMPL}
\alias{chronoMPL}
\title{Molecular Dating With Mean Path Lengths}
\usage{
chronoMPL(phy, se = TRUE, test = TRUE)
}
\arguments{
\item{phy}{an object of class \code{"phylo"}.}
\item{se}{a logical specifying whether to compute the standard-errors
of the node ages (\code{TRUE} by default).}
\item{test}{a logical specifying whether to test the molecular clock
at each node (\code{TRUE} by default).}
}
\description{
This function estimates the node ages of a tree using the mean path
lengths method of Britton et al. (2002). The branch lengths of the
input tree are interpreted as (mean) numbers of substitutions.
}
\details{
The mean path lengths (MPL) method estimates the age of a node with
the mean of the distances from this node to all tips descending from
it. Under the assumption of a molecular clock, standard-errors of the
estimates node ages can be computed (Britton et al. 2002).
The tests performed if \code{test = TRUE} is a comparison of the MPL
of the two subtrees originating from a node; the null hypothesis is
that the rate of substitution was the same in both subtrees (Britton
et al. 2002). The test statistic follows, under the null hypothesis, a
standard normal distribution. The returned \emph{P}-value is the
probability of observing a greater absolute value (i.e., a two-sided
test). No correction for multiple testing is applied: this is left to
the user.
Absolute dating can be done by multiplying the edge lengths found by
calibrating one node age.
}
\note{
The present version requires a dichotomous tree.
}
\value{
an object of class \code{"phylo"} with branch lengths as estimated by
the function. There are, by default, two attributes:
\item{stderr}{the standard-errors of the node ages.}
\item{Pval}{the \emph{P}-value of the test of the molecular clock for
each node.}
}
\references{
Britton, T., Oxelman, B., Vinnersten, A. and Bremer, K. (2002)
Phylogenetic dating with confidence intervals using mean path
lengths. \emph{Molecular Phylogenetics and Evolution}, \bold{24},
58--65.
}
\author{Emmanuel Paradis}
\seealso{
\code{\link{chronopl}}
}
\examples{
tr <- rtree(10)
tr$edge.length <- 5*tr$edge.length
chr <- chronoMPL(tr)
layout(matrix(1:4, 2, 2, byrow = TRUE))
plot(tr)
title("The original tree")
plot(chr)
axisPhylo()
title("The dated MPL tree")
plot(chr)
nodelabels(round(attr(chr, "stderr"), 3))
title("The standard-errors")
plot(tr)
nodelabels(round(attr(chr, "Pval"), 3))
title("The tests")
layout(1)
}
\keyword{models}
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