3 \title{Molecular Dating With Mean Path Lengths}
5 chronoMPL(phy, se = TRUE, test = TRUE)
8 \item{phy}{an object of class \code{"phylo"}.}
9 \item{se}{a logical specifying whether to compute the standard-errors
10 of the node ages (\code{TRUE} by default).}
11 \item{test}{a logical specifying whether to test the molecular clock
12 at each node (\code{TRUE} by default).}
15 This function estimates the node ages of a tree using the mean path
16 lengths method of Britton et al. (2002). The branch lengths of the
17 input tree are interpreted as (mean) numbers of substitutions.
20 The mean path lengths (MPL) method estimates the age of a node with
21 the mean of the distances from this node to all tips descending from
22 it. Under the assumption of a molecular clock, standard-errors of the
23 estimates node ages can be computed (Britton et al. 2002).
25 The tests performed if \code{test = TRUE} is a comparison of the MPL
26 of the two subtrees originating from a node; the null hypothesis is
27 that the rate of substitution was the same in both subtrees (Britton
28 et al. 2002). The test statistic follows, under the null hypothesis, a
29 standard normal distribution. The returned \emph{P}-value is the
30 probability of observing a greater absolute value (i.e., a two-sided
31 test). No correction for multiple testing is applied: this is left to
34 Absolute dating can be done by multiplying the edge lengths found by
35 calibrating one node age.
38 The present version requires a dichotomous tree.
41 an object of class \code{"phylo"} with branch lengths as estimated by
42 the function. There are, by default, two attributes:
44 \item{stderr}{the standard-errors of the node ages.}
45 \item{Pval}{the \emph{P}-value of the test of the molecular clock for
49 Britton, T., Oxelman, B., Vinnersten, A. and Bremer, K. (2002)
50 Phylogenetic dating with confidence intervals using mean path
51 lengths. \emph{Molecular Phylogenetics and Evolution}, \bold{24},
54 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
56 \code{\link{chronogram}}, \code{\link{ratogram}},
57 \code{\link{NPRS.criterion}}, \code{\link{chronopl}}
61 tr$edge.length <- 5*tr$edge.length
63 layout(matrix(1:4, 2, 2, byrow = TRUE))
65 title("The original tree")
68 title("The dated MPL tree")
70 nodelabels(round(attr(chr, "stderr"), 3))
71 title("The standard-errors")
73 nodelabels(round(attr(chr, "Pval"), 3))