chronoMPL {ape} | R Documentation |
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.
chronoMPL(phy, se = TRUE, test = TRUE)
phy |
an object of class |
se |
a logical specifying whether to compute the standard-errors
of the node ages ( |
test |
a logical specifying whether to test the molecular clock
at each node ( |
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 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 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.
an object of class "phylo"
with branch lengths as estimated by
the function. There are, by default, two attributes:
stderr |
the standard-errors of the node ages. |
Pval |
the P-value of the test of the molecular clock for each node. |
The present version requires a dichotomous tree.
Emmanuel Paradis
Britton, T., Oxelman, B., Vinnersten, A. and Bremer, K. (2002) Phylogenetic dating with confidence intervals using mean path lengths. Molecular Phylogenetics and Evolution, 24, 58–65.
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)