# chronoMPL

From ape v4.1
0th

Percentile

##### Molecular Dating With Mean Path Lengths

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.

Keywords
models
##### Usage
chronoMPL(phy, se = TRUE, test = TRUE)
##### Arguments
phy

an object of class "phylo".

se

a logical specifying whether to compute the standard-errors of the node ages (TRUE by default).

test

a logical specifying whether to test the molecular clock at each node (TRUE by default).

##### 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 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.

##### Value

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.

##### Note

The present version requires a dichotomous tree.

##### References

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.

chronopl

• chronoMPL
##### Examples
# NOT RUN {
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")
# }

Documentation reproduced from package ape, version 4.1, License: GPL (>= 2)

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