# chronoMPL

##### 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.

##### See Also

##### 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")
```

*Documentation reproduced from package ape, version 2.6-3, License: GPL (>= 2)*