chronoMPL | 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 |

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.

`chronopl`

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)

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