gammaStat {ape}

Gamma-Statistic of Pybus and Harvey

Description

This function computes the gamma-statistic which summarizes the information contained in the inter-node intervals of a phylogeny. It is assumed that the tree is ultrametric. Note that the function does not check that the tree is effectively ultrametric, so if it is not, the returned result may not be meaningful.

Usage

gammaStat(phy)

Arguments

phy

an object of class "phylo".

Details

The gamma-statistic is a summary of the information contained in the inter-node intervals of a phylogeny; it follows, under the assumption that the clade diversified with constant rates, a normal distribution with mean zero and standard-deviation unity (Pybus and Harvey 2000). Thus, the null hypothesis that the clade diversified with constant rates may be tested with 2*(1 - pnorm(abs(gammaStat(phy)))) for a two-tailed test, or 1 - pnorm(abs(gammaStat(phy))) for a one-tailed test, both returning the corresponding P-value.

Value

a numeric vector of length one.

Author(s)

Emmanuel Paradis

References

Pybus, O. G. and Harvey, P. H. (2000) Testing macro-evolutionary models using incomplete molecular phylogenies. Proceedings of the Royal Society of London. Series B. Biological Sciences, 267, 2267–2272.

See Also

branching.times, ltt.plot, skyline