gammaStat {ape} | R Documentation |
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.
gammaStat(phy)
phy |
an object of class |
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.
a numeric vector of length one.
Emmanuel Paradis
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.
branching.times
, ltt.plot
, skyline