phylosignal {picante}R Documentation

Measure phylogenetic signal

Description

Calculates K statistic of phylogenetic signal as well as P-value based on variance of phylogenetically independent contrasts relative to tip shuffling randomization.

Usage

phylosignal(x, phy, reps = 999, ...)

Arguments

x Trait vector (same order as phy$tip.label)
phy phylo object
reps Number of randomizations
... Additional arguments passed to pic

Value

Data frame with columns:

K K statistic
PIC.variance Mean observed PIC variance
PIC.variance.P P-value of observed vs. random variance of PICs
PIC.variance.z Z-score of observed vs. random variance of PICs

Warning

Assumes that trait data are sorted in the same order as phylo$tip.label

Author(s)

Steven Kembel <skembel@uoregon.edu>

References

Blomberg, S. P., and T. Garland, Jr. 2002. Tempo and mode in evolution: phylogenetic inertia, adaptation and comparative methods. Journal of Evolutionary Biology 15:899-910.

Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717-745.

See Also

Kcalc

Examples

randtree <- rcoal(20)
randtraits <- evolve.brownian(randtree)
phylosignal(randtraits[randtree$tip.label],randtree)

[Package picante version 0.6-1 Index]