phylosignal: Measure phylogenetic signal

In picante: Integrating Phylogenies and Ecology

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, checkdata=TRUE, ...)

Arguments

x	Trait vector (same order as phy\$tip.label)
phy	phylo object
reps	Number of randomizations
checkdata	Check for match between trait and phylogeny taxa labels using match.phylo.data? (default=TRUE)
...	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

Author(s)

Steven Kembel <[e-mail]>

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 <- rTraitCont(randtree)
phylosignal(randtraits[randtree$tip.label],randtree)

picante documentation built on July 1, 2020, 10:57 p.m.