picante (version 1.8)

phylosignal: 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, 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

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

# NOT RUN {
randtree <- rcoal(20)
randtraits <- rTraitCont(randtree)
phylosignal(randtraits[randtree$tip.label],randtree)
# }