picante (version 0.7-1)

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, ...)

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

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)