picante: phylosignal – R documentation

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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

Author(s)

Steven Kembel <steve.kembel@gmail.com>

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.

Examples

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

picante

Integrating Phylogenies and Ecology

v1.8.2

GPL-2

Authors

Steven W. Kembel <steve.kembel@gmail.com>, David D. Ackerly <dackerly@berkeley.edu>, Simon P. Blomberg <s.blomberg1@uq.edu.au>, Will K. Cornwell <cornwell@zoology.ubc.ca>, Peter D. Cowan <pdc@berkeley.edu>, Matthew R. Helmus <mrhelmus@wisc.edu>, Helene Morlon <morlon.helene@gmail.com>, Campbell O. Webb <cwebb@oeb.harvard.edu>

Initial release

2020-06-08