phy.signal: Calculate phylogenetic 'signal'

In pez: Phylogenetics for the Environmental Sciences

Calculate phylogenetic ‘signal’

Description

Calculate phylogenetic ‘signal’

Usage

phy.signal(data, method = c("lambda", "delta", "kappa", "blom.k"))

Arguments

data	comparative.comm object
method	what kind of signal to calculate, one of Pagel's lambda(default), delta, and kappa, or Blomberg's K.

Details

Phylogenetic ‘signal’ is one of those concepts that is said a lot in community ecology, but some do not full consider its meaning. Think carefully before rushing to report a value whether: (1) it makes sense to assess phylogenetic ‘signal’ in your datasets, and (2) what the phrase ‘phylogenetic signal’ actually means. This code makes use of caper::pgls to get estimates of fit; alternatives that offer more flexibility exist (see below).

Value

Named numeric vector, where each element is a trait or community.

Author(s)

Will Pearse, Jeannine Cavender-Bares

References

Blomberg S.P., Garland T. & Ives A.R. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57(4): 717–745.

R. P. Freckleton, P. H. Harvey, and M. Pagel. Phylogenetic analysis and comparative data: A test and review of evidence. American Naturalist, 160:712-726, 2002.

Mark Pagel (1999) Inferring the historical patterns of biological evolution. Nature 6756(401): 877–884.

See Also

fitContinuous fitDiscrete pgls phylosignal

Examples

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits)
phy.signal(data, "lambda")

pez documentation built on Sept. 1, 2022, 1:09 a.m.