pez (version 1.2-4)

phy.signal: Calculate phylogenetic `signal'

Description

Calculate phylogenetic `signal'

Usage

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

Value

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

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.

Author

Will Pearse, Jeannine Cavender-Bares

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).

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")