| phy.signal {pez} | R Documentation |
Calculate phylogenetic ‘signal’
Description
Calculate phylogenetic ‘signal’
Usage
phy.signal(data, method = c("lambda", "delta", "kappa", "blom.k"))
Arguments
data |
|
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")