Calculate phylogenetic ‘signal’
what kind of signal to calculate, one of Pagel's lambda (default), delta, and kappa, or Blomberg's K.
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
Named numeric vector, where each element is a trait or community.
Will Pearse, Jeannine Cavender-Bares
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.
fitContinuous fitDiscrete pgls phylosignal
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