Just to clarify, force.ultrametric is not a formal rate-smoothing method
or anything like that. It is intended only for use to resolve numerical
precision issues such as the one raised in this thread.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profesor A
I'll just add that it is always a really good idea to view the trees you
(think you) are using, not just rely on the variance-covariance matrices
derived from them and used in PGLS analyses, etc. Several times when I was
compiling trees and data from the literature authors sent me tree files
(e.g.
I haven't been closing following this thread, so I'm not sure that this
is relevant - but phytools has a function called 'force.ultrametric' (I
believe) that does precisely what its name suggests it might.
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
& Profe
Hmm. I hope that isn't the case - branching.times() is used pretty
widely in ape-dependent packages for getting node ages from dated
ultrametric trees, and if such minimally non-ultrametric trees can
cause branching.times throw negative node ages, then I'm really
concerned what impact that might ha
