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 Asociado, Programa de Biología
Universidad del Rosario
web: http://faculty.umb.edu/liam.revell/

On 5/3/2018 4:21 PM, Theodore Garland wrote:
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., Nexus) that did not match what they showed in a paper or described in the methods.  Sometimes this was because the default display in Mesquite is NOT "branches proportional to lengths," but I am sure potentially misleading displays occur in some other programs as well.

If one does force a tree to become ultrametric, then make sure you provide that tree and the original in the Online Supplemental Material or whatever, and clearly say what you did.

Cheers,
Ted



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On Thu, May 3, 2018 at 1:09 PM, Liam J. Revell <liam.rev...@umb.edu <mailto:liam.rev...@umb.edu>> wrote:

    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
    & Profesor Asociado, Programa de Biología
    Universidad del Rosario
    web: http://faculty.umb.edu/liam.revell/
    <http://faculty.umb.edu/liam.revell/>

    On 5/3/2018 3:34 PM, David Bapst wrote:

        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 have elsewhere in the R-phylo
        universe.
        -Dave

        On Wed, May 2, 2018 at 2:30 PM, Brian O'Meara <bome...@utk.edu
        <mailto:bome...@utk.edu>> wrote:

            On Wed, May 2, 2018 at 2:53 PM, David Bapst
            <dwba...@tamu.edu <mailto:dwba...@tamu.edu>> wrote:


                Given that your tree appears to be non-ultrametric
                enough to cause
                branching.times to throw some nonsensical node ages, if
                it is supposed
                to be ultrametric. I recommend checking it carefully to
                figure out why
                the tips seem to not quite be at the same distance from
                the root.


               Sometimes this happens with tree import from a file -- it
            could be a newick
            tree with branch lengths precise to the hundredths but a lot
            of the R
            ultrametric tests by default use higher precision (1e-08, iirc).

            Best,
            Brian





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