Unless it does something internally already, you might need to do something
like: options(digits=10) before running the node.depth.edgelength(tree) to
identify your problem.

Yes, I wasn't referring to branching.times. I was talking about various
methods, e.g., BAMM, that don't perform well (or at all) with zero-length
branches.

Cheers,
Eliot

On Mon, May 7, 2018 at 5:27 PM, David Bapst <dwba...@tamu.edu> wrote:

> Interesting, Rafael. Perhaps it is just barely within tolerance for
> force.ultrametric, but not within the zone to avoid issues with
> branching.times?
>
> What did
>
> node.depth.edgelength(tree)
>
> return? That should give us an idea how far each tip is from the root.
>
> As a note, Eliot, I don't think I've seen branching.times have
> problems with tree with zero-length branches, although that is pretty
> unusual with the ultrametric trees valid with branching.times.
>
> Cheers,
> -Dave
>
> On Fri, May 4, 2018 at 8:32 AM, Rafael S Marcondes
> <raf.marcon...@gmail.com> wrote:
> > Hi Elliot et al,
> >
> > Thanks for all the helpful answers, and sorry for my delay in getting
> back.
> > min(tree$edge.length) returns a nonzero positive number, but running
> > force.ultrametric on the tr did not cause that warning message to go
> away...
> >
> > --
> > Rafael Sobral Marcondes
> > PhD Candidate (Systematics, Ecology and Evolution/Ornithology)
> >
> > Museum of Natural Science
> > Louisiana State University
> > 119 Foster Hall
> > Baton Rouge, LA 70803, USA
> >
> > Twitter: @brown_birds
> >
> >
> >
> > On Fri, May 4, 2018 at 8:22 AM Eliot Miller <eliot.is...@gmail.com>
> wrote:
> >>
> >> I suggest calling min(tree$edge.length) on any tree you plan to use for
> >> comparative methods, including the one you're having trouble with
> Rafael. If
> >> you get a negative value, then something is really funny and you need to
> >> solve it. If you get a zero then various comparative methods will throw
> >> errors, but it's not the end of the world--there are workarounds. If
> neither
> >> of these things is true, and the tree is still returning FALSE to
> >> is.ultrametric, then assuming the tree is supposed to be ultrametric,
> it's
> >> almost certainly a tolerance thing (which you can check directly by
> tweaking
> >> the tol method in the is.ultrametric function). In that case, I've had
> good
> >> experiences using the phangorn/phytools approach to force the tree
> >> ultrametric.
> >>
> >> Eliot
> >>
> >> On Thu, May 3, 2018 at 5:08 PM, Liam J. Revell <liam.rev...@umb.edu>
> >> wrote:
> >>>
> >>> 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
> >>>>
> >>>>
> >>>>
> >>>> Theodore Garland, Jr., Distinguished Professor
> >>>>
> >>>> Department of Evolution, Ecology, and Organismal Biology (EEOB)
> >>>>
> >>>> University of California, Riverside
> >>>>
> >>>> Riverside, CA 92521
> >>>>
> >>>> Office Phone: (951) 827-3524 <tel:%28951%29%20827-3524>
> >>>>
> >>>> Facsimile: (951) 827-4286 <tel:%28951%29%20827-4286> (not
> confidential)
> >>>>
> >>>> Email: tgarl...@ucr.edu <mailto:tgarl...@ucr.edu>
> >>>>
> >>>> http://www.biology.ucr.edu/people/faculty/Garland.html
> >>>>
> >>>> http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ
> >>>>
> >>>>
> >>>> Director, UCR Institute for the Development of
> >>>> <http://idea.ucr.edu/>Educational Applications <http://idea.ucr.edu/>
> >>>>
> >>>>
> >>>> Editor in Chief, /Physiological and Biochemical Zoology
> >>>> <http://www.press.uchicago.edu/ucp/journals/journal/pbz.html>/
> >>>>
> >>>>
> >>>> Fail Lab: Episode One
> >>>>
> >>>> _https://www.youtube.com/watch?v=c0msBWyTzU0_
> >>>>
> >>>>
> >>>> 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
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>     _______________________________________________
> >>>>     R-sig-phylo mailing list - R-sig-phylo@r-project.org
> >>>>     <mailto:R-sig-phylo@r-project.org>
> >>>>     https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> >>>>     <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>
> >>>>     Searchable archive at
> >>>>     http://www.mail-archive.com/r-sig-phylo@r-project.org/
> >>>>     <http://www.mail-archive.com/r-sig-phylo@r-project.org/>
> >>>>
> >>>>
> >>
> >
>
>
>
> --
> David W. Bapst, PhD
> Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville
> Lecturer, Geology & Geophysics, Texas A & M University
> https://github.com/dwbapst/paleotree
> Google Calender: https://goo.gl/EpiM4J
>

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