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>
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>>>>     <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo>
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>>>>     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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