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 <http://sites01.lsu.edu/wp/mns/>
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @brown_birds <https://twitter.com/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
>>>
>>>
>>>
>>>
>>>
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>>>
>>>
>

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