Hi Rafael,

I found the source of the error, I think, and filed an issue at github
on the OUwie repo. There are issues with how the code in OUwie handles
non-ultrametric trees if a root.age isn't given by the user, causing
problems for the paleotree function dateNodes, and your tree is
apparently non-ultrametric enough to run afoul of these issues.

https://github.com/thej022214/OUwie/issues/3

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.

Cheers,
-Dave.

On Wed, May 2, 2018 at 1:35 PM, David Bapst <dwba...@tamu.edu> wrote:
> Rafael,
>
> That error message is from paleotree's dateNodes function, which is
> called as part of OUwie's approach to getting node dates. I think I
> see what Elliot is trying to get at, but this might be quicker:
>
> node.depth.edgelength(tree)
>
> That should tell us how far each node, including the tips, are from the root.
>
> Cheers,
> -Dave
>
> On Wed, May 2, 2018 at 1:26 PM, Eliot Miller <eliot.is...@gmail.com> wrote:
>> What does: min(tree$edge.length) say?
>>
>> Eliot
>>
>> On Wed, May 2, 2018 at 2:22 PM, Rafael S Marcondes <raf.marcon...@gmail.com>
>> wrote:
>>
>>> Here's a little more info that may be relevant: the tree is not supposed to
>>> have negative dates. Although when I do is.ultrametric(tr) I get FALSE, I
>>> have always been just ascribing that to lack of precision, in part because
>>> it has never been a problem with OUwie().
>>>
>>>
>>> *--*
>>> *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 Wed, May 2, 2018 at 1:08 PM Rafael S Marcondes <raf.marcon...@gmail.com
>>> >
>>> wrote:
>>>
>>> > Hi all,
>>> >
>>> > I need some help with a warning message I've been getting when running
>>> > parametric bootstrapping in OUwie.
>>> >
>>> > >OUwie.boot(nboot=1, simmap.tree=F...)
>>> > Beginning parametric bootstrap -- performing 1 replicates
>>> > Warning: Some dates are negative? rootAge may be incorrectly defined or
>>> > you are using a time-scaling method that warps the tree, like aba or
>>> zbla.
>>> > Initializing...
>>> > Finished. Begin thorough search...
>>> > Finished. Summarizing results.
>>> >
>>> > Initially I didn't give it much thought, but my bootstrapping results are
>>> > quite unexpected, and I'm starting to think that may be related to that
>>> > warning.
>>> >
>>> > I don't get that warning when I run OUwie() with the same
>>> > tree/dataset/settings, and I've been able to trace it to the function
>>> > dateNodes in the package paleotree, but haven't been able to go any
>>> further
>>> > than that.
>>> >
>>> > Thanks in advance for any help!
>>> >
>>> >
>>> >
>>> > *--*
>>> > *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>
>>> >
>>> >
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>
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>>
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>
>
> --
> 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



-- 
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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