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>
>> >
>> >
>>
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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

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