Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Eliot Miller]

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  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
>  wrote:
> > Hi Elliot et al,
> >
> > Thanks for all the helpful answers, and sorry for my delay in getting
> back.
> > min(tree$edge.length) returns a nonzero positive number, but running
> > force.ultrametric on the tr did not cause that warning message to go
> away...
> >
> > --
> > Rafael Sobral Marcondes
> > PhD Candidate (Systematics, Ecology and Evolution/Ornithology)
> >
> > Museum of Natural Science
> > Louisiana State University
> > 119 Foster Hall
> > Baton Rouge, LA 70803, USA
> >
> > Twitter: @brown_birds
> >
> >
> >
> > On Fri, May 4, 2018 at 8:22 AM Eliot Miller 
> wrote:
> >>
> >> I suggest calling min(tree$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 
> >> 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 
> 
>  Facsimile: (951) 827-4286  (not
> confidential)
> 
>  Email: tgarl...@ucr.edu 
> 
>  http://www.biology.ucr.edu/people/faculty/Garland.html
> 
>  http://scholar.google.com/citations?hl=en=iSSbrhwJ
> 
> 
>  Director, UCR Institute for the Development of
>  Educational Applications 
> 
> 
>  Editor in Chief, /Physiological and Biochemical Zoology
>  /
> 
> 
>  Fail Lab: Episode One
> 
>  _https://www.youtube.com/watch?v=c0msBWyTzU0_
> 
> 
>  On Thu, May 3, 2018 at 1:09 PM, Liam J. Revell 

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[David Bapst]

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
 wrote:
> Hi Elliot et al,
>
> Thanks for all the helpful answers, and sorry for my delay in getting back.
> min(tree$edge.length) returns a nonzero positive number, but running
> force.ultrametric on the tr did not cause that warning message to go away...
>
> --
> Rafael Sobral Marcondes
> PhD Candidate (Systematics, Ecology and Evolution/Ornithology)
>
> Museum of Natural Science
> Louisiana State University
> 119 Foster Hall
> Baton Rouge, LA 70803, USA
>
> Twitter: @brown_birds
>
>
>
> On Fri, May 4, 2018 at 8:22 AM Eliot Miller  wrote:
>>
>> I suggest calling min(tree$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 
>> 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 

 Facsimile: (951) 827-4286  (not confidential)

 Email: tgarl...@ucr.edu 

 http://www.biology.ucr.edu/people/faculty/Garland.html

 http://scholar.google.com/citations?hl=en=iSSbrhwJ


 Director, UCR Institute for the Development of
 Educational Applications 


 Editor in Chief, /Physiological and Biochemical Zoology
 /


 Fail Lab: Episode One

 _https://www.youtube.com/watch?v=c0msBWyTzU0_


 On Thu, May 3, 2018 at 1:09 PM, Liam J. Revell > 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/
 

 On 5/3/2018 3:34 PM, David Bapst wrote:

 Hmm. I 

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Rafael S Marcondes]

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  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 
> 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 
>>>
>>> Facsimile: (951) 827-4286  (not confidential)
>>>
>>> Email: tgarl...@ucr.edu 
>>>
>>> http://www.biology.ucr.edu/people/faculty/Garland.html
>>>
>>> http://scholar.google.com/citations?hl=en=iSSbrhwJ
>>>
>>>
>>> Director, UCR Institute for the Development of 
>>> Educational
>>> Applications 
>>>
>>>
>>> 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 >> > 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/
>>> 
>>>
>>> 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 >> > wrote:
>>>
>>> On Wed, May 2, 2018 at 2:53 PM, David Bapst
>>> 

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Eliot Miller]

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  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 
>>
>> Facsimile: (951) 827-4286  (not confidential)
>>
>> Email: tgarl...@ucr.edu 
>>
>> http://www.biology.ucr.edu/people/faculty/Garland.html
>>
>> http://scholar.google.com/citations?hl=en=iSSbrhwJ
>>
>>
>> Director, UCR Institute for the Development of > >Educational Applications 
>>
>>
>> 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 > > 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/
>> 
>>
>> 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 > > wrote:
>>
>> On Wed, May 2, 2018 at 2:53 PM, David Bapst
>> > 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 

Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Liam J. Revell]

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 

Facsimile: (951) 827-4286  (not confidential)

Email: tgarl...@ucr.edu 

http://www.biology.ucr.edu/people/faculty/Garland.html

http://scholar.google.com/citations?hl=en=iSSbrhwJ


Director, UCR Institute for the Development of 
Educational Applications 



Editor in Chief, /Physiological and Biochemical Zoology 
/



Fail Lab: Episode One

_https://www.youtube.com/watch?v=c0msBWyTzU0_


On Thu, May 3, 2018 at 1:09 PM, Liam J. Revell > 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/


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 > wrote:

On Wed, May 2, 2018 at 2:53 PM, David Bapst
> 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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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Theodore Garland]

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

Facsimile:  (951) 827-4286 (not confidential)

Email:  tgarl...@ucr.edu

http://www.biology.ucr.edu/people/faculty/Garland.html

http://scholar.google.com/citations?hl=en=iSSbrhwJ


Director, UCR Institute for the Development of
Educational
Applications 


Editor in Chief, *Physiological and Biochemical Zoology
*


Fail Lab: Episode One

*https://www.youtube.com/watch?v=c0msBWyTzU0
*

On Thu, May 3, 2018 at 1:09 PM, Liam J. Revell  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/
>
> 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  wrote:
>>
>>> On Wed, May 2, 2018 at 2:53 PM, David Bapst  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
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at http://www.mail-archive.com/r-
> sig-ph...@r-project.org/
>

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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Liam J. Revell]

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/

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  wrote:

On Wed, May 2, 2018 at 2:53 PM, David Bapst  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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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[David Bapst]

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  wrote:
> On Wed, May 2, 2018 at 2:53 PM, David Bapst  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
>



-- 
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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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Brian O'Meara]

On Wed, May 2, 2018 at 2:53 PM, David Bapst  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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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[David Bapst]

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  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  wrote:
>> What does: min(tree$edge.length) say?
>>
>> Eliot
>>
>> On Wed, May 2, 2018 at 2:22 PM, Rafael S Marcondes 
>> 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 
>>> Louisiana State University
>>> 119 Foster Hall
>>> Baton Rouge, LA 70803, USA
>>>
>>> Twitter: @brown_birds 
>>>
>>>
>>>
>>> On Wed, May 2, 2018 at 1:08 PM Rafael S Marcondes >> >
>>> 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 
>>> > Louisiana State University
>>> > 119 Foster Hall
>>> > Baton Rouge, LA 70803, USA
>>> >
>>> > Twitter: @brown_birds 
>>> >
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ___
>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>>> Searchable archive at http://www.mail-archive.com/r-
>>> sig-ph...@r-project.org/
>>>
>>
>> [[alternative HTML version deleted]]
>>
>> ___
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>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at 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



-- 
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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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[David Bapst]

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  wrote:
> What does: min(tree$edge.length) say?
>
> Eliot
>
> On Wed, May 2, 2018 at 2:22 PM, Rafael S Marcondes 
> 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 
>> Louisiana State University
>> 119 Foster Hall
>> Baton Rouge, LA 70803, USA
>>
>> Twitter: @brown_birds 
>>
>>
>>
>> On Wed, May 2, 2018 at 1:08 PM Rafael S Marcondes > >
>> 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 
>> > Louisiana State University
>> > 119 Foster Hall
>> > Baton Rouge, LA 70803, USA
>> >
>> > Twitter: @brown_birds 
>> >
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at http://www.mail-archive.com/r-
>> sig-ph...@r-project.org/
>>
>
> [[alternative HTML version deleted]]
>
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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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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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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Eliot Miller]

What does: min(tree$edge.length) say?

Eliot

On Wed, May 2, 2018 at 2:22 PM, Rafael S Marcondes 
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 
> Louisiana State University
> 119 Foster Hall
> Baton Rouge, LA 70803, USA
>
> Twitter: @brown_birds 
>
>
>
> On Wed, May 2, 2018 at 1:08 PM Rafael S Marcondes  >
> 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 
> > Louisiana State University
> > 119 Foster Hall
> > Baton Rouge, LA 70803, USA
> >
> > Twitter: @brown_birds 
> >
> >
>
> [[alternative HTML version deleted]]
>
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>

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Re: [R-sig-phylo] Problem with negative ages in OUwie.boot?

[Rafael S Marcondes]

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 
Louisiana State University
119 Foster Hall
Baton Rouge, LA 70803, USA

Twitter: @brown_birds 



On Wed, May 2, 2018 at 1:08 PM Rafael S Marcondes 
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 
> Louisiana State University
> 119 Foster Hall
> Baton Rouge, LA 70803, USA
>
> Twitter: @brown_birds 
>
>

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