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
>>>
>>>
>>
>>
>>
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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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