To pile a little bit more after David's message, ape has the function
ltt.plot.coords which does the same thing than phytools::ltt but with
different options, including 'tol' which specifies the tolerance for
considering a tree as ultrametric or not.
Best,
Emmanuel
Le 13/01/2016 03:29, Liam J. Revell a écrit :
Hi Lev.
You could also look at ltt in phytools. The object returned has the time
of all the events on the tree - including the end of lineages that go
extinct before the present. To access these, you can do:
obj<-ltt(tree,plot=FALSE)
obj$times
obj$ltt
& to see how these are associated with events, you can do:
plot(obj,show.tree=TRUE)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 1/12/2016 10:22 PM, Dan Rabosky wrote:
Dear Lev-
I don't think branching.times can compute these for non-ultrametric
trees.
You can do this with package BAMMtools, but you need a "hidden"
internal function. You can access it as
"BAMMtools:::NU.branching.times"
It returns branching times relative to the most recently-occurring tip
in the tree. It's a R-based recursion that is a little slower that the
ape function, so it's not recommended as a replacement for
branching.times if you have an ultrametric tree.
I'm not actively maintaining laser, but getBtimes returns the output
of branching.times after sorting the times and stripping out the node
names (this was useful for something many years ago!). If you plot
sort(getBtimes(x)) and sort(branching.times(x)) they should be identical.
~Dan Rabosky
On Jan 12, 2016, at 7:37 PM, Yampolsky, Lev <yampo...@mail.etsu.edu>
wrote:
Dear Colleagues,
Does anyone know what is the difference between ape�s
branching.times() and laser�s getBtimes()?
And why they may be giving rather different results, particularly for
internal branches? (From an ultrametric tree created by
chronotree <- chronos(tree, lambda = 1, model = "correlated", quiet =
FALSE, calibration = makeChronosCalib(tree), control =
chronos.control())
Thank you very much in advance for your help!
PS. A related but less important question: I am curious how does
branching.times() calculate branching times from a non-ultrametric tree?
--
Lev Yampolsky
Professor
Department of Biological Sciences
East Tennessee State University
Box 70703
Johnson City TN 37614-1710
Cell 423-676-7489
Office/lab 423-439-4359
Fax 423-439-5958
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_____________________
Dan Rabosky
Assistant Professor & Curator of Herpetology
Museum of Zoology &
Department of Ecology and Evolutionary Biology
University of Michigan
Ann Arbor, MI 48109-1079 USA
drabo...@umich.edu
http://www-personal.umich.edu/~drabosky
http://www.lsa.umich.edu/ummz/
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