Lev,
This is easy, if the newick strings are structured the same so that
the resulting edge matrix and tip labels are identical. Here's a
worked example:
```
library(ape)
# with edge lengths
newick1<-"(Homo:30,(Echinus:18,(Cephalodiscus:12,(Rhabdopleura:8,(Dictyonema:1,(Rhabdinopora:1,Dicellograptus:3):1):1):4):4):10);"
# with node names
newick2<-"(Homo,(Echinus,(Cephalodiscus,(Rhabdopleura,(Dictyonema,(Rhabdinopora,Dicellograptus)Graptoloida)Eugraptolithina)Graptolithina)Pterobranchia)Ambulacraria)Deuterostomia;"
# convert newick strings to phylo objects
tree1<-read.tree(text=newick1)
plot(tree1)
tree2<-read.tree(text=newick2)
plot(tree2)
nodelabels(tree2$node.label)
# combine
if(identical(tree1$edge,tree2$edge) &
identical(tree1$tip.label,tree2$tip.label)){
tree3<-tree1
tree3$node.label<-tree2$node.label
}
plot(tree3)
nodelabels(tree3$node.label)
```
If $edge and $tip.label are not identical, then this is a somewhat
more complex issue.
Cheers,
-Dave
On Wed, Jan 13, 2016 at 4:39 PM, Yampolsky, Lev <yampo...@mail.etsu.edu> wrote:
> Dear Colleagues,
>
> Thank you very much for your help, it’s all clear now. (I got way more
> than I asked for, for example, my trees include only extant taxa). And
> yes, branching.times() and getBtimes() return exact same numbers of
> course, I just didn’t understand ow indexing works.
>
> Next question, a very simple one again.
>
> I have two newick trees, identical topology. In one I have branch lengths,
> in the other I have node names. I would like a tree with both. How do I do
> this?
>
> Thanks in advance!
>
> --
> Lev Yampolsky
>
> Professor
> Department of Biological Sciences
> East Tennessee State University
> Box 70703
> Johnson City TN 37614-1710
> Cell 423-676-7489
> Office/lab 423-439-4359
> Fax 423-439-5958
>
>
>
>
> On 1/13/16, 4:20 AM, "Emmanuel Paradis" <emmanuel.para...@ird.fr> wrote:
>
>>To pile a little bit more after David's message, ape has the function
>>ltt.plot.coords which does the same thing than phytools::ltt but with
>>different options, including 'tol' which specifies the tolerance for
>>considering a tree as ultrametric or not.
>>
>>Best,
>>
>>Emmanuel
>>
>>Le 13/01/2016 03:29, Liam J. Revell a écrit :
>>> Hi Lev.
>>>
>>> You could also look at ltt in phytools. The object returned has the time
>>> of all the events on the tree - including the end of lineages that go
>>> extinct before the present. To access these, you can do:
>>>
>>> obj<-ltt(tree,plot=FALSE)
>>> obj$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
>>>>>
>>>>> _______________________________________________
>>>>> 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-phylo@r-project.org/
>>>>
>>>> _____________________
>>>> 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/
>>>>
>>>>
>>>>
>>>> [[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-phylo@r-project.org/
>>>>
>>>
>>> _______________________________________________
>>> 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-phylo@r-project.org/
>>
>
> _______________________________________________
> 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-phylo@r-project.org/
--
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701
http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
_______________________________________________
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-phylo@r-project.org/
