Hi all,
To complete the previous suggestions from David and Santiago, the
function makeNodeLabel with its option method = "md5sum" creates node
labels depending only the composition of the tip labels descending from
each node. Then using match(), it is possible to find nodes representing
iden
uot; mailto:yampo...@mail.etsu.edu>>
To: Emmanuel Paradis mailto:emmanuel.para...@ird.fr>>,
"Liam J. Revell"
mailto:liam.rev...@umb.edu>>, Dan Rabosky
mailto:drabo...@umich.edu>>
Cc: "r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>"
ps://sites.google.com/site/santiagosnchezrmirez/
>
> Message: 1
> Date: Wed, 13 Jan 2016 23:39:21 +
> From: "Yampolsky, Lev"
> To: Emmanuel Paradis , "Liam J. Revell"
> , Dan Rabosky
> Cc: "r-sig-phylo@r-project.org"
> Subject: Re: [R-sig-p
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,Dicellogra
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 v
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
Dear Lev and all,
First, to answer the actual question in your postscriptum, ape's
branching.times() is not for non-ultrametric trees, but it does
silently accept them as input, unfortunately. The branching.times it
returns assume that some tip (the first tip?) is at time=0, which
means that often
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 e
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 ti
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 = "correl
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