Hi, George,
Ape package do not read tree with singletons, yet. New version will read.
You can use readTree from phytools package for while.
Best regards,
Mario
On 5 Sep 2017 5:53 p.m., "George Vega Yon" wrote:
Hi,
When trying to read this tree with the ape::read.tree
Dears,
I'm studying the structure of phylo object to work it in my functions. I'm
using read.newick to read tree with singletons. I do not know why the
number of node is not equal to length of node.labels. For instance:
I have this tree (the same annexed):
/drop.clade.label.r
I leaned a lot working on it!
p.s.: drop.tip function remove singletons in the last code. Maybe this
behaviour could be optional with a new argument
All the best,
Mario
Mario José Marques-Azevedo
Ph.D. Candidate
June 2017 at 16:13, Mario José Marques-Azevedo <mariojm...@gmail.com>
wrote:
> Dear Eliot,
>
> Thank you for your answer! My tree is ok, but to plot is needed to
> collapse singles, as you said.
>
> I use ape/phytools to manipulate my tree for date it after with ph
tted. See:
>
> plot(t1)
>
> Error in plot.phylo(t1) :
> there are single (non-splitting) nodes in your tree; you may need to use
> collapse.singles()
>
> On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo <
> mariojm...@gmail.com> wrote:
>
>> De
without
problem. Maybe some update that I did, but I'm not sure.
Thank you again!
Best regards,
Mario
Mario José Marques-Azevedo
Ph.D. Candidate in Ecology
Department of Plant Biology, Institute of Biology
University of Campinas