So sorry for the silly question, I overlooked your show.node=T.
Many thanks.
Kamila
On Aug 22, 2013, at 12:29 PM, "Naxerova, Kamila"
wrote:
> Thank you Klaus, this works like a charm. One more if I may: If I still want
> to have bootstrap values in my plot, how do I go about plotting those f
Sorry - this is the correct source file. (I just neglected
"as.phylo.formula<-" from the start of the source file.)
- Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phyt
Thank you Klaus, this works like a charm. One more if I may: If I still want to
have bootstrap values in my plot, how do I go about plotting those for my new
tree?
Kamila
On Aug 22, 2013, at 12:12 PM, Klaus Schliep
mailto:klaus.schl...@gmail.com>>
wrote:
Hi Kamila,
try function pruneTree in
-- Forwarded message --
From: Klaus Schliep
Date: Thu, Aug 22, 2013 at 6:12 PM
Subject: Re: [R-sig-phylo] Collapsing branches with low bootstrap values
To: "Naxerova, Kamila"
Hi Kamila,
try function pruneTree in phangorn.
data(woodmouse)
f <- function(x) nj(dist.dna(x))
tr <- f
On Thu, Aug 22, 2013 at 5:09 PM, Naxerova, Kamila
wrote:
> Dear list,
>
> is there a function that will take a tree and the output of boot.phylo()
> and collapse branches below a chosen bootstrap value cutoff?
>
> Many thanks.
> Kamila
>
> ___
> R-sig-ph
Hi Francois.
The reason that this is the case because the algorithm in
as.phylo.formula is to build a Newick string without "singles" (that is,
nodes with only one descendant), and then read it into memory using
read.tree (which can only read Newick trees without singles). In the
attached ver
Dear list,
is there a function that will take a tree and the output of boot.phylo() and
collapse branches below a chosen bootstrap value cutoff?
Many thanks.
Kamila
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/
Hi all,
I 'm trying to build a taxonomic tree from a taxonomic matrix using the
function as.phylo.formula of the ape package. It works well but it
returns a phylo object without branch length. This is problematic in
that it can lead to misleading graphic representation (eg with
plot.phylo). Fo
