Hi Maria.
I believe I just fixed this on GitHub. There was a bug in phytools for
the circumstance in which some but not all nodes are labeled. You can
install phytools directly from GitHub using devtools as follows:
library(devtools)
install_github("liamrevell/phytools")
& then you can test as follows:
library(phytools)
tree<-read.newick(text='((((((a))A),(((b),(b1)))B)))C;')
tree$edge.length<-rep(1,nrow(tree$edge))
plotTree.singletons(tree)
nodelabels(tree$node.label)
All the best, Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 6/22/2017 9:22 AM, Mario José Marques-Azevedo wrote:
Dears,
I'm studying the structure of phylo object to work it in my functions.
I'm using read.newick to read tree with singletons. I do not know why
the number of node is not equal to length of node.labels. For instance:
I have this tree (the same annexed):
tree<-read.newick(text='((((((a))A),(((b),(b1)))B)))C;')
tree$Nnode
[1] 10
tree$tip.label
[1] "a" "b" "b1"
tree$node.label
[1] "C" "" "" "" "A" "" "B"
length(tree$node.label)
[1] 7
Why nodes 11, 12 and 13 not have labels, even if it is "", in
tree$node.lable, but node 9 has?
Best regards,
Mario
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