It was recently
reported
that there can be a mismatch between the number of nodes & the length of the node label
vector in an object class "phylo"
produced by the function read.newick
in phytools. This appears to be a bug that is produced when some nodes have labels, but the
node with the largest-valued index does not have a label. I just pushed a
fix
to GitHub & it appears to work. Here's a demo using the case submitted on R-sig-phylo:
library(phytools)
## Loading required package: ape
## Loading required package: maps
packageVersion("phytools")
## [1] '0.6.17'
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)
That's it.
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