Hi Andrew.
This is because the numbers in tre$edge are node & tip numbers, not tip
labels (which also can be numbers). The translation between tip numbers
and tip labels is given by tre$tip.label. Here, tip labels are indexed
by their numbers in tre$edge.
For instance, in your case we have:
> tre$edge
[,1] [,2]
[1,] 10 11
[2,] 11 12
[3,] 12 13
[4,] 13 1
[5,] 13 2
... (some rows excluded)
and:
> tre$tip.label
[1] "8" "9" "3" "1" "6" "7" "2" "4" "5"
This tells us, to take your example, that node 13 should be connected to
tips 1 & 2, which tre$tip.label tells us have labels "8" & "9", just as
we see with:
> plot(tre); nodelabels()
I hope this clears things up somewhat.
All the best, Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 9/9/2011 7:51 AM, Andrew Barr wrote:
library(ape)
tre<-read.tree(text="((((8:2.850732306,9:0.1789410068):1.147884602,3:0.8848821048):1.411242805,(1:3.869881809,((6:0.6904865854,7:0.02044458561):1.984259398,2:0.04497273798):0.3022512176):0.09298177296):0.3029547699,(4:0.8015431218,5:1.467916249):2.117025776);")
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