[R-sig-phylo] edge representation of trees produced by birthdeath.tree() in geiger

Andrew Barr wabarr at gmail.com
Fri Sep 9 13:51:19 CEST 2011


Hi all,

While simulating some trees using the birthdeath.tree() function in
geiger I noticed an inconsistency between the node/tip labels in the
edge matrix and in a plot of the tree.  I dumped in the text of one of
the trees I produced as an example.

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);")

plot(tre)
nodelabels()
tre$edge

Note that the edge matrix contains edges that shouldn't exist based on
the plot. For instance, there should be no edge between node 13 and
tip 1 based on the plot, but there it is in the fourth row of the edge
matrix.  My feeling is this has to do with the way the tips are
getting labeled by the birthdeath.tree() function but I can't quite
figure it out. Any ideas?

Thanks,

Andrew Barr
PhD Candidate
University of Texas at Austin



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