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 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
