OK, I think I've figured out what the trouble is, it's a problem with the way the input Nexus files are being written. The trouble is with the data in the translation table. If I extract the Newick tree structure by itself, without the translation labels, the tree can be read and processed normally (though of course the tip labels are anonymous now).
Is there some way of getting read.nexus() to ignore the translation table? cheers, Gabe On Wed, Nov 12, 2014 at 7:03 PM, Gabriel Yedid <[email protected]> wrote: > Hello all, > > I'm having a curious problem in that I have trees that seem to have > more nodes than tips. They're part of a time series of trees (not > generated with an R package) that I'm reading in and doing tree shape > analyses of. Not all of the trees have this problem, but once it > crops up it persists in all trees generated after that point. > > The tree file (in Nexus format) is read in OK, but when I try to plot it I > see: > >> plot(INTREE, show.tip.label=FALSE) > Error in plot.phylo(INTREE, show.tip.label = FALSE) : > tree badly conformed; cannot plot. Check the edge matrix. >> summary(INTREE) > > Phylogenetic tree: INTREE > > Number of tips: 5796 > Number of nodes: 5797 > Branch lengths: > mean: 9.617864 > variance: 149.9489 > distribution summary: > Min. 1st Qu. Median 3rd Qu. Max. > 0.000 2.480 6.213 12.740 188.200 > Root edge: 17.5434 > First ten tip labels: taxa_1000 > taxa_10001 > taxa_10002 > taxa_10003 > taxa_10004 > taxa_10005 > taxa_10006 > taxa_10008 > taxa_10009 > taxa_10019 > No node labels. > > And when I try to drop all of the extinct tips of the tree, all tips > are dropped! > > What could be causing this behaviour? How can it be fixed (in R)? > > cheers, > > Gabe _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
