Hi, I was recently splitting some massive phylo class objects with extract.clade() and noticed what appears to be a bug in how tip labels are copied from the full tree to the pruned tree. This possible bug was also mentioned here:
http://www.mail-archive.com/r-sig-ph...@r-project.org/msg00537.html An example: library(ape) set.seed(5) x <- matrix(rnorm(100), ncol=10) p <- as.phylo(hclust(dist(x))) p.new <- extract.clade(p, 14) par(mfcol=c(1,2), mar=c(1,1,5,1)) plot(p) title('original') nodelabels() plot(p.new) title('cut at node 14') I have noticed that this error is present only sometimes... i.e. when I use a different seed for the random matrix 'x', the results are correct in some cases. Any ideas? Thanks for the very useful 'ape' package! Cheers, Dylan -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
