Hello all, I am trying to drop extinct taxa from a large phylogeny generated with a non-R-based tree simulation program. The tree was saved in a Nexus file which was read in with read.nexus. It's quite large--10911 leaves, but only 2055 are "alive" i.e. lineages that survived to the end of the simulation. It's these lineages I want to keep around for further analysis.
I've tried both the drop.fossil (from APE) and drop.extinct(from geiger) functions, but both of them give problems. If I use the customary low tolerance for either of these functions, drop.fossil produces the following error: > INTREE_EXTANT = drop.fossil(INTREE, tol=1e-6) Error in xmat[, 1] : incorrect number of dimensions Lowering the tolerance value to 1e-4 trims off some of the living tips I wanted kept (the resulting tree is smaller than it's supposed to be). drop.extinct just seems to hang and doesn't return even after about 10 minutes, no matter what tolerance value I supply. Is there some other way I can remove extinct lineages from a large tree like this? cheers, Gabe _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
