Hi Lev, I recently released a package that is robust to reading trees that includes singletons by relying on the NEXUS class library. It can read newick files.
The package is on CRAN here: http://cran.r-project.org/web/packages/rncl/index.html after installation: library(rncl) read_newick_phylo(file="tree.tre") Cheers, -- François On Tue, Feb 17, 2015 at 2:19 PM, Yampolsky, Lev <yampo...@mail.etsu.edu> wrote: > Dear Colleagues, > > I need to remove singleton nodes from a tree; trying to do it by this script: > > require(phytools) > source("read.newick.R") > tree<-read.newick(file="tree,tre") > tree<-collapse.singles(tree) > plotTree(tree,type="fan") > > (https://stat.ethz.ch/pipermail/r-sig-phylo/2013-June/002783.html) > > read.newick.R returns warnings that look like this: > 1: In getEdgeLength(text, i) : NAs introduced by coercion > (and then the same for every node). > And of course the resulting tree has 0 edge lengths. > > Anyone has any idea why this may be happening? > > Thank you very much in advance, > > Lev Yampolsky > > _______________________________________________ > 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/ _______________________________________________ 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/
