Dear Eliot, Thank you for your answer! My tree is ok, but to plot is needed to collapse singles, as you said.
I use ape/phytools to manipulate my tree for date it after with phylocom. Then, all node is important, including single one. For this, collapse singletons do not work for me. For instance. This trees: ((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R; (((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),(F1)F)G)R; 'collapsed' is: ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R; I lost 'F' node, as I said early. D1 is now in 'right' way. This tree: ((((((A_1,A_2,)A,(B1,B2,B3)B)C)ABC,((D1,(E1,E2)E)D))DE,(F1)F)G)R; 'collapsed' is: ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D)DE,F1)G; I lost 'F', 'R' and 'ABC' node. I have a big tree and some families has polytomies. Then, I extract each family (remove tips of this node), resolve plytomies, and I bind families tree again. After that, I date tree with phylocon. Phylocon use ages file with node age, then each node in my tree is important and collapse singletons would be a lost of information. I created one function to help me with extract node because I have issues using drop.tips (https://github.com/MarioJose/r-functions/blob/master/drop. clade.label/example.md). As I said, extract.node was working months ago. I don't know if this error is some updated that I did. Best regards, Mario On 1 June 2017 at 11:41, Eliot Miller <eliot.is...@gmail.com> wrote: > Your Newick string is badly formatted. See: > > plot(t1) > > Error in plot.phylo(t1) : > there are single (non-splitting) nodes in your tree; you may need to use > collapse.singles() > > On Thu, Jun 1, 2017 at 1:31 AM, Mario José Marques-Azevedo < > mariojm...@gmail.com> wrote: > >> Dears, >> >> I'm using extract.clade from ape package and get some issues. I'm using >> phytools package to load tree with single clade like above: >> >> library(phytools) >> >> t1 <- read.newick(text='(((((A_1,A_2,)A,(B1,B2,B3)B)C,(D1,(E1,E2) >> E)D),(F1)F)G)R;') >> >> t2 <- read.newick(text='((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),( >> E1,E2)E)D),(F1)F)R; >> >> When I extract 'F' clade, for instance: >> >> c1 <- extract.clade(t1, 'F') >> >> or >> >> c2 <- extract.clade(t2, 'F') >> >> I have this error: >> >> Error in prop.part(phy) : attempt to set index 8/8 in SET_VECTOR_ELT >> >> I have one tree with mode than 300 tips. When I try extract any clade, I >> have the same error. If I repeat the command I have this one: >> >> *** Error in `/usr/lib/rstudio/bin/rsession': malloc(): memory >> corruption: >> 0x000000000a3aaa40 *** >> >> My configurations was: >> >> platform x86_64-pc-linux-gnu >> arch x86_64 >> os linux-gnu >> system x86_64, linux-gnu >> language R >> version.string R version 3.3.3 (2017-03-06) >> >> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10) >> >> I try update R to 3.4 and recompile all my packages, but I get the same >> error. >> >> My new configurations: >> >> platform x86_64-pc-linux-gnu >> arch x86_64 >> os linux-gnu >> system x86_64, linux-gnu >> language R >> version.string R version 3.4.0 (2017-04-21) >> >> phytools (0.6.0), ape (4.1), maps (3.1.1), Rcpp (0.12.10) >> >> I don't know why I have this error if I can extract with the same commands >> some time ago. >> >> I have the same error if I run in RStudio or in terminal. When I use >> RStudio, it abort after the error. >> >> I try Google, but I don't found nothing that can help me. >> >> Thank you and best regards, >> >> Mario >> >> >> .................................................................... >> Mario José Marques-Azevedo >> Ph.D. Candidate in Ecology >> Department of Plant Biology, Institute of Biology >> University of Campinas, Campinas, São Paulo, Brazil >> https://github.com/mariojose <http://www.github.com/mariojose> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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-ph...@r-project.org/ > > > [[alternative HTML version deleted]] _______________________________________________ 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/
