Dear Klaus, Thank you for your answer and good news that ape/phangorn will load tree with singletons! Can I send the tree to your email?
My problem with collapse.singles is, for instance, when I have only one genus/specie. I want the node name with genus and a tip name with species. When I collapse, genus node name is removed. For instance: This tree: ((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R; when 'collapsed' will be: ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R; Note that I lost node name 'F'. I don't know why, but month ago I ran extract.clade of my tree without problem. Maybe some update that I did, but I'm not sure. Thank you again! 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 On 1 June 2017 at 11:43, Mario José Marques-Azevedo <mariojm...@gmail.com> wrote: > Dear Klaus, > > Thank you for your answer and good news that ape/phangorn will load tree > with singletons! Can I send the tree to your email? > > My problem with collapse.singles is, for instance, when I have only one > genus/specie. I want the node name with genus and a tip name with species. > When I collapse, genus node name is removed. For instance: > > This tree: > > ((((A_1,A_2,)A,(B1,B2,B3)B)C,((((D1))),(E1,E2)E)D),(F1)F)R; > > when 'collapsed' will be: > > ((((A_1,A_2)A,(B1,B2,B3)B)C,(D1,(E1,E2)E)D),F1)R; > > Note that I lost node name 'F'. > > I don't know why, but month ago I ran extract.clade of my tree without > problem. Maybe some update that I did, but I'm not sure. > > Thank you again! > > 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 > > > > > On 1 June 2017 at 11:17, Klaus Schliep <klaus.schl...@gmail.com> wrote: > >> Dear Mario, >> Emmanuel and I are working to allow singletons in ape / phangorn. In the >> next version will read the tree in with read.tree(). >> Can you send me your larger tree for testing purposes, as it is one which >> would fail at the moment? >> Regards, >> Klaus >> >> >> >> >> >> >> On Thu, Jun 1, 2017 at 8:51 AM, Klaus Schliep <klaus.schl...@gmail.com> >> wrote: >> >>> Hi Mario, >>> >>> the problem with your tree is that it contains singleton (nodes of >>> degree 2). Try collapse.singles() before using extract.clade(). >>> >>> Cheers, >>> Klaus >>> >>> >>> >>> >>> 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/ >>> >>> >>> >>> >>> -- >>> Klaus Schliep >>> Postdoctoral Fellow >>> Revell Lab, University of Massachusetts Boston >>> http://www.phangorn.org/ >>> >>> >> >> >> -- >> Klaus Schliep >> Postdoctoral Fellow >> Revell Lab, University of Massachusetts Boston >> http://www.phangorn.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/
