Thanks Nathan, I was right now able to figure out the problem. I noticed that the species list I was using had one blank space after each species' epithet. It was invisible at the original csv file, but after Klaus identified the trees were not in the downloaded file, it made me think there was something wrong with the species names. I deleted that blank space and now the trees work fine.
Best regards, Agus 2018-02-14 0:33 GMT-02:00 Upham, Nathan <nathan.up...@yale.edu>: > Hi Agus > I work next to the main developer for the birdtree.org site— glad to help > figure the error if its on our end. I just downloaded a test file (Ericson > sequenced, 100 trees) and it worked as intended including full trees. What > species and settings did you choose for your download, and using what web > browser? > > Reply to me off list and we’ll get this sorted. > > All the best > —nate > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > *Nathan S. Upham, Ph.D. *Postdoctoral Associate, Yale University, Ecology > and Evolutionary Biology > 165 Prospect Street > <https://maps.google.com/?q=165+Prospect+Street&entry=gmail&source=g>, > OML 122, New Haven, CT, 06511, USA > > personal web: Home <https://n8upham.github.io/> | Research Gate > <https://www.researchgate.net/profile/Nathan_Upham> | Google Scholar > <https://scholar.google.com/citations?user=zIn4NoUAAAAJ&hl=en> > lab pages: Jetz Lab <http://jetzlab.yale.edu/> | NSF VertLife grant > <http://vertlife.org/> > > Research Associate, Integrative Research Center, Field Museum of Natural > History > Chair, Biodiversity Committee, American Society of Mammalogists > ~> Check out the new Mammal Diversity Database > <https://mammaldiversity.org/> > Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group > > e: nathan.up...@yale.edu | Skype: nate_upham | Twitter: @n8_upham > > > > > > > On Feb 13, 2018, at 9:11 PM, Agus Camacho <agus.cama...@gmail.com> wrote: > > Thanks for that, Klaus! > Regards > Agus > > 2018-02-13 22:51 GMT-02:00 Klaus Schliep <klaus.schl...@gmail.com>: > > Dear Agustín, > > the nexus file on dropbox does not contain any trees. > If you open it in an editor you see this: > > > #NEXUS > > [Tree distribution from: The global diversity of birds in space and time; > W. Jetz, G. H. Thomas, J. B. Joy, K. Hartmann, A. O. Mooers > doi:10.1038/nature11631] > [Subsampled and pruned from birdtree.org on 2018-02-13T21:49:59Z ] > [Data: "Hackett All Species" (see Jetz et al. 2012 supplement for details)] > > BEGIN TREES; > TREE tree_4104 = > TREE tree_9438 = > ... > TREE tree_1868 = > TREE tree_0011 = > END; > > > Looks like your download did not work and the error message from > read.nexus could improve. > > Cheers, > Klaus > > > On Tue, Feb 13, 2018 at 5:11 PM, Agus Camacho <agus.cama...@gmail.com> > wrote: > > Dear list, > > I am puzzled with this error when importing a bird tree subset from > https://urldefense.proofpoint.com/v2/url?u=https-3A__ > birdtree.org_subsets_&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r= > Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=QCx_ > EErW5SnutNdxWnXm65RyRGtG1st3m0iAmNiulmU&e= . > > The subset is supposed to be in nexus format. However, > > trees<-read.nexus("output.nex") > > Error in if (tp[3] != "") obj$node.label <- tp[3] : > > missing value where TRUE/FALSE needed > > > read.tree gives the same error > read.newick gets stuck, it never ends reading in the tree > > I tried scanning the file and then several notes appear before the actual > trees Thus, I tried read.annotated.nexus from OutbreakTools. > But it gives another error: > > Error in read.annotated.nexus("C:/Users/agusc/Dropbox/output.nex") : > .annotated.clado.build is not yet implemented. > > > I tried with several different subsets from different backbones and none > worked. > Here is one: https://urldefense.proofpoint.com/v2/url?u=https- > 3A__www.dropbox.com_s_037u6pjr4006o6r_output.nex-3Fdl-3D0&d=DwIFaQ&c= > cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s= > BfBnKVjZjCJ1C8YumcqEIf2FGIDH2pRzLaqMU8gm01g&e= > > Somebody has reported this error previously in the internet, but it still > seems to be unsolved. > > Thanks in advance and best regards. > Agus > > > -- > Agustín Camacho Guerrero. > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > agustincamacho.com&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r= > Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=jSdLapf5K-3pnA7_OTck6Zt- > 60GpMrs1IZ0AAh8B34E&e= > Doutor em Zoologia. > Laboratório de Herpetologia, Departamento de Zoologia, Instituto de > Biociências, USP. > Rua do Matão, trav. 14, nº 321, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwIFaQ&c= > cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s= > KE5rlr3daja6JHbUqJvP2AlAphe78oeV_0vZiCCNRYw&e= > Searchable archive at https://urldefense.proofpoint.com/v2/url?u=http- > 3A__www.mail-2Darchive.com_r-2D&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r= > Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s= > szj7UYL8tC9dS7P9aTAKywcv5WlOuztpY7wJzVlAtQk&e= > sig-ph...@r-project.org/ > > > > > -- > Klaus Schliep > Postdoctoral Fellow > Revell Lab, University of Massachusetts Boston > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > phangorn.org_&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r= > Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=ZLALoSqYWiPRC_ > eOJCMWrhZgF0GgiIY5NOxGc-3IQCg&e= > > > > > -- > Agustín Camacho Guerrero. > https://urldefense.proofpoint.com/v2/url?u=http-3A__www. > agustincamacho.com&d=DwIFaQ&c=cjytLXgP8ixuoHflwc-poQ&r= > Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=jSdLapf5K-3pnA7_OTck6Zt- > 60GpMrs1IZ0AAh8B34E&e= > Doutor em Zoologia. > Laboratório de Herpetologia, Departamento de Zoologia, Instituto de > Biociências, USP. > Rua do Matão, trav. 14, nº 321, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat. > ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwIFaQ&c= > cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s= > KE5rlr3daja6JHbUqJvP2AlAphe78oeV_0vZiCCNRYw&e= > Searchable archive at https://urldefense.proofpoint.com/v2/url?u=http- > 3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject.org_&d=DwIFaQ&c= > cjytLXgP8ixuoHflwc-poQ&r=Q5p7Th8M0OGrWt3H3QohAlhP-5Yx0wuJ0zlxqhR3rfM&m=_ > wK9RgVNWrHAUkqxAjALq8J5PLRUQSEz8B6CFf47GuU&s=SC-Xjwva_ > CCOqErppkn_aTAS5qlebRD_WFlMFAaIaKM&e= > > > -- Agustín Camacho Guerrero. http://www.agustincamacho.com Doutor em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. [[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/
