Hi Agus I work next to the main developer for the birdtree.org<http://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, 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<mailto:nathan.up...@yale.edu> | Skype: nate_upham | Twitter: @n8_upham On Feb 13, 2018, at 9:11 PM, Agus Camacho <agus.cama...@gmail.com<mailto: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<mailto: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<http://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<mailto: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<mailto: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<mailto: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<mailto: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= [[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/
