[R-sig-phylo] problem calculating independent contrasts
Dear look your data the "tree.phy" Inside BEGIN TAXA; the name of tax need be exactly equals in as TRANSLATE see my .phy example bellow the same error are occurring to me (the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis.) I solve it by change the taxon macularius, this taxon was with an extra h at the end in the section TRANSLATE. a just remove this "h" and tried to run the command again, and no error/warning message. #NEXUS BEGIN TAXA; DIMENSIONS ntax=5 TAXLABELS macularius pusilla collaris semipalmatus antilarum ; END; BEGIN TREES; TRANSLATE 1 maculariush, 2 pusilla, 3 collaris, 4 semipalmatus, 5 antilarum, ; TREE tree_1 = [] ((1:0.10820559,2:0.07532207):0.04591014,(3:0.55047517,4:0.01800012):0.07815226,5:0.07346231); END; -- Patrick Douglas Corrêa Pereira Laboratório de Biologia Molecular e Neuroecologia - Instituto Federal do Pará Campus Bragança. Rua da Escola Agrícola s/n, Vila Sinhá, Bragança, Pará, Brasil. Telefone: +55 (91) 9 85404339 E-mail: patrickpereira...@gmail.com patr...@ufpa.br patrickpereira...@hotmail.com [[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/
[R-sig-phylo] problem calculating independent contrasts
Hello, I keep getting the following error when trying to calculate independent contrasts: pic.log_repertoire_data - pic(log_repertoire_data, t.100species) Warning message: In pic(log_repertoire_data, t.100species) : the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis. However, unless I'm misunderstanding what this means, then it is not correct. My data is in: log_repertoire_data Alouatta_palliata Alouatta_seniculus Aotus_nigricepsAotus_trivirgatus 0.778151 0.778151 0.778151 0.778151 Ateles_belzebuth Ateles_fusciceps Ateles_geoffroyi Brachyteles_arachnoides 0.778151 0.954243 1.322219 0.903090 Cacajao_calvusCallicebus_moloch Callicebus_torquatusCallimico_goeldii 1.079181 1.041393 0.845098 0.845098 Callithrix_jacchus Callithrix_penicillata Callithrix_pygmaea Cebus_capucinus 0.954243 0.602060 1.176091 1.414973 Cebus_olivaceus Lagothrix_lagotricha Leontopithecus_rosaliaPithecia_pithecia 1.079181 1.146128 1.00 1.00 Saguinus_fuscicollis Saguinus_geoffroyi Saguinus_midas Saguinus_oedipus 1.113943 1.00 0.903090 0.954243 Saimiri_oerstedii Saimiri_sciureus Cercocebus_torquatus_atys Cercopithecus_ascanius 0.602060 1.301030 1.079181 0.845098 Cercopithecus_campbelli Cercopithecus_cephus Cercopithecus_mitis Cercopithecus_neglectus 1.176091 1.204120 0.845098 0.778151 Cercopithecus_pogonias Chlorocebus_aethiops Colobus_angolensis_palliatus Colobus_guereza 1.230449 1.322219 0.903090 0.845098 Colobus_polykomos Erythrocebus_patas Lophocebus_albigena Macaca_arctoides 0.903090 1.079181 1.079181 1.230449 Macaca_fascicularis Macaca_mulatta Macaca_nemestrina Macaca_radiata 1.176091 1.204120 1.371068 1.397940 Macaca_silenus Macaca_sylvanus Mandrillus_leucophaeusMandrillus_sphinx 1.322219 1.041393 1.041393 1.00 Miopithecus_talapoin Nasalis_larvatus Papio_anubis Papio_cynocephalus 1.230449 0.698970 1.204120 1.00 Papio_hamadryas Papio_papio Piliocolobus_badius Presbytis_comata 0.477121 1.176091 1.079181 1.041393 Procolobus_verus Semnopithecus_entellus Theropithecus_gelada Trachypithecus_cristatus 0.903090 1.204120 1.342423 1.113943 Trachypithecus_johnii Chlorocebus pygerythrus Gorilla_gorilla_gorilla Hylobates_agilis 1.204120 1.322219 1.361728 0.778151 Hylobates_moloch Pan_paniscus Pan_troglodytes_troglodytes Pongo_abelii 0.954243 1.146128 1.531479 1.505150 Pongo_pygmaeus Arctocebus_calabarensis Avahi_laniger Avahi_occidentalis 1.204120 0.301030 0.477121 0.477121 Cheirogaleus_major Cheirogaleus_medius Daubentonia_madagascariensisEulemur_coronatus 0.477121 0.845098 0.954243 1.00 Eulemur_fulvus_fulvusEulemur_macaco_macaco
Re: [R-sig-phylo] problem calculating independent contrasts
Hi Tom, have you tried running name.check(t.100species, log_repertoire_data) to confirm that the names perfectly match in both? If there is even a slight mismatch, then pic will ignore all the names in the data and assume that they are in the same order as the tip labels in the tree. Thus the pics returned would be random. Graham Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669 gsla...@ucla.edu www.eeb.ucla.edu/gslater On Feb 20, 2012, at 3:54 PM, Tom Schoenemann wrote: Hello, I keep getting the following error when trying to calculate independent contrasts: pic.log_repertoire_data - pic(log_repertoire_data, t.100species) Warning message: In pic(log_repertoire_data, t.100species) : the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis. However, unless I'm misunderstanding what this means, then it is not correct. My data is in: log_repertoire_data Alouatta_palliata Alouatta_seniculus Aotus_nigricepsAotus_trivirgatus 0.778151 0.778151 0.778151 0.778151 Ateles_belzebuth Ateles_fusciceps Ateles_geoffroyi Brachyteles_arachnoides 0.778151 0.954243 1.322219 0.903090 Cacajao_calvusCallicebus_moloch Callicebus_torquatusCallimico_goeldii 1.079181 1.041393 0.845098 0.845098 Callithrix_jacchus Callithrix_penicillata Callithrix_pygmaea Cebus_capucinus 0.954243 0.602060 1.176091 1.414973 Cebus_olivaceus Lagothrix_lagotricha Leontopithecus_rosaliaPithecia_pithecia 1.079181 1.146128 1.00 1.00 Saguinus_fuscicollis Saguinus_geoffroyi Saguinus_midas Saguinus_oedipus 1.113943 1.00 0.903090 0.954243 Saimiri_oerstedii Saimiri_sciureus Cercocebus_torquatus_atys Cercopithecus_ascanius 0.602060 1.301030 1.079181 0.845098 Cercopithecus_campbelli Cercopithecus_cephus Cercopithecus_mitis Cercopithecus_neglectus 1.176091 1.204120 0.845098 0.778151 Cercopithecus_pogonias Chlorocebus_aethiops Colobus_angolensis_palliatus Colobus_guereza 1.230449 1.322219 0.903090 0.845098 Colobus_polykomos Erythrocebus_patas Lophocebus_albigena Macaca_arctoides 0.903090 1.079181 1.079181 1.230449 Macaca_fascicularis Macaca_mulatta Macaca_nemestrina Macaca_radiata 1.176091 1.204120 1.371068 1.397940 Macaca_silenus Macaca_sylvanus Mandrillus_leucophaeusMandrillus_sphinx 1.322219 1.041393 1.041393 1.00 Miopithecus_talapoin Nasalis_larvatus Papio_anubis Papio_cynocephalus 1.230449 0.698970 1.204120 1.00 Papio_hamadryas Papio_papio Piliocolobus_badius Presbytis_comata 0.477121 1.176091 1.079181 1.041393 Procolobus_verus Semnopithecus_entellus Theropithecus_gelada Trachypithecus_cristatus 0.903090 1.204120 1.342423 1.113943 Trachypithecus_johnii Chlorocebus pygerythrus Gorilla_gorilla_gorilla Hylobates_agilis 1.204120 1.322219 1.361728 0.778151 Hylobates_moloch
Re: [R-sig-phylo] problem calculating independent contrasts
Graham is absolutely right. If you did this you would find that Chlorocebus pygerythrus has an underscore separating genus specific epithet in your tree, but not in your data vector: require(geiger) name.check(tree,x) $Tree.not.data [1] Chlorocebus_pygerythrus $Data.not.tree [1] Chlorocebus pygerythrus - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 2/20/2012 7:30 PM, Graham Slater wrote: Hi Tom, have you tried running name.check(t.100species, log_repertoire_data) to confirm that the names perfectly match in both? If there is even a slight mismatch, then pic will ignore all the names in the data and assume that they are in the same order as the tip labels in the tree. Thus the pics returned would be random. Graham Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669 gsla...@ucla.edu www.eeb.ucla.edu/gslater On Feb 20, 2012, at 3:54 PM, Tom Schoenemann wrote: Hello, I keep getting the following error when trying to calculate independent contrasts: pic.log_repertoire_data- pic(log_repertoire_data, t.100species) Warning message: In pic(log_repertoire_data, t.100species) : the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis. However, unless I'm misunderstanding what this means, then it is not correct. My data is in: log_repertoire_data Alouatta_palliata Alouatta_seniculus Aotus_nigricepsAotus_trivirgatus 0.778151 0.778151 0.778151 0.778151 Ateles_belzebuth Ateles_fusciceps Ateles_geoffroyi Brachyteles_arachnoides 0.778151 0.954243 1.322219 0.903090 Cacajao_calvusCallicebus_moloch Callicebus_torquatusCallimico_goeldii 1.079181 1.041393 0.845098 0.845098 Callithrix_jacchus Callithrix_penicillata Callithrix_pygmaea Cebus_capucinus 0.954243 0.602060 1.176091 1.414973 Cebus_olivaceus Lagothrix_lagotricha Leontopithecus_rosaliaPithecia_pithecia 1.079181 1.146128 1.00 1.00 Saguinus_fuscicollis Saguinus_geoffroyi Saguinus_midas Saguinus_oedipus 1.113943 1.00 0.903090 0.954243 Saimiri_oerstedii Saimiri_sciureus Cercocebus_torquatus_atys Cercopithecus_ascanius 0.602060 1.301030 1.079181 0.845098 Cercopithecus_campbelli Cercopithecus_cephus Cercopithecus_mitis Cercopithecus_neglectus 1.176091 1.204120 0.845098 0.778151 Cercopithecus_pogonias Chlorocebus_aethiops Colobus_angolensis_palliatus Colobus_guereza 1.230449 1.322219 0.903090 0.845098 Colobus_polykomos Erythrocebus_patas Lophocebus_albigena Macaca_arctoides 0.903090 1.079181 1.079181 1.230449 Macaca_fascicularis Macaca_mulatta Macaca_nemestrina Macaca_radiata 1.176091 1.204120 1.371068 1.397940 Macaca_silenus Macaca_sylvanus Mandrillus_leucophaeusMandrillus_sphinx 1.322219 1.041393 1.041393 1.00 Miopithecus_talapoin Nasalis_larvatus Papio_anubis Papio_cynocephalus 1.230449 0.698970 1.204120 1.00 Papio_hamadryas Papio_papio Piliocolobus_badius Presbytis_comata 0.477121 1.176091 1.079181 1.041393 Procolobus_verus Semnopithecus_entellus
Re: [R-sig-phylo] problem calculating independent contrasts
Nice! Thanks Graham and Liam, -Tom On Feb 20, 2012, at 9:07 PM, Liam J. Revell wrote: Graham is absolutely right. If you did this you would find that Chlorocebus pygerythrus has an underscore separating genus specific epithet in your tree, but not in your data vector: require(geiger) name.check(tree,x) $Tree.not.data [1] Chlorocebus_pygerythrus $Data.not.tree [1] Chlorocebus pygerythrus - Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 2/20/2012 7:30 PM, Graham Slater wrote: Hi Tom, have you tried running name.check(t.100species, log_repertoire_data) to confirm that the names perfectly match in both? If there is even a slight mismatch, then pic will ignore all the names in the data and assume that they are in the same order as the tip labels in the tree. Thus the pics returned would be random. Graham Graham Slater Department of Ecology and Evolutionary Biology University of California, Los Angeles 621 Charles E Young Drive South Los Angeles CA 90095-1606 (310) 825-4669 gsla...@ucla.edu www.eeb.ucla.edu/gslater On Feb 20, 2012, at 3:54 PM, Tom Schoenemann wrote: Hello, I keep getting the following error when trying to calculate independent contrasts: pic.log_repertoire_data- pic(log_repertoire_data, t.100species) Warning message: In pic(log_repertoire_data, t.100species) : the names of argument 'x' and the tip labels of the tree did not match: the former were ignored in the analysis. However, unless I'm misunderstanding what this means, then it is not correct. My data is in: log_repertoire_data Alouatta_palliata Alouatta_seniculus Aotus_nigricepsAotus_trivirgatus 0.778151 0.778151 0.778151 0.778151 Ateles_belzebuth Ateles_fusciceps Ateles_geoffroyi Brachyteles_arachnoides 0.778151 0.954243 1.322219 0.903090 Cacajao_calvusCallicebus_moloch Callicebus_torquatusCallimico_goeldii 1.079181 1.041393 0.845098 0.845098 Callithrix_jacchus Callithrix_penicillata Callithrix_pygmaea Cebus_capucinus 0.954243 0.602060 1.176091 1.414973 Cebus_olivaceus Lagothrix_lagotricha Leontopithecus_rosaliaPithecia_pithecia 1.079181 1.146128 1.00 1.00 Saguinus_fuscicollis Saguinus_geoffroyi Saguinus_midas Saguinus_oedipus 1.113943 1.00 0.903090 0.954243 Saimiri_oerstedii Saimiri_sciureus Cercocebus_torquatus_atys Cercopithecus_ascanius 0.602060 1.301030 1.079181 0.845098 Cercopithecus_campbelli Cercopithecus_cephus Cercopithecus_mitis Cercopithecus_neglectus 1.176091 1.204120 0.845098 0.778151 Cercopithecus_pogonias Chlorocebus_aethiops Colobus_angolensis_palliatus Colobus_guereza 1.230449 1.322219 0.903090 0.845098 Colobus_polykomos Erythrocebus_patas Lophocebus_albigena Macaca_arctoides 0.903090 1.079181 1.079181 1.230449 Macaca_fascicularis Macaca_mulatta Macaca_nemestrina Macaca_radiata 1.176091 1.204120 1.371068 1.397940 Macaca_silenus Macaca_sylvanus Mandrillus_leucophaeusMandrillus_sphinx 1.322219 1.041393 1.041393 1.00 Miopithecus_talapoin Nasalis_larvatus Papio_anubis Papio_cynocephalus 1.230449 0.698970 1.204120 1.00 Papio_hamadryas Papio_papio Piliocolobus_badius Presbytis_comata
