[R-sig-phylo] problem calculating independent contrasts

Graham Slater gslater at ucla.edu
Tue Feb 21 01:30:02 CET 2012


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
gslater at 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_nigriceps            Aotus_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_calvus            Callicebus_moloch         Callicebus_torquatus            Callimico_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_rosalia            Pithecia_pithecia 
>                    1.079181                     1.146128                     1.000000                     1.000000 
>        Saguinus_fuscicollis           Saguinus_geoffroyi               Saguinus_midas             Saguinus_oedipus 
>                    1.113943                     1.000000                     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_leucophaeus            Mandrillus_sphinx 
>                    1.322219                     1.041393                     1.041393                     1.000000 
>        Miopithecus_talapoin             Nasalis_larvatus                 Papio_anubis           Papio_cynocephalus 
>                    1.230449                     0.698970                     1.204120                     1.000000 
>             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_madagascariensis            Eulemur_coronatus 
>                    0.477121                     0.845098                     0.954243                     1.000000 
>       Eulemur_fulvus_fulvus        Eulemur_macaco_macaco               Eulemur_mongoz          Eulemur_rubriventer 
>                    1.000000                     0.845098                     0.954243                     0.698970 
>        Euoticus_elegantulus                Galago_alleni                Galago_moholi          Galago_senegalensis 
>                    0.778151                     0.698970                     0.477121                     1.255273 
>         Galagoides_demidoff            Hapalemur_griseus              Hapalemur_simus                  Indri_indri 
>                    1.041393                     0.954243                     0.845098                     0.602060 
>                 Lemur_catta       Lepilemur_ruficaudatus            Loris_tardigradus           Microcebus_murinus 
>                    1.342423                     0.477121                     0.778151                     0.477121 
>          Nycticebus_coucang          Nycticebus_pygmaeus           Otolemur_garnettii           Perodicticus_potto 
>                    0.845098                     0.903090                     0.845098                     0.698970 
>             Phaner_furcifer          Propithecus_diadema  Varecia_variegata_variegata             Tarsius_bancanus 
>                    0.778151                     0.845098                     0.698970                     0.845098 
> 
> My phylogeny reports the same names:
> 
>> t.100species$tip.label
>  [1] "Cercopithecus_ascanius"       "Cercopithecus_campbelli"      "Cercopithecus_cephus"        
>  [4] "Cercopithecus_mitis"          "Cercopithecus_neglectus"      "Cercopithecus_pogonias"      
>  [7] "Chlorocebus_aethiops"         "Chlorocebus_pygerythrus"      "Erythrocebus_patas"          
> [10] "Miopithecus_talapoin"         "Avahi_laniger"                "Avahi_occidentalis"          
> [13] "Cheirogaleus_major"           "Cheirogaleus_medius"          "Daubentonia_madagascariensis"
> [16] "Eulemur_coronatus"            "Eulemur_fulvus_fulvus"        "Eulemur_macaco_macaco"       
> [19] "Eulemur_mongoz"               "Eulemur_rubriventer"          "Hapalemur_griseus"           
> [22] "Hapalemur_simus"              "Indri_indri"                  "Lemur_catta"                 
> [25] "Lepilemur_ruficaudatus"       "Microcebus_murinus"           "Phaner_furcifer"             
> [28] "Propithecus_diadema"          "Varecia_variegata_variegata"  "Alouatta_palliata"           
> [31] "Alouatta_seniculus"           "Ateles_belzebuth"             "Ateles_fusciceps"            
> [34] "Ateles_geoffroyi"             "Brachyteles_arachnoides"      "Lagothrix_lagotricha"        
> [37] "Aotus_nigriceps"              "Aotus_trivirgatus"            "Callimico_goeldii"           
> [40] "Callithrix_jacchus"           "Callithrix_penicillata"       "Callithrix_pygmaea"          
> [43] "Cebus_capucinus"              "Cebus_olivaceus"              "Leontopithecus_rosalia"      
> [46] "Saguinus_fuscicollis"         "Saguinus_geoffroyi"           "Saguinus_midas"              
> [49] "Saguinus_oedipus"             "Saimiri_oerstedii"            "Saimiri_sciureus"            
> [52] "Arctocebus_calabarensis"      "Loris_tardigradus"            "Nycticebus_coucang"          
> [55] "Nycticebus_pygmaeus"          "Perodicticus_potto"           "Gorilla_gorilla_gorilla"     
> [58] "Hylobates_agilis"             "Hylobates_moloch"             "Pan_paniscus"                
> [61] "Pan_troglodytes_troglodytes"  "Pongo_abelii"                 "Pongo_pygmaeus"              
> [64] "Cacajao_calvus"               "Callicebus_moloch"            "Callicebus_torquatus"        
> [67] "Pithecia_pithecia"            "Cercocebus_torquatus_atys"    "Lophocebus_albigena"         
> [70] "Macaca_arctoides"             "Macaca_fascicularis"          "Macaca_mulatta"              
> [73] "Macaca_nemestrina"            "Macaca_radiata"               "Macaca_silenus"              
> [76] "Macaca_sylvanus"              "Mandrillus_leucophaeus"       "Mandrillus_sphinx"           
> [79] "Papio_anubis"                 "Papio_cynocephalus"           "Papio_hamadryas"             
> [82] "Papio_papio"                  "Theropithecus_gelada"         "Colobus_angolensis_palliatus"
> [85] "Colobus_guereza"              "Colobus_polykomos"            "Nasalis_larvatus"            
> [88] "Piliocolobus_badius"          "Presbytis_comata"             "Procolobus_verus"            
> [91] "Semnopithecus_entellus"       "Trachypithecus_cristatus"     "Trachypithecus_johnii"       
> [94] "Euoticus_elegantulus"         "Galago_alleni"                "Galago_moholi"               
> [97] "Galago_senegalensis"          "Galagoides_demidoff"          "Otolemur_garnettii"          
> [100] "Tarsius_bancanus"            
>> 
> 
> Is it that the data have to be in the same order as the tree tips listed in the tree file?
> 
> Doing a search in the manual:
> 
> Package Œape‚
> February 14, 2012
> Version 3.0
> 
> Does not report any lines matching: "tip labels of the tree did not match"
> 
> Not sure what it means that "the former were ignored in the analysis"?  Does this mean that the independent contrasts were random with respect to the tree? (not sure why this would be the default∑)  
> 
> Any clarification or help on how to proceed would be appreciated!
> 
> -Tom
> _________________________________________________
> P. Thomas Schoenemann
> 
> Associate Professor
> Department of Anthropology
> Indiana University
> Bloomington, IN  47405
> Phone: 812-855-8800
> E-mail: toms at indiana.edu
> 
> Open Research Scan Archive (ORSA) Co-Director
> Consulting Scholar
> Museum of Archaeology and Anthropology
> University of Pennsylvania
> 
> Homepage: http://mypage.iu.edu/~toms/
> 
> 
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