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_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: t...@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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