[R-sig-phylo] problem with fitcontinuos function
Dear all, fitcontinuous is giving me a warning generally related to non correspondence between tree tips and data. However name.check and the tree tips seems ok. Anybody has a hint on this? Thanks in advance. Agus name.check(tree, tp)[1] OK BMfit - fitContinuous(tree, tp$temperature, model=BM)Warning: no tip labels, order assumed to be the same as in the tree Fitting BM model: tree Phylogenetic tree with 11 tips and 10 internal nodes. Tip labels: C.leiolepis, C.nicterus, C.sinebrachiatus, S.catimbau, N.ablephara, P.erythrocercus, ... Node labels: 1, 2, 3, 4, 5, 6, ... Rooted; includes branch lengths. -- Agustín Camacho Guerrero. Doutorando em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] problem with fitcontinuos function
Hello Agus, I believe your problem will be solved if you set row names to the object tp$temperature. An example follows: names(temperature)-row.names(tp) Please let me know if it worked. Cheers, Renata -- Renata Brandt Departamento de Biologia - FFCLRP Universidade de São Paulo Ribeirão Preto - SP - Brasil (11) 92756353 (16) 82039533 /..) ( ( ) ) ( ( ) ) _( (_ ) ) \ ) \ On Wed, May 23, 2012 at 5:16 PM, Agus Camacho agus.cama...@gmail.comwrote: Dear all, fitcontinuous is giving me a warning generally related to non correspondence between tree tips and data. However name.check and the tree tips seems ok. Anybody has a hint on this? Thanks in advance. Agus name.check(tree, tp)[1] OK BMfit - fitContinuous(tree, tp$temperature, model=BM)Warning: no tip labels, order assumed to be the same as in the tree Fitting BM model: tree Phylogenetic tree with 11 tips and 10 internal nodes. Tip labels: C.leiolepis, C.nicterus, C.sinebrachiatus, S.catimbau, N.ablephara, P.erythrocercus, ... Node labels: 1, 2, 3, 4, 5, 6, ... Rooted; includes branch lengths. -- Agustín Camacho Guerrero. Doutorando em Zoologia. Laboratório de Herpetologia, Departamento de Zoologia, Instituto de Biociências, USP. Rua do Matão, trav. 14, nº 321, Cidade Universitária, São Paulo - SP, CEP: 05508-090, Brasil. [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] problem with fitcontinuos function
Thanks to all for your fast answer, this list is amazing! Graham's answer was perfectly satisfactory, once onnly that eliminated the warning. Thanks to all again. Agus 2012/5/23 Graham Slater gsla...@ucla.edu This doesn't indicate that they don't match - rather it's telling you that there are no names associated with the tip data (as tp$temperature is just a vector of numerical values) and so it is assuming that those values are in the same order as the tip labels in the tree. Assuming the taxon names are the rownames of your dataframe tp, try fitContinuous(phy = tree, data = tp$temperature, model=BM, data.names = rownames(tp) that should work without a warning. If your tip data are in the same order as the tip labels, the model output won't change. If they're not. Graham On May 23, 2012, at 1:16 PM, Agus Camacho wrote: Dear all, fitcontinuous is giving me a warning generally related to non correspondence between tree tips and data. However name.check and the tree tips seems ok. Anybody has a hint on this? Thanks in advance. Agus name.check(tree, tp)[1] OK BMfit - fitContinuous(tree, tp$temperature, model=BM)Warning: no tip labels, order assumed to be the same as in the tree Fitting BM model: tree Phylogenetic tree with 11 tips and 10 internal nodes. Tip labels: C.leiolepis, C.nicterus, C.sinebrachiatus, S.catimbau, N.ablephara, P.erythrocercus, ... Node labels: 1, 2, 3, 4, 5, 6, ... Rooted; includes branch lengths. -- Agustín Camacho Guerrero. Doutorando 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 Graham Slater Ph. D. Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E. Young Drive South Los Angeles, CA 90095-1606 (424) 442-4348 gsla...@ucla.edu www.eeb.ucla.edu/gslater -- Agustín Camacho Guerrero. Doutorando 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
