Re: [R-sig-phylo] trees to matrix and gamma-statistic
Hi all, Thank you for your help, I resolve my first problem (tree convert to matrix) and the second one I think I must to calculate the gamma-statistics with the ultrametric tree. Thank you people, Cheers Bryan Morales Pallero Licenciado en Biología Biólogo Laboratorio de Diversidad Genómica y Filoinformática Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción - Chile On 03/12/10 03:45, Joe Felsenstein wrote: Folks -- Now that I have had a chance to look up the history: 1. Sokal and Rohlf in 1962 (in Taxon) introduced the cophenetic correlation. 2. They had a distance called the dendrogrammatic distance which was (for the ultrametric trees they considered), half of the patristic distance. 3. Wartren Wagner mentions patristic distance in a 1968 review in Bioscience, but does not claim it. 4. JS Farris's paper showing that the cophenetic correlation is minimized when we achieve a least squares fit of tree to distances is in 1969 in Systematic Zoology. Joe Joe Felsenstein, j...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] trees to matrix and gamma-statistic
Hello all, I'm working in the evolution of lizards in Chile, and I will very grateful if you can help me with the next questions: 1. I need to transform the sample of trees generated by bayesian inference into a matrix whose values are the branch lenght between tips, Can I do this? 2. I understand that the gamma-statistic index of Pybus and Harvey applies only to ultrametric trees, there is a similar index for trees that are not ultrametric? Thank you very much for any help that you can give me and I'm sorry for my bad english. Thanks -- Bryan Morales Pallero Licenciado en Biología Biólogo Laboratorio de Diversidad Genómica y Filoinformática Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción - Chile ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] trees to matrix and gamma-statistic
Hi Bryan, On Thu, 02 Dec 2010 03:06:39 -0300 Bryan Morales Pallero feano...@gmail.com wrote: Hello all, I'm working in the evolution of lizards in Chile, and I will very grateful if you can help me with the next questions: 1. I need to transform the sample of trees generated by bayesian inference into a matrix whose values are the branch lenght between tips, Can I do this? Yes. See the function vcv in ape. 2. I understand that the gamma-statistic index of Pybus and Harvey applies only to ultrametric trees, there is a similar index for trees that are not ultrametric? The 'ultrametricity' of the tree gives it a temporal feature (if done properly, of course), so that methods considering the tempo of evolution can be used to analyse such trees. If you cannot get ultrametric dated trees, see the package apTreeshape which has methods to analyse tree shapes, but the range of inferences will usually be less than with dated trees. Best, EP Thank you very much for any help that you can give me and I'm sorry for my bad english. Thanks -- Bryan Morales Pallero Licenciado en Biología Biólogo Laboratorio de Diversidad Genómica y Filoinformática Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción - Chile ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] trees to matrix and gamma-statistic
Folks -- I believe that the distances predicted from the tree are called patristic distance. They are a quite old concept. I don't have the literature accessible right now but believe they were first described by JS Farris or by Jim Rohlf. Searching on Google using that phrase yields more tools. Cophenetic correlation is the correlation coefficient (the ordinary Pearson correlation) between the observed distances and the patristic distances. Farris pointed out in the early 1970s that minimizing it chooses the same tree as minimizing the unweighted least squares fit of the distances. Joe --- Joe Felsenstein, j...@gs.washington.edu Department of Genome Sciences and Department of Biology University of Washington Box 355065 Seattle WA 98195-5065 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] trees to matrix and gamma-statistic
Hi Liam, You are right: thanks for correcting me. Cheers, Emmanuel On Thu, 02 Dec 2010 23:18:39 -0500 Liam J. Revell lrev...@nescent.org wrote: I would also add that C-vcv.phylo(tree) gives a matrix, C, containing the distances from the root to the common ancestor of each pair of species. From this you can of course compute the distances between tips using D[i,j]-C[i,i]+C[j,j]-2*C[i,j]. But if you are just after the distances, you can also compute D-cophenetic(tree) which yields a matrix containing the distances between all the tips in the tree, I think. - Liam Liam J. Revell NESCent, Duke University web: http://anolis.oeb.harvard.edu/~liam/ NEW email: lrev...@nescent.org On 12/2/2010 10:01 PM, Emmanuel Paradis wrote: Hi Bryan, On Thu, 02 Dec 2010 03:06:39 -0300 Bryan Morales Pallero feano...@gmail.com wrote: Hello all, I'm working in the evolution of lizards in Chile, and I will very grateful if you can help me with the next questions: 1. I need to transform the sample of trees generated by bayesian inference into a matrix whose values are the branch lenght between tips, Can I do this? Yes. See the function vcv in ape. 2. I understand that the gamma-statistic index of Pybus and Harvey applies only to ultrametric trees, there is a similar index for trees that are not ultrametric? The 'ultrametricity' of the tree gives it a temporal feature (if done properly, of course), so that methods considering the tempo of evolution can be used to analyse such trees. If you cannot get ultrametric dated trees, see the package apTreeshape which has methods to analyse tree shapes, but the range of inferences will usually be less than with dated trees. Best, EP Thank you very much for any help that you can give me and I'm sorry for my bad english. Thanks -- Bryan Morales Pallero Licenciado en Biolog?a Bi?logo Laboratorio de Diversidad Gen?mica y Filoinform?tica Facultad de Ciencias Naturales y Oceanogr?ficas Universidad de Concepci?n Concepci?n - Chile ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ 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] trees to matrix and gamma-statistic
Emmanuel wrote -- 2. I understand that the gamma-statistic index of Pybus and Harvey applies only to ultrametric trees, there is a similar index for trees that are not ultrametric? The 'ultrametricity' of the tree gives it a temporal feature (if done properly, of course), so that methods considering the tempo of evolution can be used to analyse such trees. If you cannot get ultrametric dated trees, see the package apTreeshape which has methods to analyse tree shapes, but the range of inferences will usually be less than with dated trees. To rephrase what he said (but probably not change the meaning), if the intent of the gamma statistic is to measure the change through time of the speciation rate (or the difference between the speciation and extinction rates) then you need some way to associate a time with each point in the tree. Lacking an ultrametric tree, you don't have a non-arbitrary way to do that. Joe Joe Felsenstein, j...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] trees to matrix and gamma-statistic
Folks -- Now that I have had a chance to look up the history: 1. Sokal and Rohlf in 1962 (in Taxon) introduced the cophenetic correlation. 2. They had a distance called the dendrogrammatic distance which was (for the ultrametric trees they considered), half of the patristic distance. 3. Wartren Wagner mentions patristic distance in a 1968 review in Bioscience, but does not claim it. 4. JS Farris's paper showing that the cophenetic correlation is minimized when we achieve a least squares fit of tree to distances is in 1969 in Systematic Zoology. Joe Joe Felsenstein, j...@gs.washington.edu Dept. of Genome Sciences, Univ. of Washington Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] trees to matrix and gamma-statistic
Hello all, I'm working in the evolution of lizards in Chile, and I will very grateful if you can help me with the next questions: 1. I need to transform the sample of trees generated by bayesian inference into a matrix whose values are the branch lenght between tips, Can I do this? 2. I understand that the gamma-statistic index of Pybus and Harvey applies only to ultrametric trees, there is a similar index for trees that are not ultrametric? Thank you very much for any help that you can give me and I'm sorry for my bad english. Thanks -- Bryan Morales Pallero Licenciado en Biología Biólogo Laboratorio de Diversidad Genómica y Filoinformática Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción - Chile ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
