Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-03 Thread Bryan Morales Pallero
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

[R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Bryan Morales Pallero
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

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Emmanuel Paradis
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

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Joe Felsenstein
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

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Emmanuel Paradis
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.

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Joe Felsenstein
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

Re: [R-sig-phylo] trees to matrix and gamma-statistic

2010-12-02 Thread Joe Felsenstein
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.

[R-sig-phylo] trees to matrix and gamma-statistic

2010-12-01 Thread Bryan Morales Pallero
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