Re: [R-sig-phylo] fitting multiple OU optima
Hi Paolo, the method for doing what you want is called 'SURFACE' and there is an associated R package: http://cran.r-project.org/web/packages/surface/index.html The paper describing the method can be found here: http://onlinelibrary.wiley.com/doi/10./2041-210X.12034/abstract Cheers, Florian 2014-04-22 11:54 GMT+02:00 Paolo Piras paolo.pi...@uniroma3.it: Dear list, I write to ask you if it is possible to look for multiple optima in OU process as in OUwie. However, i would like to tun the analysis WITHOUT specifing a priori the selective regime group for innner nodes or taxa. Do you know if this approach is possible? thankyou in advance paolo piras ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Florian Boucher Postdoctoral researcher, Institute of Systematic Botany, Zürich [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] fitting multiple OU optima
Hi Paolo, I'm not sure if what you ask has been implemented yet in any package, but something that you can do, in the case it hasn't, is to set up models with as many regimes as you consider realistic and feasible and then compare them using AIC. Cheers, Santiago ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] Ape package.
You need put the path of the directory with this simbol / and not this \, so the correct path is F:*/*tetrapods_tree.txt. Cheers! On Sun, Apr 20, 2014 at 5:17 PM, Alexey Fomin lesh...@rambler.ru wrote: Hi! Whether someone work with ape package? I have long tree (see attached, it is in newick format, it is ultra metric, it is from http://www.onezoom.org/user/tetrapods_tree.js ). I need dates of nodes. Someone advised me to do: 1) library(ape) 2) tree-read.tree(?yourtree.nex?) 3) br.times-branching.times(tree) But I can not not do the second step. I tried (after library(ape)) tree-read.tree(F:\tetrapods_tree.txt) But it is gives: Error: unexpected input in tree-read.tree(F:\ What can I do? Alexey. ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
