[R-sig-phylo] help with dist.multiPhylo needed
Hello I would like to compute geodesic distances from random trees for comparison and hypothesis testing with those produced from a given set of trees. I am using dist.multiPhylo() in the 'distory' package, but it seems to be too compute-intensive. To illustrate my point: lin4 #object consisting of 4 randomly generated trees [1] "(S8: 1.0, (((S4: 0.28596, S5: 0.28596): 0.63211, (S10: 0.88214, ((S6: 0.49245, S7: 0.49245): 0.24813, S9: 0.74058): 0.14156): 0.03592): 0.03859, ((S1: 0.16950, S2: 0.16950): 0.61358, S3: 0.78308): 0.17357): 0.04335);" [2] "((S6: 0.10938, S2: 0.10938): 0.89062, ((S7: 0.79060, ((S4: 0.31389, S8: 0.31389): 0.31812, (((S1: 0.06153, S3: 0.06153): 0.08642, S10: 0.14795): 0.47444, S9: 0.62238): 0.00962): 0.15860): 0.01336, S5: 0.80396): 0.19604);" [3] "((S7: 0.98617, (S4: 0.90628, (S3: 0.86179, ((S1: 0.17650, S6: 0.17650): 0.48270, ((S10: 0.28064, S5: 0.28064): 0.06352, (S9: 0.00968, S8: 0.00968): 0.33448): 0.31505): 0.20259): 0.04449): 0.07990): 0.01383, S2: 1.0);" [4] "(S6: 0.42675, S3: 0.42675): 0.16273, S8: 0.58948): 0.00542, S5: 0.59490): 0.05023, (S4: 0.19208, S7: 0.19208): 0.45305): 0.35486, (S9: 0.90829, (S10: 0.64179, (S2: 0.36191, S1: 0.36191): 0.27988): 0.26649): 0.09171);" dist.multiPhylo(lin4) Error: evaluation nested too deeply: infinite recursion / options(expressions=)? If I increase the value of "expressions" from 5000 (default) to 25000 then options(expressions=25000) dist.multiPhylo(lin4) Error: protect(): protection stack overflow Is there a way to circumvent these errors? Thank you very much for your time. Juan A. Balbuena -- Dr. Juan A. Balbuena Marine Zoology Unit Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia http://www.uv.es/~balbuena P.O. Box 22085 http://www.uv.es/cavanilles/zoomarin/index.htm 46071 Valencia, Spain http://cetus.uv.es/mullpardb/index.html e-mail: j.a.balbu...@uv.es tel. +34 963 543 658 fax +34 963 543 733 NOTE! For shipments by EXPRESS COURIER use the following street address: C/ Catedrtico Jos Beltrn 2, 46980 Paterna (Valencia), Spain. ___ 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] help with dist.multiPhylo needed
Hi Klaus You are right. The problem was that my lin4 object was a list. I have saved the same trees in a text file as "(S8: 1.0, (((S4: 0.28596, S5: 0.28596): 0.63211, (S10: 0.88214, ((S6: 0.49245, S7: 0.49245): 0.24813, S9: 0.74058): 0.14156): 0.03592): 0.03859, ((S1: 0.16950, S2: 0.16950): 0.61358, S3: 0.78308): 0.17357): 0.04335);" "((S6: 0.10938, S2: 0.10938): 0.89062, ((S7: 0.79060, ((S4: 0.31389, S8: 0.31389): 0.31812, (((S1: 0.06153, S3: 0.06153): 0.08642, S10: 0.14795): 0.47444, S9: 0.62238): 0.00962): 0.15860): 0.01336, S5: 0.80396): 0.19604);" "((S7: 0.98617, (S4: 0.90628, (S3: 0.86179, ((S1: 0.17650, S6: 0.17650): 0.48270, ((S10: 0.28064, S5: 0.28064): 0.06352, (S9: 0.00968, S8: 0.00968): 0.33448): 0.31505): 0.20259): 0.04449): 0.07990): 0.01383, S2: 1.0);" "(S6: 0.42675, S3: 0.42675): 0.16273, S8: 0.58948): 0.00542, S5: 0.59490): 0.05023, (S4: 0.19208, S7: 0.19208): 0.45305): 0.35486, (S9: 0.90829, (S10: 0.64179, (S2: 0.36191, S1: 0.36191): 0.27988): 0.26649): 0.09171);" and tree4 - read.tree(file.choose()) dist.multiPhylo(tree4) 1 2 3 2 2.452629 3 2.441263 2.362859 4 1.598451 2.050473 2.259690 Excellent! Thank you very much for your help! Juan El 23/01/2014 16:54, Klaus Schliep escribi: I also checked it for a multiPhylo object the function works fine, but not for a list or vector of characters. On Thu, Jan 23, 2014 at 4:49 PM, Juan Antonio Balbuena j.a.balbu...@uv.es wrote: Hello Thank you very much for your interest. Yes, it does read newick and works with similar trees. So the problem seems "architectural" instead of not applying the function correctly. Cheers Juan El 23/01/2014 16:35, Klaus Schliep escribi: Sorry, should also read newick format, sorry for my comment. On Thu, Jan 23, 2014 at 4:30 PM, Klaus Schliep klaus.schl...@gmail.com wrote: Dear Juan, lin4 is not an object of class multiPhylo but vector of characters. Read in the trees with read.tree from the ape package. Regards, Klaus On Thu, Jan 23, 2014 at 4:20 PM, Juan Antonio Balbuena j.a.balbu...@uv.es wrote: Hello I would like to compute geodesic distances from random trees for comparison and hypothesis testing with those produced from a given set of trees. I am using dist.multiPhylo() in the 'distory' package, but it seems to be too compute-intensive. To illustrate my point: lin4 #object consisting of 4 randomly generated trees [1] "(S8: 1.0, (((S4: 0.28596, S5: 0.28596): 0.63211, (S10: 0.88214, ((S6: 0.49245, S7: 0.49245): 0.24813, S9: 0.74058): 0.14156): 0.03592): 0.03859, ((S1: 0.16950, S2: 0.16950): 0.61358, S3: 0.78308): 0.17357): 0.04335);" [2] "((S6: 0.10938, S2: 0.10938): 0.89062, ((S7: 0.79060, ((S4: 0.31389, S8: 0.31389): 0.31812, (((S1: 0.06153, S3: 0.06153): 0.08642, S10:
[R-sig-phylo] OUwie $solution.se
Hi, How is it possible to get approximate standard errors of alpha and sigma^2 ($solution.se) in OUwie? Maybe, diagn=T should show me this element, but it does not work:Â Error in dim(edges) : 'edges' is missing Thank you! [[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/
