Hi Nick, You can fix the value of alpha in corMartins:
corMartins(1, tree, fixed=TRUE) You can try with different values to see which one gives the best fit. Best, Emmanuel -----Original Message----- From: Nicholas Mason <nicholas.albert.ma...@gmail.com> Sender: r-sig-phylo-boun...@r-project.org Date: Thu, 22 Mar 2012 12:57:59 To: <r-sig-phylo@r-project.org> Subject: [R-sig-phylo] Error with PGLS under OU model using corMartins Dear Rsigphylo users, I am having issues running PGLS (with nlme function gls()) under an OU model using the corMartins command from ape. I've included links to a reproducible example via my dropbox account below. Previous posts have been made about the same error I've encounter, but neither thread seems to have relevant replies or have resolved the issue. Apologies if I've missed something else from previous rsigphylo threads. https://stat.ethz.ch/pipermail/r-sig-phylo/2011-January/000875.html http://www.mail-archive.com/r-sig-phylo@r-project.org/msg00577.html In short, the data set I've linked to will run gls() under a correlation structure as defined by corBrownian and corPagel but not corMartins. The following error is encountered with corMartins: Error in recalc.corStruct(object[[i]], conLin) : NA/NaN/Inf in foreign function call (arg 4) Has anyone else experienced this issue or know how to resolve it? What does this message mean? This happens with each variable I examine, not just the example included here. Thanks in advance for any help or answers provided. Cheers, Nick Mason The R object below contains a list called sampledata. sampledata[[1]] is a data frame with tip values and sampledata[[2]] is the corresponding tree. Link to R objects: http://db.tt/ablyDBt1 Link to Rscript via public dropbox: http://db.tt/tJ8jg0JQ require(ape) require(nlme) load("sampledata.Rdata") sampledata[[1]]->tipdata sampledata[[2]]->tree gls(TraitA~TraitB,data=tipdata,correlation=corMartins(1,tree)) gls(TraitA~TraitB,data=tipdata,correlation=corBrownian(1,tree)) gls(TraitA~TraitB,data=tipdata,correlation=corPagel(1,tree)) --------------------------------- Nicholas Albert Mason MS Candidate, Burns Lab http://kevinburnslab.com/ Department of Biology - EB Program San Diego State University 5500 Campanile Drive San Diego, CA 92182-4614 845-240-0649 (cell) [[alternative HTML version deleted]] _______________________________________________ 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
