Hi all I have a dataset of 5 PC axes for a phylogeny with 52 tips and I would like to get the variance-covariance matrix under a global OU model of evolution. I find that OU is strongly favored over BM, based on fitContinuous in GEIGER. However, I am having issues with convergence when trying to fit a hansen model to my data. What can I do to get around this problem? Alternatively, is there another way to get at the multivariate VCV matrix other than with the OUCH package?
The error is: *unsuccessful convergence, code 1, see documentation for `optim'* *Warning message:* *In hansen(tree = ot, data = otd[varnames], regimes = otd["regimes"], :* * unsuccessful convergence* I have posted a small file that contains the following R script along with the data here <http://dl.dropbox.com/u/34644229/OUhansen.zip>. Any advice would be greatly appreciated! Thanks! require(ouch) require(ape) tree<-read.nexus('tree.nex') data<-read.csv('data.csv') rownames(data)<-data$X data$X<-NULL tree head(data) colnames(data)->varnames #for hansen() ot<-ape2ouch(tree) otd<-as(ot,"data.frame") data$labels<-rownames(data) otd<-merge(otd,data,by="labels",all=TRUE) rownames(otd)<-otd$nodes ot<-with(otd,ouchtree(nodes=nodes,ancestors=ancestors,times=times,labels=labels)) otd$regimes<-as.factor("global") h1<-hansen(tree=ot,data=otd[varnames],regimes=otd["regimes"],sqrt.alpha=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1),sigma=c(1,0,0,0,0,1,0,0,0,1,0,0,1,0,1)) -- Pascal Title Graduate Student Burns Lab http://kevinburnslab.com/ Department of Evolutionary Biology San Diego State University 5500 Campanile Drive San Diego, CA 92182-4614 [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
