Hi Rafael.I don't want to speak on behalf of the authors who are also on this list, but OUwie can read in modified "phylo" objects created by the phytools functions read.simmap & make.simmap.
All the best, Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://phytools.blogspot.com On 3/13/2012 4:35 PM, Rafael Maia wrote:
Speaking of OUwie, the paper just came out today: Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger & Brian C. O’Meara. MODELING STABILIZING SELECTION: EXPANDING THE ORNSTEIN-UHLENBECK MODEL OF ADAPTIVE EVOLUTION. Evolution, Accepted Article, DOI: 10.1111/j.1558-5646.2012.01619.x (link: http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01619.x/abstract ) Has anyone tried it out yet? Is there a way of converting SIMMAP trees to the format to be used with the OUwie function? Thanks! Abraços, Rafael Maia --- webpage: http://gozips.uakron.edu/~rm72 "A little learning is a dangerous thing; drink deep, or taste not the Pierian spring." (A. Pope) Graduate Student - Integrated Bioscience University of Akron http://gozips.uakron.edu/~shawkey/ On Mar 12, 2012, at 2:39 PM, Liam J. Revell wrote:You might want to try the OUWie package by Beaulieu & O'Meara (http://cran.r-project.org/web/packages/OUwie/index.html). I have not tried it yet, but it promises to do multi-optimum OU model fitting as well. All the best, Liam -- Liam J. Revell University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu <mailto:liam.rev...@umb.edu> blog: http://phytools.blogspot.com On 3/12/2012 2:31 PM, Pascal Title wrote: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))_______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org <mailto:R-sig-phylo@r-project.org> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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