Hi, I’m interested in using the OUCH package to estimate BM and OU parameters for a specific trait among many different trees. My goal is to determined which model is the most suitable for each tree, applying likelihood ratio test.

As I’m a new user in R when it comes to phylogenetic analysis, I started by running the documentation example (Hansen, documentation page 11) and was surprised to see that the loglikelihood was a positive number BM: $call brown(data = otd[c("tarsusL", "beakD")], tree = ot) $sigma.squared [,1] [,2] [1,] 0.02878091 0.08897504 [2,] 0.08897504 0.43711838 $theta $theta$tarsusL [1] 3.020419 $theta$beakD [1] 1.826695 $loglik [1] 9.90115 As this number is crucial for further analysis - Is this a transformation of the resulting log likelihood? (e.g. -2 * log(L) as described in the paper) or am I missing something here..? In addition I have another issue, I have a tree constructed of ~400 viral genomes and their corresponding trait values. When I’m running the documentation script with my own data (in the same format) I get the following error: Error in solve.default(v, e) : system is computationally singular: reciprocal condition number = 1.59061e-17 I guess it says that my variance covariance matrix is not inversable, hence I manually tried to adjust the retol parameter in the Hansen function in order to make it work (however I’ll need to second guess my results?), but I still get the same error. Code example: h1 <- hansen( + tree=ot, + data=otd[c("k5")], + regimes=otd["regimes"], + fit=TRUE, + sqrt.alpha=1, + sigma=1, + maxit=500000, + reltol=1e-20, + method="Nelder-Mead" + ) I’ll be thankful for any advice or answer, Danielle _______________________________________________ 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/