Hi, I am interested in estimating discrete ancestral states in ace using the calls: fitER<-ace(tipRegion,tree,model="ER",type="discrete") fitARD<-ace(tipRegion,tree,model="ARD",type="discrete", use.expm=TRUE)
When I fit the ARD model (with either use.expm=TRUE or use.eigen=TRUE), I get the following warning: 1: In nlminb(rep(ip, length.out = np), function(p) dev(p), lower = rep(0, : imaginary parts discarded in coercion Additionally, the two rates which I expect to be the highest are estimated as 0. There are 3 tip states for a tree of 146 tips and 145 internal nodes. A likelihood ratio test supports the ARD model, but I cannot trust model results. I am wondering: 1) is there an obvious error that is creating this warning and unexpected output? 2) should I use a simpler model (i.e. SYM)? Or should I reclassify tip states so that I examine transitions between only 2 states? Thank you in advance for your help! This is a fantastic package! Best, [[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/