I am interested in estimating discrete ancestral states in ace using the
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
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!

        [[alternative HTML version deleted]]

R-sig-phylo mailing list - R-sig-phylo@r-project.org
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/

Reply via email to