Re: [R-sig-phylo] Nonsensical likelihoods returned when using the 'ace' function and the 'all rates different' model in the R package: 'Ape'

Hi Joe, I'd say this issue is related to these particular data: there are four states so the ARD model has 12 parameters which is quite a lot considering that one state ('3') is overwhelming represented in the data. If you simulate data with two states, then the ARD model has only 2 parameters

[R-sig-phylo] Nonsensical likelihoods returned when using the 'ace' function and the 'all rates different' model in the R package: 'Ape'

Dear R-sig-phylo mailing group I'm having some problems using the 'all rates different' (ARD) model of the 'ace' function. The function seems to return different errors / warnings depending on the specified method for computing the exponential of the rate matrix. Most notably, its returning