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 and the fit converges most
of the times.
Best,
Emmanuel
----- Le 29 Jan 21, à 5:49, Joseph Keating joe.keat...@bristol.ac.uk a écrit :
> 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 likelihoods for states that are >1 or <0.
> I
> don't get the same errors if using the 'SYM' or "ER" models.
>
> Please see my post on stackoverflow for an example. Link below:
> https://stackoverflow.com/questions/65944177/nonsensical-likelihoods-returned-when-using-the-ace-function-and-the-all-rate
>
> If anyone could provide any help or advice, it would be hugely appreciated.
> And
> thanks to Ben Bolker for pointing me to this mailing group.
>
> Kind Regards
>
> Joe Keating
> [https://cdn.sstatic.net/Sites/stackoverflow/Img/apple-touch-i...@2.png?v=73d79a89bded]<https://stackoverflow.com/questions/65944177/nonsensical-likelihoods-returned-when-using-the-ace-function-and-the-all-rate>
> phylogeny - Nonsensical likelihoods returned when using the 'ace' function and
> the 'all rates different' model in the R package: 'Ape' - Stack
> Overflow<https://stackoverflow.com/questions/65944177/nonsensical-likelihoods-returned-when-using-the-ace-function-and-the-all-rate>
> 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.
> stackoverflow.com
>
>
>
> Dr Joseph Keating
> Palaeobiology Research Group
> University of Bristol
> Bristol Life Sciences Building
> 24 Tyndall Avenue
> Bristol
> BS8 1TQ
>
> [[alternative HTML version deleted]]
>
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