Re: [R-sig-phylo] model averaging using brownie.lite

[Karla Shikev]

Thanks so much, Liam! Just one quick follow-up question: what do you
suggest should be the sample size for transforming AIC into AICc? the
number of tips on the tree?

Karla

On Thu, Sep 5, 2019 at 10:27 AM Liam Revell <liam.rev...@umb.edu> wrote:

> Dear Karla.
>
> You could try & create your own logLik method for the object class
> "brownie.lite" as follows:
>
> ## method
> logLik.brownie.lite<-function(object,...){
>         lik<-setNames(
>                 c(object$logL1,object$logL.multiple),
>                 c("single-rate","multi-rate"))
>         attr(lik,"df")<-c(object$k1,object$k2)
>         lik
> }
> ## fit model
> fit<-brownie.lite(tree,x)
> ## use it
> logLik(fit)
> AIC(fit)
>
> All the best, Liam
>
> Liam J. Revell
> Associate Professor, University of Massachusetts Boston
> Profesor Asistente, Universidad Católica de la Ssma Concepción
> web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org
>
> Academic Director UMass Boston Chile Abroad (starting 2019):
> https://www.umb.edu/academics/caps/international/biology_chile
>
> On 9/5/2019 9:13 AM, Karla Shikev wrote:
> > [EXTERNAL SENDER]
> >
> > Dear all,
> >
> > I've been trying to use brownie.lite to implement the tutorial available
> > here (
> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftreethinkers.org%2Ftutorials%2Fmorphological-evolution-in-r%2F&amp;data=02%7C01%7Cliam.revell%40umb.edu%7Cacb98c128374458b48a708d73202efd0%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032860521435814&amp;sdata=rOvlxUCu350av35%2F0BzDM4Zh9H7qYgM12wxrY%2BUxjUE%3D&amp;reserved=0)
> to
> > calculate model-averaged rates of evolution and for model selection (1
> > versus 2 rates). However, the current version of phytools 0.6-99 won't
> > produce AICc estimates. Does anyone know a way around this? Any help
> would
> > be greatly appreciated.
> >
> > thanks a bunch,
> >
> > Karla
> >
> >          [[alternative HTML version deleted]]
> >
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