Dear Karla. In my opinion, it is probably correct to use the number of tips on the tree as the sample size for AICc when estimating the Brownian rate: as the number of independent pieces of information is n-1, just like with an ordinary variance. For other parameters in phylogenetic comparative analyses, the effective sample size may be different, however.
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 9:49 AM, Karla Shikev wrote: > [EXTERNAL SENDER] > > 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/, >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org&data=02%7C01%7Cliam.revell%40umb.edu%7C04607945a9f74968c14e08d73207f67f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032882107478464&sdata=ofsem4h4SNk6g6QFUwD%2BJKO3TsTArNfH9%2BAyYDEjCvY%3D&reserved=0 >> >> 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&data=02%7C01%7Cliam.revell%40umb.edu%7C04607945a9f74968c14e08d73207f67f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032882107478464&sdata=64k6WMtazzmyn0SLRrx2wEA%2F2wkk3%2B%2F3dBS0HtjlUT8%3D&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]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> >> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C04607945a9f74968c14e08d73207f67f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032882107478464&sdata=ZZxjUW5cV1gb9De3yOjb54RCNlFv2WHWr01lnaeEf54%3D&reserved=0 >>> Searchable archive at >> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C04607945a9f74968c14e08d73207f67f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032882107488458&sdata=NUqbn4Yz9gYilJAs7K2mW%2BIANK1%2FmXcpvuIo0Q0h0hw%3D&reserved=0 >>> >> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C04607945a9f74968c14e08d73207f67f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032882107488458&sdata=S0vvcWinbTdWb4T%2BwD9Fk7gFn6gdhpycbArMGgd7cYI%3D&reserved=0 > Searchable archive at > https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C04607945a9f74968c14e08d73207f67f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C0%7C637032882107488458&sdata=NUqbn4Yz9gYilJAs7K2mW%2BIANK1%2FmXcpvuIo0Q0h0hw%3D&reserved=0 > _______________________________________________ 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/
