Hi Franz, If you try the "logistic_MPLE" method, please keep in mind that the result might be a local maximum, not the global maximum. So, you should try several starting points and pick the result returning the maximum penalized likelihood. An ideal situation is all the starting points have the same result.
Lam On Mon, Jul 6, 2015 at 9:24 AM, Cécile Ané <[email protected]> wrote: > Hi Franz, > Could this be a separation issue? Even if you cannot trust the output, > looking at the estimates is informative. It can tell you where the region > of high likelihood might be, and if the convergence problem comes from > alpha going to an extreme, or from the estimated probabilities going to 0 > or 1 (that would indicate a separation issue). > I don't recommend increasing the btol value. > > You could also try the "logistic_MPLE" method, rather than > "logistic_IG10". In my experience, maximizing the penalized likelihood > directly (MPLE) converges better and has better accuracy. > Cecile. > > > On 07/06/2015 03:49 AM, [email protected] wrote: > >> Hello, >> >> after a discussion with Brian (see [R-sig-phylo] corDISC binary coding >> problems, 04/15) I used the method from Ives and Garland (2010), >> which is implemented in the R package phylolm. >> >> The problem is, that the likelihood estimator does not converge. >> Here is my code: >> >> fit <- phyloglm(rot.fill ~ Acrogymnospermae + Magnoliophyta, >> data=dat, phy=data$phy, method = "logistic_IG10", >> btol=20, >> log.alpha.bound = 4, start.beta=NULL, start.alpha=NULL) >> >> And the warning message: >> >> In phyloglm(rot.fill ~ Acrogymnospermae + Magnoliophyta, data = dat, : >> phyloglm failed to converge. >> >> So the function produces an output but the results are not reliable since >> the global maximum is very likely not reached... >> >> I set the btol value to 20 by try and error-increasing (which I don’t >> really understand since I thought the bounds converge to 0 and 1 at about >> btol=10 ??) >> >> Now I have to find suitable start.beta and start.alpha values. But I have >> no clue how to approach them. Can anyone help? >> Why doesn’t phyloglm has a option for iterating starting values? >> >> All the Best, >> Franz >> >> >> >> Franz Krah >> Personal Webpage: http://franzkrah.github.io <http://franzkrah.github.io/ >> > >> University: http://www.biodiv.wzw.tum.de/index.php?id=18 < >> http://www.biodiv.wzw.tum.de/index.php?id=18> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> R-sig-phylo mailing list - [email protected] >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> Searchable archive at >> http://www.mail-archive.com/[email protected]/ >> >> > -- > Cecile Ane > Departments of Statistics and of Botany > University of Wisconsin - Madison > www.stat.wisc.edu/~ane/ > > CALS statistical consulting lab: > www.cals.wisc.edu/calslab/stat_consulting.php > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
