Re: [R] What happen for Negative binomial link in Lmer fonction?
Dear R users, As I have no answer to my las reply i try again. If the binomal negative link has never been implemented in the lmer fonction, and as it was working when I did it some months ago, What kind of result did I get? This is the exemple of the answer of R when i was using lmer with negative binomal family: m1a<-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method="Laplace",data=manu) summary(m1a) Generalized linear mixed model fit using Laplace Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) Data: manu Family: Negative Binomial(log link) AIC BIC logLik deviance 125.1 147.6 -54.57109.1 Thank you for your answers, Best Regards Emmanuelle E. Robardet wrote: > > Thank you for your answers, > > I have an exemple of that i was using: > > m1a<-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method="Laplace",data=manu) > summary(m1a) > Generalized linear mixed model fit using Laplace > Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) >Data: manu > Family: Negative Binomial(log link) >AIC BIC logLik deviance > 125.1 147.6 -54.57109.1 > > I think It was the version lme4 0.9975-10. > Unfortunately, I have this version no more available on my computer.. > I wonder if this old results are still valid.. > > > Ben Bolker wrote: >> >> >> >> ROBARDET Emmanuelle wrote: >>> >>> Dear R users, >>> I'm performing some GLMMs analysis with a negative binomial link. >>> I already performed such analysis some months ago with the lmer() >>> function but when I tried it today I encountered this problem: >>> Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative >>> Binomial' >>> >>> Does anyone know if the negative binomial family has been removed from >>> this function? >>> I really appreciate any response. >>> Emmanuelle >>> >>> >> >> I would be extremely surprised if this worked in the past; to >> the best of my knowledge the negative binomial family has >> never been implemented in lmer. One could in principle >> do a glmmPQL fit with the negative binomial family >> (with a fixed value of the overdispersion parameter). >> glmmADMB is another option. >> Can you say which version etc. you were using??? >> >> Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org >> >> > > -- View this message in context: http://old.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26439076.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What happen for Negative binomial link in Lmer
Patrick Giraudoux wrote: > > Seems the message below and the thread have reveived no attention/answer. > The output presented is quite tricky. Looks like if lmer (lme4 0.9975-10) > has accepted a negative binomial link with reasonable estimates, although > it was not designed for... > > What can one think about result validity ? > > Well, I can believe that lme4 0.9975-10 may have allowed families that were not hard-coded (e.g., negative binomial with a fixed overdispersion parameter). I would expect the results to be reasonable. However, lme4 has gone through a lot of changes. If you have an old copy around and your results pass all the sanity checks you can think of, I might go ahead and use them -- otherwise you will have to deal with glmmADMB, WinBUGS, AD Model Builder (or lme4 with quasipoisson family) ... -- View this message in context: http://old.nabble.com/Re%3A-What-happen-for-Negative-binomial-link-in-Lmer-tp26194594p26198718.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What happen for Negative binomial link in Lmer
Seems the message below and the thread have reveived no attention/answer. The output presented is quite tricky. Looks like if lmer (lme4 0.9975-10) has accepted a negative binomial link with reasonable estimates, although it was not designed for... What can one think about result validity ? Best Patrick Message: 34 Date: Thu, 29 Oct 2009 06:51:24 -0700 (PDT) From: "E. Robardet" Subject: Re: [R] What happen for Negative binomial link in Lmer fonction? To: r-help@r-project.org Message-ID: <26113408.p...@talk.nabble.com> Content-Type: text/plain; charset=us-ascii Thank you for your answers, I have an exemple of that i was using: m1a<-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method="Laplace",data=manu) summary(m1a) Generalized linear mixed model fit using Laplace Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) Data: manu Family: Negative Binomial(log link) AIC BIC logLik deviance 125.1 147.6 -54.57109.1 I think It was the version lme4 0.9975-10. Unfortunately, I have this version no more available on my computer.. I wonder if this old results are still valid.. Ben Bolker wrote: > > > > > > > > ROBARDET Emmanuelle wrote: > >> >> >> >> Dear R users, >> >> I'm performing some GLMMs analysis with a negative binomial link. >> >> I already performed such analysis some months ago with the lmer() >> >> function but when I tried it today I encountered this problem: >> >> Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative >> >> Binomial' >> >> >> >> Does anyone know if the negative binomial family has been removed from >> >> this function? >> >> I really appreciate any response. >> >> Emmanuelle >> >> >> >> >> > > > > I would be extremely surprised if this worked in the past; to > > the best of my knowledge the negative binomial family has > > never been implemented in lmer. One could in principle > > do a glmmPQL fit with the negative binomial family > > (with a fixed value of the overdispersion parameter). > > glmmADMB is another option. > > Can you say which version etc. you were using??? > > > > Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org > > > > > -- View this message in context: http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26113408.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What happen for Negative binomial link in Lmer fonction?
Thank you for your answers, I have an exemple of that i was using: m1a<-lmer(atpos~ninter+saison+milieu*zone+(1|code),family=neg.bin(0.429),method="Laplace",data=manu) summary(m1a) Generalized linear mixed model fit using Laplace Formula: atpos ~ ninter + saison + milieu * zone + (1 | code) Data: manu Family: Negative Binomial(log link) AIC BIC logLik deviance 125.1 147.6 -54.57109.1 I think It was the version lme4 0.9975-10. Unfortunately, I have this version no more available on my computer.. I wonder if this old results are still valid.. Ben Bolker wrote: > > > > ROBARDET Emmanuelle wrote: >> >> Dear R users, >> I'm performing some GLMMs analysis with a negative binomial link. >> I already performed such analysis some months ago with the lmer() >> function but when I tried it today I encountered this problem: >> Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative >> Binomial' >> >> Does anyone know if the negative binomial family has been removed from >> this function? >> I really appreciate any response. >> Emmanuelle >> >> > > I would be extremely surprised if this worked in the past; to > the best of my knowledge the negative binomial family has > never been implemented in lmer. One could in principle > do a glmmPQL fit with the negative binomial family > (with a fixed value of the overdispersion parameter). > glmmADMB is another option. > Can you say which version etc. you were using??? > > Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org > > -- View this message in context: http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26113408.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What happen for Negative binomial link in Lmer fonction?
On Thu, Oct 22, 2009 at 1:39 PM, Ben Bolker wrote: > ROBARDET Emmanuelle wrote: >> >> Dear R users, >> I'm performing some GLMMs analysis with a negative binomial link. >> I already performed such analysis some months ago with the lmer() function >> but when I tried it today I encountered this problem: >> Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative >> Binomial' >> >> Does anyone know if the negative binomial family has been removed from >> this function? >> I really appreciate any response. >> Emmanuelle >> >> > > I would be extremely surprised if this worked in the past; to > the best of my knowledge the negative binomial family has > never been implemented in lmer. I too would be extremely surprised if it had worked in the past, considering that I have never implemented it. I did exchange email with Bill Venables about it and we formulated what seems to be a reasonable approach but it hasn't made it to the top of the "To Do" list yet. Right now the big push is on code to profile the log-likelihood with respect to the parameters so we can actually get confidence intervals and, the holy grail of mixed-modeling, p-values. > One could in principle > do a glmmPQL fit with the negative binomial family > (with a fixed value of the overdispersion parameter). > glmmADMB is another option. > Can you say which version etc. you were using??? > > Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org > -- > View this message in context: > http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26015140.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] What happen for Negative binomial link in Lmer fonction?
ROBARDET Emmanuelle wrote: > > Dear R users, > I'm performing some GLMMs analysis with a negative binomial link. > I already performed such analysis some months ago with the lmer() function > but when I tried it today I encountered this problem: > Erreur dans famType(glmFit$family) : unknown GLM family: 'Negative > Binomial' > > Does anyone know if the negative binomial family has been removed from > this function? > I really appreciate any response. > Emmanuelle > > I would be extremely surprised if this worked in the past; to the best of my knowledge the negative binomial family has never been implemented in lmer. One could in principle do a glmmPQL fit with the negative binomial family (with a fixed value of the overdispersion parameter). glmmADMB is another option. Can you say which version etc. you were using??? Follow-ups should probably be sent to r-sig-mixed-mod...@r-project.org -- View this message in context: http://www.nabble.com/What-happen-for-Negative-binomial-link-in-Lmer-fonction--tp26013041p26015140.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
