[R-sig-ME] Overdispersion and model selection: glmmadmb vs. glmer

Paul Johnson paul.johnson at glasgow.ac.uk
Mon Sep 2 13:03:57 CEST 2013 

PS This paper discusses in detail how to assess Poisson-lognormal model fit by plotting residuals at each heirarchical level: 
Elston, D.A., Moss, R., Boulinier, T., Arrowsmith, C. & Lambin, X. (2001). Analysis of aggregation, a worked example: numbers of ticks on red grouse chicks. Parasitology, 122, 563–9.
http://abdn.ac.uk/lambin-group/Papers/Paper%2041%202001%20Elston%20Tick%20aggregation%20Parasitology.pdf



On 2 Sep 2013, at 11:34, Paul Johnson <Paul.Johnson at glasgow.ac.uk> wrote:

> Hi Luca,
> 
> (To avoid confusion, I'm the Glasgow Paul Johnson, not the Kansas one - incidentally there's also a statistician of the same name in Oxford, a former colleague, whom we can only hope stays out of this discussion).
> 
> Below is some code for comparing residuals between Poisson-lognormal glmer and NB glmmadmb fits. I find this useful as a quick way of spotting bad fits (aiming, roughly, for homoscedasticity and absence of a trend). However I agree with the other PJ that plotting the predictions and prediction intervals from both models over the data is a better way to compare the two fits.
> 
> Best wishes,
> Paul
> 
> 
>  plot.glmer<-
>    function(mer.fit,type="pearson",overdispersion.term=NULL)
>    {
>      require(AICcmodavg)
>      if(is.null(overdispersion.term))
>      {
>        Fitted<-fitted(mer.fit)
>        Residuals=resid(mer.fit,type)
>      } else
>        {
>          response<-model.frame(mer.fit)[[1]]
>          od.ranef<-lme4::ranef(mer.fit)[[overdispersion.term]][[1]]
>          if(length(response)!=length(od.ranef) || fam.link.mer(mer.fit)$family!="poisson" || fam.link.mer(mer.fit)$link!="log")
>            stop("Model is not lognormal-Poisson. Cannot use overdispersion term.")
>          Fitted<-exp(log(fitted(mer.fit))-od.ranef)
>          Residuals<-(response - Fitted)/sqrt(Fitted+(Fitted^2)*c(exp(lme4::VarCorr(mer.fit)[[overdispersion.term]])-1))
>        }
>      plot.data<-data.frame(Fitted=Fitted,Residuals=Residuals)
>      plot.data$loess.line<-predict(loess(Residuals~Fitted,data=plot.data))
>      plot.data<-plot.data[order(plot.data$Fitted),]
>      plot(plot.data[,c("Fitted","Residuals")])
>      abline(h=0)
>      points(plot.data[,c("Fitted","loess.line")],type="l",col="red")
>      hist(plot.data$Residuals,xlab="Residuals",main="")
>    }
> 
>  par(mfrow=c(3,2))
>  plot.glmer(pois.glmm)  # overdispersion effects in the fitted values, so expect a trend
>  plot.glmer(pois.glmm,overdispersion.term="ons")   # 'detrended' by moving OD effects to the residuals
>  plot.glmer(nb.glmm)  # compare with residuals from NB GLMM
> 
> On 2 Sep 2013, at 08:32, Luca Corlatti <luca.corlatti at boku.ac.at> wrote:
> 
>> Dear Paul, thanks for your answer. Surely I can offer a link to the data, here it is:
>> https://www.dropbox.com/s/3i22ovc588kahsk/dataset.csv
>> 
>> 
>> obs=observation level
>> id=animal identity
>> age=age class of the ind.
>> mat_be=individual mating behavior (territorial vs non-territorial)
>> month, year, elevation=when & at which elevation (a.s.l.) the sampling occurred
>> testosterone, cortisol=testosterone and cortisol levels registered for each individual
>> hr=home range of each individual (on a monthly basis)
>> larvae=number of parasite larvae counted (response variable, on a monthly basis)
>> 
>> 
>> The key point, here, is that not being statistician (I'm a behavioral ecologist) I don't quite get why 2 methods which should ideally yield similar results, in fact do not. I realize the question may seem to vague, and likely fairly trivial, but I guess other researchers, in my same situation, would simply ask "ok, I have overdispersed data, shall I go for glmer with (1|obs) or glmmadmb?".
>> 
>> 
>> Without getting too complicated (e.g. model selection and averaging), even if you run a very simple model, just to check if the number of counted larvae differ between age classes, the estimates differ between glmmadmb and glmer:
>> 
>> 
>> mod1<-glmmadmb(larvae~age+(1|year:month)+(1|id), family="nbinom", zeroInflation=FALSE, data=dataset)
>> mod2<-glmer(larvae~age+(1|year:month)+(1|id)+(1|obs), family=poisson, data=dataset)
>> 
>> 
>> 
>> If you try with the full additive models:
>> 
>> 
>> mod1<-glmmadmb(larvae~age+mat_be+elevation+log(cortisol)+log(testosterone)+log(hr)+(1|year:month)+(1|id), family="nbinom", zeroInflation=FALSE, data=dataset)
>> mod2<-glmer(larvae~age+mat_be+elevation+log(cortisol)+log(testosterone)+log(hr)+(1|year:month)+(1|id)+(1|obs), family=poisson, data=dataset)
>> 
>> 
>> 
>> the summary, just as well, gives different results (I used log-transformation as it seems to linearize the relationship with the response variable).
>> 
>> 
>> Hope this can help!
>> Luca
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>>>>> Paul Johnson <pauljohn32 at gmail.com> 01/09/13 22.04 >>>
>> Hi, I'm a different Paul Johnson :) (Had a shock reviewing this thread thinking I'd posted a message that I did not recognize at all).
>> 
>> 
>> The question is too vague now.  Aside from agreeing with another Paul Johnson that there are differences between the negative binomial and random-effects interpretations, I can't see where this is leading. The negative binomial model magnifies variance for larger values of the expected outcome, but it does not, by design, include "clustering" of variances. On the other hand, the glmer model you describe is a model of a "clustered" random effect that generates variety among outcomes for a given set of other predictors.  Both can cause "overdispersion" in the sense you notice, but they really are substantively different explanations of it.
>> 
>> How about you show us the estimated models to let us see what's so different, in your view?
>> 
>> Apart from the residual diagnostics you are concerned about, what about the substantively important parameters and predicted values?  I guess that's a little interesting because, when I last checked, glmer did not have a predict version in the CRAN package (was in testing Rforge version in 2012).
>> 
>> Are the predicted values of outcomes similar in the 2 models? How does it look when you create a scatterplot of the predicted values of the GLMMADMB model versus the glmer model?
>> 
>> 
>> If you post the code that leads to the different diagnostic scatterplots and offer a link to the data, this might be interesting to make into one of the working examples for the mixed models wiki.  I could assign some grad students on this to work it out fully.
>> 
>> 
>> 
>> 
>> 
>> On Wed, Aug 28, 2013 at 4:46 AM, Luca Corlatti <luca.corlatti at boku.ac.at> wrote:
>> Thanks, Paul, it's somewhat consoling to read somebody else had the same thoughts!
>> Thanks a lot for your advice. What I miss here, though, is why the results of the model selection differ so much between glmmadmb and glmer, hence what is preferable between the two approaches...
>> Cheers,
>> Luca
>> 
>> 
>> 
>> 
>>>>> Paul Johnson <paul.johnson at glasgow.ac.uk> 26/08/13 0.29 >>>
>> Hi Luca,
>> 
>> I've also seen this difference in residuals from a glmmadmb nbinom2 fit and a lognormal-Poisson fit with glmer. Generally the residuals X fitted plot from glmmadmb looks good (homoscedastic, no trend) while that from the lognormal-Poisson looks wrong (strong curve climbing sharply from negative to positive before plateauing). After some head-scratching I've decided that this isn't a problem.
>> 
>> The reason for the discrepancy is that the fitted values from the lognormal-Poisson fit include the overdispersion random effects, i.e. everything expect the Poisson variation, while the NB fitted values don't, because overdispersion is intrinsic to the NB, not an added random effect. Because the obs-level random effect is there to increase the spread of the Poisson distribution, it's almost inevitable with strong overdispersion that the residuals with low fitted values will be negative while those with high fitted values will be positive.
>> 
>> The way to get a fair comparison between the two is to remove the obs-level random effect from the fitted values of the lognormal-Poisson, leaving just the fixed effects and any other random effects. I find this generally gives a residual pattern much more similar to NB in glmmadmb:
>> 
>>  Fitted <- exp(log(fitted(mod)) - ranef(mod)$obs[[1]])
>>  Resid <- (dat$response - Fitted) / sqrt(Fitted + (Fitted^2) * c(exp(VarCorr(mod)$obs) - 1))
>>  plot(Fitted, Resid)
>> 
>> # obs is the name of the factor used for the obs-level random effect,
>> # mod is the glmer fit of the lognormal-Poisson model, dat$response are the responses, and
>> # the bit inside the sqrt() is the variance function for the lognormal-Poisson
>> 
>> Generally I don't find that the model estimates and SEs differ much though.
>> 
>> Best wishes,
>> Paul
>> 
>> 
>> Paul Johnson
>> 
>> Institute of BAH&CM
>> Graham Kerr Building
>> University of Glasgow
>> Glasgow G12 8QQ
>> 
>> http://www.gla.ac.uk/researchinstitutes/bahcm/staff/pauljohnson/
>> http://www.stats.gla.ac.uk/~paulj/index.html
>> 
>> 
>> ________________________________________
>> From: r-sig-mixed-models-bounces at r-project.org [r-sig-mixed-models-bounces at r-project.org] On Behalf Of Luca Corlatti [luca.corlatti at boku.ac.at]
>> Sent: 25 August 2013 20:18
>> To: r-sig-mixed-models at r-project.org
>> Subject: [R-sig-ME] Overdispersion and model selection: glmmadmb vs. glmer
>> 
>> Dear all,
>> 
>> 
>> I recently ran a model selection (AIC-based) to investigate the role of several etho-ecological factors in shaping the emission of parasites in my study species. My data are counts showing overdispersion. I therefore fitted my models using the function glmmadmb with family=nbinom. Visual inspection of residuals (normality, heteroschedasticity, independence) suggested the global model fitted the data adequately, and I'm pretty happy with the results of my analysis. For the sake of curiosity, however, I tried to re-run the model selection using the function glmer, with family=poisson, adding the observation-level as a random factor (1|obs) to account for overdispersion, as recently suggested. In this case, however, visual inspection of residuals for the global model were not very satisfactory. After running the model selection, the results were quite different from those obtained with glmmadmb (not dramatically different, but still...). Given I have no deep knowledge into th!
> e philosophy behind the use of glmer with (1|obs), I was wondering:
>> 1) when one should rely on the use of glmer with (1|obs) to account for overdispersion? (i.e. is the check of residuals for the global model the key issue here?)
>> 2) why did I find such a difference in the outcome of the 2 model selections?
>> Kind regards,
>> Luca
>> 
>> 
>> 
>> 
>> 
>> 
>> _______________________________________________
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>> 
>> 
>> 
>> 
>> 
>> --
>> Paul E. Johnson
>> Professor, Political Science      Assoc. Director
>> 1541 Lilac Lane, Room 504      Center for Research Methods
>> University of Kansas                 University of Kansas
>> http://pj.freefaculty.org               http://quant.ku.edu
>> 
>> 
>> 
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