[R-sig-ME] glmmADMB error messages with percentage cover data (Elwyn Sharps)

[Highland Statistics Ltd]

>
> I have collected data on % cover of a variety of
> plant species on heathland (in relation to nesting birds) and am interested in
> testing the effect of density of grazing ponies, the proximity to nest site
> (%cover measured at 1 and 10m from the nest) and the age of the nest (as a
> control for vegetation being measured at nests of different ages). The
> response is percentage cover and contains many zeros (see attached
> data for an example).
>
>
> I have tried using glmmADMB, with family=
> binomial and zero inflation=T. The response was created using cbind e.g.
> y<-(cbind(Data$Plant_cover, Data$Plant_empty)), where Plant cover = % cover
> and Plant empty = 100-Plant cover.
>
>
> Example model:
>
> Fit1<-glmmadmb(y~Grazing*proximity+Age+(1|site),data=Heath,zeroInflation=TRUE,family="binomial")
>


See the help file of glmmadmb:

zeroInflation:   whether a zero-inflated model should be fitted (only 
"poisson" and "nbinom" families).

With emphasis on the last part in this sentence.

Kind regards,


Alain


> The majority of the models for Species
> 1 have been running fine, however I have been getting the occasional error
> message and for Species 2, all models give an error message.
>
>
> Example error messages:
>
> Parameters were estimated, but not standard errors
> were not: the most likely problem is that the curvature at MLE was zero or
> negative
>
> Error in glmmadmb(w ~ Grazing * proximity + Age + (1 | site), data =
> heathland,  :
>
>    The function maximizer failed (couldn't find STD file) Troubleshooting
> steps include (1) run with 'save.dir' set and inspect output files; (2) change
> run parameters: see '?admbControl'
>
> Warning message:
>
> In glmmadmb(w ~ 1 + (1 | site), data = heathland, zeroInflation = T,  :
>
>    Convergence failed:log-likelihood of gradient= -0.269018
>
>
>
> I just wanted to check that this is a sensible
> way to deal with these data and if there is anything that I should be doing to
> remedy the error messages? I've tried some other options, e.g. Arc sine
> transformation couldn't deal with the excess zeros. I've also considered
> quasibinomial in lme4, but have seen Doug Bates comments on the unreliability
> of the model output.
>
>   
>
> Any advice would be very much appreciated.
> All the best
> Elwyn 		 	   		   		 	   		
>
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> End of R-sig-mixed-models Digest, Vol 95, Issue 24
> **************************************************
>

-- 
Dr. Alain F. Zuur

First author of:
1. Beginner's Guide to GAMM with R (2014).
2. Beginner's Guide to GLM and GLMM with R (2013).
3. Beginner's Guide to GAM with R (2012).
4. Zero Inflated Models and GLMM with R (2012).
5. A Beginner's Guide to R (2009).
6. Mixed effects models and extensions in ecology with R (2009).
7. Analysing Ecological Data (2007).

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