[R-sig-ME] zero-inflation beta or gamma model?

[Highland Statistics Ltd]

> Hi,
>
> I have a response variable expressed as proportion that varies from 0 to 1. The variable is highly left skewed, and about half of the values are zeros. I found a previous question related to a possible use of beta family together with a zero-inflation, to which B. Bolker replied it was possible using a hurdle approach in the glmmTMB package. I rescaled the response to 0 - 0.999 (only 1 value is = 1) and tried this approach.
>
> However, when I run
>
> mod<-glmmTMB(TerrBeta2 ~ 1 + (1|Family/Genus/Species) + (1|Site/Year/Month), family=beta_family(), ziformula=~., data=data2)
>
> I get the following error message (looks like the ziformula argument is ignored)
>
> Error in eval(family$initialize) : y values must be 0 < y < 1
>
> I also tried to specify the family differently
>
> mod<-glmmTMB(TerrBeta2 ~ 1 + (1|Family/Genus/Species) + (1|Site/Year/Month), family=list(family="beta",link="logit"), ziformula=~., data=data2)
>
> But I get this

Your model is very complication in terms of the random effects. 
Besides...I am not a fan of using year and month as random effects.

As to the zero inflation aspect of the beta GLMM....apologies for 
self-citing here, but Chapter 16 in this book:

http://highstat.com/index.php/beginner-s-guide-to-zero-inflated-models

has a fully worked out example using the zero-inflated beta GLMM with 
2-way nested random effects.

And Chapter 23 in Volume II of this one

http://highstat.com/index.php/beginner-s-guide-to-regression-models-with-spatial-and-temporal-correlation

touches on zero-inflated beta GAMs with spatial correlation and barrier 
models.

Kind regards,
Alain




> Error in nlminb(start = par, objective = fn, gradient = gr, control = control$optCtrl) :
>    gradient function must return a numeric vector of length 15
> In addition: Warning messages:
> 1: In glmmTMB(TerrBeta2 ~ 1 + (1 | Family/Genus/Species) + (1 | Site/Year/Month),  :
>    some components missing from ‘family’: downstream methods may fail
> 2: In mkTMBStruc(formula, ziformula, dispformula, combForm, mf, fr,  :
>    specifying ‘family’ as a plain list is deprecated
> 3: In nlminb(start = par, objective = fn, gradient = gr, control = control$optCtrl) :
>    NA/NaN function evaluation
> Timing stopped at: 0.626 0.065 0.689
>
> Any suggestion?
>
> Another option to avoid rescaling the variable may be using the gamma family, but I get into the same error messages.
> Any suggestion would be greatly appreciated!
>
> Best
>
>
>
>
>          [[alternative HTML version deleted]]
>
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Dr. Alain F. Zuur
Highland Statistics Ltd.
9 St Clair Wynd
AB41 6DZ Newburgh, UK
Email: highstat using highstat.com
URL:   www.highstat.com