zero-inflation beta or gamma model?
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
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Dr. Alain F. Zuur Highland Statistics Ltd. 9 St Clair Wynd AB41 6DZ Newburgh, UK Email: highstat at highstat.com URL: www.highstat.com