[R-sig-ME] zero-inflation beta or gamma model?
|uc@@@@nt|n|@eco @end|ng |rom gm@||@com
Thu Jan 9 11:28:32 CET 2020
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$initialize) : y values must be 0 < y < 1
I also tried to specify the family differently
mod<-glmmTMB(TerrBeta2 ~ 1 + (1|Family/Genus/Species) + (1|Site/Year/Month), family=list(family="beta",link="logit"), ziformula=~., data=data2)
But I get this
Error in nlminb(start = par, objective = fn, gradient = gr, control = control$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
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!
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