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

[Luca Santini]

It works, thanks!

Luca


> On 9 Jan 2020, at 15:26, Ben Bolker <bbolker using gmail.com> wrote:
> 
>  The zero-inflation stuff is only available in the development
> version of glmmTMB at the moment ... although we hope to submit a new
> version to CRAN in the very near future.  (See
> https://github.com/glmmTMB/glmmTMB/blob/master/README.md for
> instructions on installing the development version.)
> 
> On Thu, Jan 9, 2020 at 5:28 AM Luca Santini <luca.santini.eco using gmail.com> wrote:
>> 
>> 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$initialize) : y values must be 0 < y < 1
>> 
>> I also tried to specify the family differently
>> 
>> mod<-glmmTMB(TerrBeta2 ~ 1 + (1|Family/Genus/Species) + (1|Site/Year/Month), family=list(family="beta",link="logit"), ziformula=~., data=data2)
>> 
>> But I get this
>> 
>> Error in nlminb(start = par, objective = fn, gradient = gr, control = control$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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>> 
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