[R-sig-eco] Fitting a GLMM to a zero-inflated continuous data with glmmTMB

[Mollie Brooks]

Hi Vasco,

With only 20 observations, you probably need to simplify your model. The best you can really hope for is to estimate 2 parameters. First try dropping (1|Plot:Grazing).

The Tweedie distribution is also available now. Try family=tweedie(link = "log").

cheers,
Mollie

> On 17Feb 2018, at 5:54, Vasco Silva <silvadavasco at gmail.com> wrote:
> 
> Hi,
> 
> I am trying to fit a GLMM on biomass for each individual species using
> glmmTMB but I got the following warning messages. I start to model the
> zeros in a binomial model and the non-zeros in Gamma.
> 
>> str(biomass)
> 'data.frame': 20 obs. of  15 variables:
> $ Plot           : Factor w/ 10 levels "P1","P10","P2",..: 1 3 4 5 6 7 8 9
> 10 2 ...
> $ Grazing        : Factor w/ 2 levels "Fenced","Unfenced": 1 1 1 1 1 1 1 1
> 1 1 ...
> $ sp1         : num  247.61 10.9 0 24.92 2.14 ...
> $ sp2         : num  244 0 0 2907 0 ...
> $ sp3         : num  2147 2410 1030 1227 368 ...
> $ sp3         : num  0 0 0 0 0 ...
> 
> ##
> m0<-glmmTMB(sp2.positive ~ Grazing+(1|Plot)+(1|Plot:Grazing),
>                  data=biomass,family=binomial(link="logit"))
> 
> $cond
>                 Estimate Std. Error   z value  Pr(>|z|)
> (Intercept)     -1.386333  0.9845106 -1.408144 0.1590885
> GrazingUnfenced  2.233656  1.4343891  1.557218 0.1194188
> 
> $zi
> NULL
> 
> $disp
> NULL
> 
> 
> ##
> m1<-glmmTMB(sp2~Grazing+(1|Plot)+(1|Plot:Grazing),data=biomass[biomass$sp2>0,],
> 
> family=Gamma(link="log"),control=glmmTMBControl(optCtrl=list(iter.max=1e3,eval.max=1e3)))
> 
> #Warning messages:1: In fitTMB(TMBStruc) :
>  Model convergence problem; extreme or very small eigen values
> detected. See vignette('troubleshooting')2: In fitTMB(TMBStruc) :
>  Model convergence problem; false convergence (8). See
> vignette('troubleshooting')
> 
> 
> I check the vignette (troubleshooting) of the package but I can´t fix the
> problem. Should I (re)scale the data? I saw that Tweedie is not (yet)
> implemented in glmmTMB (
> https://cran.r-project.org/web/packages/glmmTMB/vignettes/glmmTMB.pdf). Any
> alternative for modeling zero-inflated continuous data?
> 
> I would greatly appreciate it if someone could help me.
> 
> Cheers.
> 
> Vasco Silva
> 
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> 
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