[R-sig-ME] glmmADMB errors

[Mollie Brooks]

Hi Andreu,

A zero-inflated Poisson distribution is not appropriate because biomass is
not count data. I would recommend checking what distribution other
researchers in your field are using. Maybe you want to first model zero vs
non-zero and then model the non-zero biomasses separately. The log of
non-zero biomasses could be modeled with a normal distribution. Or on the
natural scale, they could be Gamma or Tweedie. Or maybe a zero-inflated
continuous positive distribution (e.g. Gamma or Tweedie) makes sense for
all of the biomasses. These zero-inflated models could be fit in glmmTMB.

cheers,
Mollie

On Thu, Oct 19, 2017 at 2:03 PM, andreu blanco <andreu.blanco at gmail.com>
wrote:

>  Dear list members, I am starting with generalized mixed models and I am
> having some trouble I hope someone could help me with.
>
> We are trying to understand the invasiveness of algae inside and outside
> MPA, to do so our sampling was set with a nested desing:
>
> Protected vs nonProtected
> 4 Locations (protected) vs 4 Locations (nonProtected)
> Exposed vs Semiexposed at each location
> 1 transect per sampling point (total 16)
> 5 quadrants per transect
>
> str(dataGLMMADMB)
> 'data.frame':   80 obs. of  4 variables:
>  $ Location: Factor w/ 4 levels "Cies1","Cies2",..: 1 1 1 1 1 1 1 1 1 1 ...
>  $ Protection: Factor w/ 2 levels "Control","Protected": 1 1 1 1 1 2 2 2 2
> 2 ...
>  $ Exposure: Factor w/ 2 levels "Exposed","Semiexposed": 1 1 1 1 1 1 1 1 1
> 1 ...
>  $ Biomass: num  124.8 104.8 139.2 102.6 62.9 ...
>
>
> First I ran it as a Poission distribution (after round the Biomass values)
> to be able to fit a zeroInflation model:
> > Model_ADMB_P<-glmmadmb(Biomass~Protection+Exposure+
> Protection:Exposure+(1|
> Protection/Location),data=GLMMADMB_P, zeroInflation=TRUE,
> family="Poisson")
> Parameters were estimated, but standard errors were not: the most likely
> problem is that the curvature at MLE was zero or negative
> Error in glmmadmb(Biomass ~ Protection + Exposure + Protection:Exposure +
> :
>   The function maximizer failed (couldn't find parameter file)
> Troubleshooting steps include (1) run with 'save.dir' set and inspect
> output files; (2) change run parameters: see '?admbControl';(3) re-run with
> debug=TRUE for more information on failure mode
> Además: Warning message:
> comando ejecutado 'C:\WINDOWS\system32\cmd.exe /c glmmadmb -maxfn 500
> -maxph 5 -noinit -shess' tiene estatus 1
>
> Then I though that since my data is continuous I'd better run the model
> with a gamma family, however, when I do run it with gamma I got the
> following error:
> > Model_ADMB_G<-glmmadmb(Biomass~Protection+Exposure+
> Protection:Exposure+(1|
> Protection/Location),data=GLMMADMB_P, family="gamma")
>
> Error in glmmadmb(Biomass ~ Protection + Exposure + Protection:Exposure +
> :
>   The function maximizer failed (couldn't find parameter file)
> Troubleshooting steps include (1) run with 'save.dir' set and inspect
> output files; (2) change run parameters: see '?admbControl';(3) re-run with
> debug=TRUE for more information on failure mode
> Además: Warning message:
> comando ejecutado 'C:\WINDOWS\system32\cmd.exe /c glmmadmb -maxfn 500
> -maxph 5 -noinit -shess' tiene estatus 1
>
> However, when I run it as a Poisson distribution with zeroInflated values
> but with no nested design and Location effect either, it ran ok
> > Model_ADMB_P1<-glmmadmb(Biomass~Protection*Exposure,data=GLMMADMB_P,
> zeroInflation=TRUE, family="Poisson")
> > summary(Model_ADMB_P1)
>
> Call:
> glmmadmb(formula = Biomass ~ Protection * Exposure, data = GLMMADMB_P,
>     family = "Poisson", zeroInflation = TRUE)
>
> AIC: 1570.7
>
> Coefficients:
>                                          Estimate Std. Error z value
> Pr(>|z|)
> (Intercept)                              4.71e+00   3.18e-02   148.0
>  <2e-16
> ProtectionProtected                     -5.53e-01   5.00e-02   -11.1
>  <2e-16
> ExposureSemiexposed                     -3.83e+01   2.22e+05     0.0
> 1
> ProtectionProtected:ExposureSemiexposed  3.64e+01   2.22e+05     0.0
> 1
>
> (Intercept)                             ***
> ProtectionProtected                     ***
> ExposureSemiexposed
> ProtectionProtected:ExposureSemiexposed
> ---
> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
>
> Number of observations: total=80
> Zero-inflation: 0.30908  (std. err.:  0.071433 )
>
> Log-likelihood: -780.37
> >
>
>
> I can not understat the solutions to these errors, can anyone please help
> me out?
> I really appreciate it!
>
> Thanks in advance,
>
> --
> Andreu Blanco Cartagena
>
>
>
> Si no és imprescindible, no imprimeixis aquest e-mail. Estalviar paper
> ajuda a protegir el medi ambient.
>
> Si no es imprescindible, no imprimas este e-mail. Ahorrar papel ayuda a
> proteger el medio ambiente.
>
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