[R-sig-ME] multiple errors when using glmmADMB
Mollie Brooks
mollieebrook@ @ending from gm@il@com
Fri Jul 27 10:46:55 CEST 2018
Hi Udita,
It looks like this is binomial data. You probably want logistic regression like this
library(lme4)
m_glmer <- glmer(cbind(No.of.chicks, Clutch.size-No.of.chicks)~ laying.date.julian.day.zscale + tmean.zscale + (1|YEAR), data = hungary_breeding, , family = binomial)
cheers,
Mollie
> On 26Jul 2018, at 22:03, Bansal, Udita <udita.bansal17 using imperial.ac.uk> wrote:
>
> I am measuring breeding success as number of chicks produced out of number of eggs laid. So, the values range from 0 to 1 including decimal values. Although, that was just a warning. Should I be too concerned about that?
>
> My model statement is as follows:
> m_admb <- glmmadmb( breeding.success ~ laying.date.julian.day.zscale + tmean.zscale + (1|YEAR) ,
> data = hungary_breeding, zeroInflation = TRUE, family = "nbinom", link = "logit")
>
> Summary for relevant columns of my data:
>
> YEAR No.of.chicks Clutch.size laying_date tmean prec
> 1988:16 Min. :0.000 Min. :2.000 Min. :1988-04-22 Min. : 3.45 Min. : 0.000
> 1989:25 1st Qu.:0.000 1st Qu.:3.000 1st Qu.:1990-05-07 1st Qu.:11.35 1st Qu.: 0.000
> 1990:45 Median :0.000 Median :3.000 Median :1991-05-09 Median :15.12 Median : 0.000
> 1991:65 Mean :1.021 Mean :2.946 Mean :1991-05-24 Mean :14.62 Mean : 2.285
> 1992:46 3rd Qu.:3.000 3rd Qu.:3.000 3rd Qu.:1992-05-15 3rd Qu.:17.95 3rd Qu.: 1.050
> 1993:24 Max. :3.000 Max. :3.000 Max. :1994-06-16 Max. :27.05 Max. :55.200
> 1994:19
> breeding.success clutch.volume laying.date.julian.day tmean.zscale.V1 prec.zscale.V1
> Min. :0.0000 Min. :15.82 Min. : 82.0 Min. :-2.5607265 Min. :-0.559014
> 1st Qu.:0.0000 1st Qu.:24.60 1st Qu.:115.0 1st Qu.:-0.7638887 1st Qu.:-0.559014
> Median :0.0000 Median :25.89 Median :129.0 Median : 0.0947269 Median :-0.559014
> Mean :0.3438 Mean :25.52 Mean :132.3 Mean :-0.0190444 Mean : 0.006583
> 3rd Qu.:1.0000 3rd Qu.:27.06 3rd Qu.:148.2 3rd Qu.: 0.7372670 3rd Qu.: 0.209975
> Max. :1.0000 Max. :29.83 Max. :186.0 Max. : 2.8070422 Max. : 3.762186
>
> laying.date.julian.day.zscale.V1
> Min. :-2.2850626
> 1st Qu.:-0.7846733
> Median :-0.1481445
> Mean : 0.0000000
> 3rd Qu.: 0.7270826
> Max. : 2.4434370
>
> I will try glmmTMB as well now.
>
> Thanks
> Udita
>
> On 26/07/18, 7:41 PM, "R-sig-mixed-models on behalf of Ben Bolker" <r-sig-mixed-models-bounces using r-project.org on behalf of bbolker using gmail.com> wrote:
>
>
> The first thing that pops out is the "non-integer response values in
> discrete family" warning. How are you measuring breeding success? Can
> you show us your whole glmmadmb() statement, and maybe a summary() of
> the relevant columns of your data set?
>
> I'll also make the now-blanket statement that you may have better
> luck moving forward with glmmTMB.
>
> cheers
> Ben Bolker
>
> On 2018-07-26 12:57 PM, Bansal, Udita wrote:
>> Hi all,
>>
>> I was trying to use the glmmADMB package but ran into some errors. I’ve
>> noticed that other people have run into similar errors but there doesn’t
>> seem to be a solution online. It would be great help if anyone could
>> provide any insights on it.
>>
>> I am using it for running a zero-inflated mixed-effects binomial model.
>> The errors are as follows:
>>
>> 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(breeding.success ~ laying.date.julian.day.zscale +
>> tmean.zscale + :
>> 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
>> In addition: Warning messages:
>> 1: In glmmadmb(breeding.success ~ laying.date.julian.day.zscale +
>> tmean.zscale + :
>> non-integer response values in discrete family
>> 2: running command './glmmadmb -maxfn 500 -maxph 5 -noinit -shess' had
>> status 1
>>
>> Any kind of help will be greatly appreciated.
>>
>> Bests
>> Udita Bansal
>>
>>
>> [[alternative HTML version deleted]]
>>
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