[R-sig-ME] multiple errors when using glmmADMB

Fri Jul 27 11:28:07 CEST 2018

Hi Mollie,

Thanks a lot, I have tried that and it runs the model. My concern is that I cannot include zero inflation of the data in this model. Any ideas for that?

Cheers
Udita

On 27/07/18, 9:47 AM, "Mollie Brooks" <mollieebrooks using gmail.com> wrote:

    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
    >> 
    >> 
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    >> 
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