[R-sig-ME] error message using glmmadmb

[Ben Bolker]

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On 12-03-05 08:52 AM, RH Gibson, School Biological Sciences wrote:
> That would make sense as I am able to fit a zero-inflated negative 
> binomial model, but not just the binomial. I have tried poisson
> too, but this gave me the same error message as trying to fit the
> binomial.
> 
> The y variable is a count, offset by a sample total. There is 
> overdispersion and a lot of zeros in the data. Does using the 
> zero-inflated negative binomial make sense here?
> 
> Thanks.

  It very rarely makes sense to use the binomial and the negative
binomial to fit the same set of data; the binomial has a fixed
(typically known) upper limit, the Poisson and NB do not.  (The
exception to this is that people will sometimes use Poisson/NB models
when the upper limit is known but the observed frequency is very low
- -- this is especially common e.g. in epidemiology.)  ZINB, or plain
old NB, probably make the most sense.

  It's more interesting that you get an error message with the
Poisson, which may indicate some glmmADMB instability.  What are the
results of summary(data1)?  How many sites do you have?

  Ben Bolker
> 
> 
> --On 05 March 2012 08:25 -0500 Ben Bolker <bbolker at gmail.com>
> wrote:
> 
>> On 12-03-05 06:00 AM, RH Gibson, School Biological Sciences
>> wrote:
>>> Updated to latest version and now having new problems:
>>> 
>>> m3<- 
>>> glmmadmb(x~nsn*Insect.type+ara*Insect.type+rap*Insect.type+fsize+offset(
>>>
>>> 
logTotal.grains)+(1|Site),data=data1, zeroInflation=TRUE,
>>> family="binomial") Error in glmmadmb(x ~ nsn * Insect.type +
>>> ara * Insect.type + rap * Insect.type +  : The function
>>> maximizer failed (couldn't find STD file) In addition: Warning
>>> message: running command 'C:\WINDOWS\system32\cmd.exe /c
>>> "C:/Program 
>>> Files/R/R-2.14.2/library/glmmADMB/bin/windows32/glmmadmb.exe"
>>> -maxfn 500 -maxph 5 -noinit -shess' had status 1
>>> 
>> 
>> This now means that the optimization failed for some reason. 
>> There are many reasons this can happen, mostly having to do with 
>> too-sparse or unusual data.  Without knowing anything about your
>> data, the one thing that pops out is you are using a binomial
>> family with zeroInflation=TRUE.  If your response is a matrix of
>> successes and failures, that's unusual but plausible; if your
>> response is a single 0/1 vector, then it doesn't make sense to
>> use zero-inflation.  (If your response is anything else it's odd
>> too, although that probably would have been caught earlier.) Try
>> working through the troubleshooting steps under ?admbControl
>> (and running with verbose=TRUE to see exactly what AD Model
>> Builder reports as the problem).
>> 
>> Ben Bolker
>> 
>> 
>>> 
>>> Can you help with this?
>>> 
>>> Many thanks, Rachel.
>>> 
>>> --On 01 March 2012 18:10 +0000 Ben Bolker <bbolker at gmail.com>
>>> wrote:
>>> 
>>>> Ben Bolker <bbolker at ...> writes:
>>>> 
>>>> [snip]
>>>> 
>>>>> If you do this:
>>>>> 
>>>>> mydata <-
>>>>> data.frame(spdiv,nsn,ara,rap,Insect.type,fsize,Site) 
>>>>> glmmadmb(spdiv~(nsn+ara+rap)*Insect.type+fsize+(1|Site),family="nbinom
>>>>>
>>>>> 
")
>>>>> 
>>>>> it ought to work.  However, it *should* work the way you
>>>>> specified -- I will work on fixing the bug.
>>>>> 
>>>>> thanks Ben Bolker
>>>> 
>>>> This should be fixed now (i.e. in glmmADMB 0.7.2.7). It's
>>>> still a good idea to use the data= argument.
>>>> 
>>>> _______________________________________________ 
>>>> R-sig-mixed-models at r-project.org mailing list 
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>>> 
>>> 
>>> 
>>> ---------------------- RH Gibson, School Biological Sciences 
>>> Rachel.Gibson at bristol.ac.uk
>> 
> 
> 
> 
> ---------------------- RH Gibson, School Biological Sciences 
> Rachel.Gibson at bristol.ac.uk

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