[R-sig-ME] error message using glmmadmb

[RH Gibson, School Biological Sciences]

here is what happens when I tried the poisson:

> 
m7<-glmmadmb(x~nsn*Insect.type+ara*Insect.type+offset(logTotal.grains)+(1|Site),data=data1, 
zeroInflation=TRUE, family="poisson")
Warning message:
In glmmadmb(x ~ nsn * Insect.type + ara * Insect.type + 
offset(logTotal.grains) +  :
  Convergence failed:log-likelihood of gradient= -223.949

I will email you the summary(data1) output separately.

I have 8 sites only.

Thanks for all the help.


--On 05 March 2012 09:22 -0500 Ben Bolker <bbolker at gmail.com> wrote:

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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+offse
>>>> t(
>>>>
>>>>
> 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="nbin
>>>>>> om
>>>>>>
>>>>>>
> ")
>>>>>>
>>>>>> 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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----------------------
RH Gibson, School Biological Sciences
Rachel.Gibson at bristol.ac.uk