error message using glmmadmb

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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.

---------------------- 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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