[R-sig-ME] glmmADMB

[Tharayil, Joseph (NIH/NINDS) [F]]

Hello all,

I am an undergraduate at the NIH summer internship program, working on
statistical models of seizure frequency. I am trying to use your R
package, glmmADMB, for zero-inflated poisson and negative binomial mixed
models. I have two questions:

  1. Does the zero inflation parameter returned by glmmadmb() refer to
     the fraction of instances in which “extra” zeros are observed?
  2. I often come across error messages containing the following phrase:
     "Error in glmmadmb(zeroinfl ~ 1 + (1 | testpatients), data = testdf,
     zeroInflation = TRUE,  : the function maximizer failed (couldn't
     find parameter file)”. It seems as though using different data sets,
     or changing the size of the data set, or using a poisson instead of
     negative binomial model, solves the problem. Two examples of a full
     error message, and a minimal code example are shown below.

I would really appreciate any assistance you are able to provide.

Thank you,
Joseph Tharayil
Summer Student
Clinical Epilepsy Section
NINDS, NIH

Minimal code example:

observations<-rnbinom(100000,size=10, mu=100000)
randzeros<-rbinom(100000,1,.80)
zeroinfl<-observations*randzeros
testpatients<-c()
k<-0
for(i in 1:1000)
{
  for(j in 1:100)
  {
    k<-k+1
    testpatients[k]<-i
  }
}
testpatients<-as.factor(testpatients)
testdf<-as.data.frame(cbind(zeroinfl,testpatients))
testdf$testpatients<-as.factor(testdf$testpatients)
testZINB<-glmmadmb(zeroinfl~1+(1|testpatients),data=testdf,zeroInflation=TRUE,family='nbinom')

Error message examples:
Example 1:
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(zeroinfl ~ 1 + (1 | testpatients), data = testdf,
zeroInflation = TRUE,  :
   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 message:
running command './glmmadmb -maxfn 500 -maxph 5 -noinit -shess' had
status 1
Example 2:
Need to increase the maximum number of separable calls allowed to at
least 20001
Current value is 20000
Use the -ndi N command line option
Error in glmmadmb(zeroinfl ~ 1 + (1 | testpatients), data = testdf,
zeroInflation = TRUE,  :
   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 message:
running command './glmmadmb -maxfn 500 -maxph 5 -noinit -shess' had
status 1


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