


Hello, list,

I have been working with a dataset that is large,
overdispersed, non-normally distributed, non-linear, spatially autocorrelated,
and zero-inflated. So far, I have been able to account for everything except
for the zero-inflation using GAMMs in R. To my knowledge, there is no general
software code available yet to incorporate zero- inflation into negative
binomial GAMMs, please correct me if I am wrong. As far as GLMMs, I have
modeled the data with glmmPQL (accounting for random effects and autocorrelation
structure), and zeroinfl{pscl} (accounting for zero-inflation). For a
zero-inflated model that includes random effects, I am attempting glmm.admb
(the example from the documentation ran smoothly), but have encountered a few
errors, all a variation of “The function maximizer failed” (below).  I am not sure if these errors are due to the
nature of the data or to a mistake that I overlooked, so I provide details
below. I would appreciate any advice.

Thank you,

Holly

 

 >
str(Data110217noFlNaRVfallsub)

'data.frame':  
9559 obs. of  18 variables:

 $ LogCRATdens  : num 
0 0 0 0 0 0 0 0 0 0 ...

 $ CRATdens     : num 
0 0 0 0 0 0 0 0 0 0 ...

 $ CRATcount    : int 
0 0 0 0 0 0 0 0 0 0 ...

 $ TransBegDate :
int  39674 39674 39674 39674 39674 39674
39674 39674 39674 39674 ...

 $ fTransBegDate:
Factor w/ 126 levels "38979","38980",..: 34 34 34 34 34 34
34 34 34 34 ...

 $ x            : num  1867 1867 1867 1867 1867 ...

 $ y            : num  320 319 318 317 316 ...

 $ fSurveyID    : Factor w/ 8 levels
"DEL0615","DEL0706",..: 4 4 4 4 4 4 4 4 4 4 ...

 $ fSurveyLeg   : Factor w/ 16 levels
"EMaug08a","EMaug08b",..: 1 1 1 1 1 1 1 1 1 1 ...

 $ Dist         : num 
26.1 26.9 27 27.8 28.6 ...

 $ ST           : num  20.9 20.9 20.9 20.8 20.4 ...

 $ DiffST1      : num 
0.03 0.06 0.07 0.38 0.38 0.22 0.22 0.16 0.12 0.12 ...

 $ Sal          : num 
31.5 31.5 31.5 31.6 31.6 ...

 $ LogTnDens    : num 
0 0 0 0 0 0 0 0 0 0 ...

 $ TnDens       : num 
0 0 0 0 0 0 0 0 0 0 ...

 $ LogDlDens    : num 
0 0 0 0 0 0 0 0 0 0 ...

 $ DlDens       : num 
0 0 0 0 0 0 0 0 0 0 ...

 $ EW           : num  9.49 8.87 8.55 9.17 9.35 9.11 8.47 8.42 8.7
9.24 ...

 

> sapply(Data110217noFlNaRVfallsub, function(i)
length(table(i)))


 
  
  LogCRATdens
  
  
  CRATdens
  
  
  CRATcount
  
  
  TransBegDate
  
  
  fTransBegDate
  
 
 
  
  51
  
  
  51
  
  
  41
  
  
  83
  
  
  126
  
 
 
  
  x
  
  
  y
  
  
  fSurveyID
  
  
  fSurveyLeg
  
  
  Dist
  
 
 
  
  9559
  
  
  9559
  
  
  8
  
  
  16
  
  
  5044
  
 
 
  
  ST
  
  
  DiffST1
  
  
  Sal
  
  
  LogTnDens
  
  
  TnDens
  
 
 
  
  1265
  
  
  266
  
  
  1445
  
  
  11
  
  
  12
  
 
 
  
  LogDlDens
  
  
  DlDens
  
  
  EW
  
  

  

 
 
  
  30
  
  
  33
  
  
  3481
  
  

  

 


 

> glmmadmbZINBrLogCRATdens5fixGrpSrvy <- glmm.admb(

+ fixed=round(LogCRATdens)~

+ Dist + 

+ DiffST1 +

+ LogTnDens +

+ LogDlDens +

+ Sal,

+ group="fSurveyID",

+ data= Data110217noFlNaRVfallsub, 

+ zeroInflation=TRUE,

+ family="nbinom")

 

0 30.22 1 14.145 0.17 0 0 30.24 1 14.861 0.08 0 0 30.25 1
14.861 0.21 0 0 30.29 1 15.665 0.22 0 0 30.4 $

size error in get_choleski

Error in glmm.admb(fixed = round(LogCRATdens) ~ Dist +
DiffST1 + LogTnDens +  : 

  The function
maximizer failed

In addition: Warning messages:

1: running command 'C:\Windows\system32\cmd.exe /c
"C:/Users/Yo/Documents/R/win-library/2.12/glmmADMB/bin/windows/nbmm.exe"
-maxfn 500 ' had status 1 

2: In shell(cmd, invisible = TRUE) :

 
'"C:/Users/Yo/Documents/R/win-library/2.12/glmmADMB/bin/windows/nbmm.exe"
-maxfn 500 ' execution failed with error code 1

 

I have tried a variety of alternatives to this model,
varying the fixed effects, the group, the random effect, the response variable,
and zeroInflation, to no avail. Changing imaxfn values anywhere from 10 to 1000000
produces the same error.

 

Using either non-integers or counts (integers) for the
response variable, I get the following error instead of the “size error in
get_choleski”:

 

1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 $

Incompatible array bounds in dvar_vector  operator * (_CONST dvar_matrix& m,_CONST
dvar_vector& x)

 

Using 3 of the variables, I don’t get either of the above
errors, but simply: “The function maximizer failed”:  

 

> glmmadmbZINBrLogCRATdens3fixGrpSrvyRand1 <-
glmm.admb(

+ fixed=round(LogCRATdens)~

+ Dist + 

+ DiffST1 +

+ LogTnDens,

+ group="fSurveyID",

+ random =~1,

+ data= Data110217noFlNaRVfallsub, 

+ zeroInflation=TRUE,

+ family="nbinom")

1 143.521 0.02 0 1 143.13 4.54 0 1 143.636 4.54 0 1
145.986 3.3 0 1 146.859 0.27 0 1 147.734 0.27 0 1 $

Error in glmm.admb(fixed = round(LogCRATdens) ~ Dist +
DiffST1 + LogTnDens,  : 

  The function
maximizer failed

In addition: Warning messages:

1: running command 'C:\Windows\system32\cmd.exe /c
"C:/Users/Yo/Documents/R/win-library/2.12/glmmADMB/bin/windows/nbmm.exe"
-maxfn 500 ' had status 1 

2: In shell(cmd, invisible = TRUE) :

 
'"C:/Users/Yo/Documents/R/win-library/2.12/glmmADMB/bin/windows/nbmm.exe"
-maxfn 500 ' execution failed with error code 1

 		 	   		  
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