Hello all;

 

I am currently attempting to model seasonal changes in aquatic invertebrate abundance (n = 1979 samples), using R package glmmADMB. 

 

Here are the details:

 

1/ I verified the excess of zeroes in the data set by the method suggested at http://glmm.wikidot.com/faq (i.e. simulating a distribution of the proportion of zeros and comparing it to the observed proportion). I’ve also verified the data has a negative binomial structure, and am thus using a ZINB model, but am having consistent problems with it.

 

2/ Data come from 2 sites (geographic regions) and 5 years, but site and year variables are confounded (i.e. there are no years for which there is data from both sites). As such, in my models, I nested years within sites (Site/Year), because the year effect can not be detected independent of site. When I originally ran these models (SAS), I used included the Site/Year term as random, but on further review of the glmm wiki, decided they were more  appropriate as fixed effects (f.e.), as there are less than 6 levels of year. 

 

3/ We sampled multiple wetlands (i.e. > 15 basins, or 'subsites') within each site. 

 

4/ I have treated this as a nested random effect (r.e.), because it is hierarchically structured, as described by Bolker et al. 2009 (TREE), and we are not interested in making any inference about the influence of these particular variables on invert. abundance.  

 

5/ When I run a ZINB model with only the random intercept effect of Basin/Site, it converges and produces similar results to what I saw in SAS:

 

A_Zinb_3<-glmmadmb(VCAmphCount~1+(1|Site/Basin), data=Amphs, zeroInflation=TRUE,family="nbinom")

 

The model also runs when I include no r.e. and only year as f.e., but as soon as I try to combine the year f.e. with the site/basin r.e., it goes haywire:

 

A_Zinb_4<-glmmadmb(VCAmphCount~1+Year+(1|Site/Basin), data=Amphs, zeroInflation=TRUE, family="nbinom")

 

producing the following error messge:

 

Error in glmmadmb(VCAmphCount ~ 1 + Year + (1 | Site/Basin), data = Amphs,  : 
  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-2.15.0/library/glmmADMB/bin/windows32/glmmadmb.exe" -maxfn 500 -maxph 5 -noinit -shess' had status 1 



I get this same error when I try to include Year/Site as f.e., with NO r.e. ...

 

I feel like there is really something wierd going on with the year effect, but I just can't figure it out... as soon as I add any "nesting" structure to it, the “function maximizer fails”

 

I feel like I need to include both SITE and YEAR, but I can’t include them independently, for the reasons I describe in point 2/. Perhaps it would be better to put them in competing models and use that which reduces deviance of the null most?

 

Any insights or suggestions would be fantastic!

 

Thanks in advance for your help...

 

kbg



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Kirsty E. B. Gurney, Ph.D.
Alaska Cooperative Fish and Wildlife Research Unit
Institute of Arctic Biology
209 Irving 1 Building
University of Alaska Fairbanks
Fairbanks, AK 99775
T: (907) 474 - 7738
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