[R] glmmADMB model fails when fixed effect interaction term is removed

Peter Claussen dakotajudo at me.com
Wed Jan 7 16:38:10 CET 2015


Cara,

Perhaps I a bit ignorant about mixed models, but I don’t understand why you have the dependent variable included as a random effect.

The variable names you are using suggest an analysis of combined trials, so (1 | Site/Block/Strip.ID) seems more appropriate. Is this a factorial or a split/strip-block design?

Peter

> On Jan 5, 2015, at 3:14 PM, cara715 <capplestein at cnlm.org> wrote:
> 
> Hello,
> 
> I am looking at a data set predicting number of plants (FERO) based on fixed
> effects sowing method (Method) and sowing rate (Rate). I also have a slope
> random effect for the site and intercept random effects for the nested
> variables Block and Strip.ID (to account for experimental design). I have
> tried running several different models using the glmmadmb function. The
> dependent variable, FERO, is a discrete count. All of my fixed and random
> effects are categorical and have the following levels:
> 
> Method: 3
> Rate: 5
> Site: 3
> Block: 18
> Strip.ID: 275
> 
> The following model runs without a problem:
> 
> fit_nbin3 <-glmmadmb(FERO ~ Method * Rate + (FERO|Site) +
> (1|Block/Strip.ID),
> data = data1, family = "nbinom")
> 
> However, when I try to run the same model without the interaction term:
> 
> fit_nbin4 <-glmmadmb(FERO ~ Method + Rate + (FERO|Site) +
> (1|Block/Strip.ID),
> + data = data1, family = "nbinom")
> 
> I get the following error message:
> 
> Parameters were estimated, but not standard errors were not: the most likely
> problem is that the curvature at MLE was zero or negative
> Error in glmmadmb(FERO ~ Method + Rate + (FERO | Site) + (1 |
> Block/Strip.ID),  : 
>  The function maximizer failed (couldn't find STD file) Troubleshooting
> steps include (1) run with 'save.dir' set and inspect output files; (2)
> change run parameters: see '?admbControl'
> In addition: Warning message:
> running command 'C:\windows\system32\cmd.exe /c
> "C:/Users/Cara/Documents/R/win-library/3.1/glmmADMB/bin/windows64/glmmadmb.exe"
> -maxfn 500 -maxph 5 -noinit -shess' had status 1
> 
> I am confused as why removing the interaction term, which should simplify
> the model is causing it to fail to run correctly. Any ideas what's going on
> here?
> 
> Here is a sample of my first few lines of data:
> 
> Site         Method         Rate  Block  Strip  FERO
> Glacial      Broadcast      A      A        H     69	
> Glacial      Broadcast      A      A        H     1
> Glacial      Broadcast      A      A        H     41
> 
> One other quick thing:
> I can't seem to the the aictab function to work on the properly run glmmadmb
> models. I get a message saying: 	
> Error in formatCands(cand.set) : 
> Functions do not support mixture of model classes
> 
> Thanks in advance for your help!
> 
> Cara Applestein
> Prairie Science Technician
> Center for Natural Lands Management
> Olympia, Washington
> 
> 
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/glmmADMB-model-fails-when-fixed-effect-interaction-term-is-removed-tp4701411.html
> Sent from the R help mailing list archive at Nabble.com.
> 
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