[R-sig-ME] lme4 and false convergence

[Ken Beath]

On 26/11/2008, at 12:46 AM, Ben Zuckerberg wrote:

> Dear R-users,
>
> I am using the most updated package of lme4 (lme4_0.999375-2).  I  
> have a data set consisting of ~900 observations at ~440 independent  
> survey sites.  There are an unbalanced number of surveys at each  
> site.  I am attempting to develop several models evaluating the  
> presence/absence of a species (PRES) at these random sites (SITE)  
> using a number of predictor variables.  The response variable (PRES)  
> is binomial and the included predictor variables are either  
> proportions (e.g., AG, FOR, OPEN, LDEV,or DEV) or numerical  
> (COUNT[min. 1 to max. 37,mean = 10]).  
> ---------------------------------------------------------------------
> PROBLEM 1:
>
> I have developed the following GLMM:
>
> mix.1<-glmer(PRES~AG+FOR+OPEN+LDEV+DEV+COUNT+(1| 
> SITE),family=binomial,data=merge1)
>
> I receive the following error:
> Warning message:
> In mer_finalize(ans) : false convergence (8)
>
> There is model output, but I am worried it might be biased.
> I have tried:
> -Data transformation of the predictor variables (e.g., log(COUNT)),  
> which does seem successful in some simpler models, but does not work  
> consistently.
> -The most updated version of lme4
>

This is difficult without the output.

Possibly there is a high correlation within sites. Try using the  
adaptive Gauss-Hermite option with nAGQ=5 or more.

It may also indicate a close to complete separation indicated by a  
large parameter estimate. There is not much that can be done if a  
parameter close to perfectly predicts.

Ken


> ---------------------------------------------------------------------
> PROBLEM #2:
> In addition, I am interested in visualizing the predicted  
> probabilities from this output using the fixed effect function, but  
> receive the following message:
>
> fixef(mix.1)
> Error in UseMethod("fixef") : no applicable method for "fixef"
>
> Any suggestions would be greatly appreciated!
>
> -- 
> Benjamin Zuckerberg, Ph.D.
> Post-doctoral Associate
> Spatial Ecologist, Citizen Science
> Cornell Laboratory of Ornithology
> 159 Sapsucker Woods Road
> Ithaca, NY 14850 Tele: 607-254-2174
> Fax: 607-254-2111
>
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