[R-sig-ME] Could not get a lmer or glmer summary

[Eric Edeline]

Dear Ben,

thank you for your feed-back. I have now tested lmer on several datasets 
and I always get the same error message when asking for model summary. 
So the problem is with lme4, not with the data. Then, I ran the exact 
same models and data on another machine and it works fine! So the lme4 
problem is specific to my machine. Then, I tried brute force: 
uninstalling and re-installing R on my machine, but the lme4 problem 
remains. Any suggestion would be greatly appreciated.

Thanks!

Eric


Ben Bolker wrote:
> Eric Edeline <edeline at ...> writes:
>
>   
>> Dear David,
>>
>> here is the Str(m11):
>>
>>  > m11<-lmer(Logl ~ 1|Species, data=Data)
>>  > str(m11)
>> Formal class 'mer' [package "lme4"] with 34 slots
>>   ..@ env     :<environment: 0xc077a5c>
>>   ..@ nlmodel : language I(x)
>>   ..@ frame   :'data.frame':    92093 obs. of  2 variables:
>>   .. ..$ Logl   : num [1:92093] 3.72 4.35 4.83 4.56 5.5 ...
>>   .. ..$ Species: Factor w/ 50 levels "ABH","ABL","ANG",..: 20 18 32 29 
>> 48 3 21 2 31 24 ...
>>     
>
>   [snip snip snip]
>
>   Nothing really obvious pops out.
>   I know your data set is really large, but can you either post
> it somewhere, or see if a subset of your data set gives you the
> same problem?  If it doesn't (i.e. if you only get problems with
> the full data set) maybe that will provide a hint.
>  
>   I made up data that looked a little bit like yours 
> and didn't have a problem:
>
>   
>> set.seed(1001)
>> Logl <- rnorm(92093)
>> Species <- factor(rep(1:50,200))[1:92093]
>> Data <- data.frame(Logl,Species)
>> m11 <- lmer(Logl~1|Species,data=Data)
>> m11
>>     
> Linear mixed model fit by REML 
> Formula: Logl ~ 1 | Species 
>    Data: Data 
>    AIC   BIC logLik deviance REMLdev
>  28375 28396 -14184    28361   28369
> Random effects:
>  Groups   Name        Variance   Std.Dev.
>  Species  (Intercept) 0.00089705 0.029951
>  Residual             0.99753902 0.998769
> Number of obs: 10000, groups: Species, 50
>
> Fixed effects:
>               Estimate Std. Error t value
> (Intercept) -0.0003448  0.0108462  -0.032
>   
>> nrow(Data)
>>     
> [1] 92093
>
>   ... although there is one weird thing, that
> "number of obs." is reported as 10000 (???)
>
>   
>> sessionInfo()
>>     
> R version 2.10.1 (2009-12-14) 
> i486-pc-linux-gnu 
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] lme4_0.999375-32   Matrix_0.999375-38 lattice_0.18-3    
>
> loaded via a namespace (and not attached):
> [1] grid_2.10.1
>
> _______________________________________________
> R-sig-mixed-models at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
>   

-- 
Eric Edeline
Assistant Professor
UMR 7618 BIOEMCO
Ecole Normale Supérieure
46 rue d'Ulm
75230 Paris cedex 05
France

Tel: +33 (0)1 44 32 38 84
Fax: +33 (0)1 44 32 38 85

http://www.biologie.ens.fr/bioemco/biodiversite/edeline.html