[R-sig-ME] Could not get a lmer or glmer summary
Eric Edeline
edeline at biologie.ens.fr
Fri Mar 26 21:26:00 CET 2010
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
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