Message-ID: <BANLkTin2tD2ATyuJxsrAVJU04WL=3Rkuzg@mail.gmail.com>
Date: 2011-06-16T13:03:35Z
From: Douglas Bates
Subject: strange interaction lme4a::lmer and lme4a::profile
In-Reply-To: <OF07FED1EF.F089A092-ONC12578B1.00342F37-C12578B1.003710EB@basf-c-s.be>
On Thu, Jun 16, 2011 at 5:01 AM, <joris.dewolf at cropdesign.com> wrote:
> Hi,
>
> I've got a strange behaviour with lme4a::lmer in combination with
> lme4a::profile()
>
> profile() seems to change the merMod object it has been calculating the
> profile for. The variance components and standard errors on fixed effects
> as returned by summary() are different before and after running profile()
> as you can see in the example below.
> >From the profile itself, the first run seems to be the correct one.
>
> Output and sessionInfo below. I can provide the data set on request.
>
> Anybody an idea what is going wrong?
Thanks for the very thorough report. It's a bug that I forgot to fix.
I'll do so now.
>
>
>
>> modL1.2 <- lmer(data=RPD15L1, value ~ transgenity +
> (transgenity|event),REML=FALSE)
>> summary(modL1.2)
> Linear mixed model fit by maximum likelihood ['summary.mer']
> Formula: value ~ transgenity + (transgenity | event)
> ? Data: RPD15L1
> ? ? ?AIC ? ? ? BIC ? ?logLik ?deviance
> ?500.6290 ?520.7116 -244.3145 ?488.6290
>
> Random effects:
> ?Groups ? Name ? ? ? ? ? ? ? ?Variance Std.Dev. Corr
> ?event ? ?(Intercept) ? ? ? ? 0.4475 ? 0.6690
> ? ? ? ? ?transgenityPositive 0.9615 ? 0.9806 ? 0.295
> ?Residual ? ? ? ? ? ? ? ? ? ? 0.2971 ? 0.5450
> Number of obs: 210, groups: event, 36
>
> Fixed effects:
> ? ? ? ? ? ? ? ? ? ?Estimate Std. Error t value
> (Intercept) ? ? ? ? ?23.2766 ? ? 0.1235 ?188.50
> transgenityPositive ? 1.0607 ? ? 0.1801 ? ?5.89
>
> Correlation of Fixed Effects:
> ? ? ? ? ? ?(Intr)
> trnsgntyPst 0.115
>> pr.modL1.2 <- profile(modL1.2)
>> summary(modL1.2)
> Linear mixed model fit by maximum likelihood ['summary.mer']
> Formula: value ~ transgenity + (transgenity | event)
> ? Data: RPD15L1
> ? ? ?AIC ? ? ? BIC ? ?logLik ?deviance
> ?500.6290 ?520.7116 -244.3145 ?488.6290
>
> Random effects:
> ?Groups ? Name ? ? ? ? ? ? ? ?Variance Std.Dev. Corr
> ?event ? ?(Intercept) ? ? ? ? 0.1964 ? 0.4432
> ? ? ? ? ?transgenityPositive 0.4376 ? 0.6615 ? 0.523
> ?Residual ? ? ? ? ? ? ? ? ? ? 0.2971 ? 0.5450
> Number of obs: 210, groups: event, 36
>
> Fixed effects:
> ? ? ? ? ? ? ? ? ? ?Estimate Std. Error t value
> (Intercept) ? ? ? ? 23.27657 ? ?0.09092 ?256.01
> transgenityPositive ?1.06065 0.13364 ? ?7.94
>
> Correlation of Fixed Effects:
> ? ? ? ? ? ?(Intr)
> trnsgntyPst 0.119
>
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Dutch_Belgium.1252 ?LC_CTYPE=Dutch_Belgium.1252
> [3] LC_MONETARY=Dutch_Belgium.1252 LC_NUMERIC=C
> [5] LC_TIME=Dutch_Belgium.1252
>
> attached base packages:
> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base
>
> other attached packages:
> [1] boot_1.2-43 ? ? ? ?lme4a_0.999375-63 ?MatrixModels_0.2-1 minqa_1.1.14
>
> [5] Rcpp_0.9.0.2 ? ? ? Matrix_0.999375-46 lattice_0.19-13 ? ?rj_0.5.0-5
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-6 grid_2.12.1 ? ? nlme_3.1-98 ? ? rJava_0.8-8
> [5] splines_2.12.1 ?stats4_2.12.1 ? tools_2.12.1
> ? ? ? ?[[alternative HTML version deleted]]
>
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