[R-sig-ME] Missing information in "name" column of Random effects output
Douglas Bates
bates at stat.wisc.edu
Thu Sep 27 19:53:16 CEST 2007
Version 0.99875-8 of the lme4 package, with this glich fixed, is now on CRAN.
On 9/26/07, Douglas Bates <bates at stat.wisc.edu> wrote:
> On 9/25/07, David Afshartous <dafshartous at med.miami.edu> wrote:
>
> > Jorge,
>
> > Awhile back I think I noticed a similar issue. I don't recall if I was able
> > to do anything different w/ the lmer statement to fix it. In any event, my
> > guess is that the first term corresponds to the intercept RE and the second
> > to the slope RE. Looking at the estimated RE's themselves supports this:
>
> Jorge is correct that the name column is no longer being filled out
> and David is correct that the order of variance components corresponds
> to the order of the terms in the model matrix for the random effects
> term. Thanks to both of you for the report.
>
> At some point I changed where the names are stored and I forgot to
> update the VarCorr method accordingly. I will release a new version
> with this fixed.
>
> > > ranef(fm1)
> > An object of class ³ranef.lmer²
> > [[1]]
> > (Intercept) Days
> > 308 2.2713451 9.1966961
> > 309 -40.3825921 -8.6223099
> > 310 -38.9403378 -5.4521894
> > 330 23.6656443 -4.8100611
> > 331 22.2391295 -3.0662861
> > 332 9.0324969 -0.2709760
> > 333 16.8277808 -0.2214775
> > 334 -7.2256113 1.0733822
> > 335 -0.3503176 -10.7492136
> > 337 34.8784025 8.6302064
> > 349 -25.1898574 1.1699674
> > 350 -13.0500361 6.6107496
> > 351 4.5697621 -3.0138529
> > 352 20.8539011 3.5376139
> > 369 3.2744289 0.8723798
> > 370 -25.5865985 4.8179542
> > 371 0.8049003 -0.9877807
> > 372 12.3075594 1.2851975
>
> > > fm1.junk = ranef(fm1)[[1]]
> > > int.ranef = fm1.junk[,1]
> > > slope.ranef = fm1.junk[,2]
> > > var(int.ranef)
> > [1] 465.8012
> > > var(slope.ranef)
> > [1] 29.75055
>
> > On 9/25/07 2:42 PM, "Jorge González" <jorge.gonzalez at psy.kuleuven.be> wrote:
> >
> > > Dear all,
> > >
> > > My apologies if this has been discussed before. When estimating a model
> > > with lmer, I can't see anymore the contents of the "name" column in the
> > > Random effects part of the output. See the example below
> > >
> > > ###### begin example ###################
> > >> sessionInfo()
> > > R version 2.5.1 (2007-06-27)
> > > i386-pc-mingw32
> > >
> > > locale:
> > > LC_COLLATE=Dutch_Belgium.1252;LC_CTYPE=Dutch_Belgium.1252;LC_MONETARY=Dutch_Be
> > > lgium.1252;LC_NUMERIC=C;LC_TIME=Dutch_Belgium.1252
> > >
> > > attached base packages:
> > > [1] "stats" "graphics" "grDevices" "utils" "datasets"
> > > "methods" "base"
> > >
> > > other attached packages:
> > > lme4 Matrix lattice
> > > "0.99875-7" "0.999375-2" "0.16-5"
> > >> fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy)
> > >> fm1
> > > Linear mixed-effects model fit by REML
> > > Formula: Reaction ~ Days + (Days | Subject)
> > > Data: sleepstudy
> > > AIC BIC logLik MLdeviance REMLdeviance
> > > 1754 1770 -871.8 1752 1744
> > > Random effects:
> > > Groups Name Variance Std.Dev. Corr
> > > Subject 610.835 24.7151
> > > 35.056 5.9208 0.067
> > > Residual 655.066 25.5943
> > > number of obs: 180, groups: Subject, 18
> > >
> > > Fixed effects:
> > > Estimate Std. Error t value
> > > (Intercept) 251.405 6.820 36.86
> > > Days 10.467 1.546 6.77
> > >
> > > Correlation of Fixed Effects:
> > > (Intr)
> > > Days -0.137
> > >>
> > > #################### end example ##################
> > > How can I know which variance correspond to the subject random
> > > intercept and which one to the subject slope Days? As far as I remember
> > > this information was available in previous versions. Is this a bug?
> > >
> > > Thank you very much in advance
> > >
> > > Jorge
> >
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
> >
>
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