[R] lme4 extracting individual variance components

[Douglas Bates]

On 6/24/05, FabbroThomas <thomas.fabbro at unifr.ch> wrote:
> Hi,
> For further calculations I need to extract indivdual Variances of
> different random effects from a fitted model.
> I found out how to extract the correlations
> (VarCorr(m1)@reSumry$group1) but I was not able to find a way to
> extract the other components individually.

Then look at

str(VarCorr(m1))

to find out what the structure is.  It contains a slot 'scale' which
is the estimated standard error of the noise term and a slot called
reSumry which is a list with components corresponding to the grouping
factors.  Each of those components has a slot named StdDev which gives
the relative standard deviation (relative to the value of the scale
slot).

> To extract the Residuals I tried: (ranef(m1)@ stdErr) which
> unfortunately did not work.
> Thank you very much for your help!
> 
> Thomas
> 
> 
> My model:
> 
>  > m1<- lmer(y ~ trtt + (trtt-1|group3) + (trtt-1|group2) +
> (trtt-1|group1), d1)
>  > m1
> Linear mixed-effects model fit by REML
> Formula: y ~ trtt + (trtt - 1 | group3) + (trtt - 1 | group2) + (trtt -
>       1 | group1)
>     Data: d1
>        AIC      BIC    logLik MLdeviance REMLdeviance
>   1819.454 2003.915 -874.7269   1736.421     1749.454
> Random effects:
>   Groups   Name                Variance Std.Dev. Corr
>   group1      trtt1/TR1       0.115094 0.33926
>            trtt1/TR2 0.338576 0.58187   0.177
>            trtt2/TR1       0.141726 0.37647  -0.002 -0.007
>            trtt2/TR2 0.327869 0.57260  -0.007 -0.002  0.321
>   group2     trtt1/TR1       0.026259 0.16205
>            trtt1/TR2 0.021771 0.14755  0.325
>            trtt2/TR1       0.025403 0.15938  0.898  0.062
>            trtt2/TR2 0.024479 0.15646  0.048  0.012  0.156
>   group3   trtt1/TR1       0.028206 0.16795
>            trtt1/TR2 0.133718 0.36567  0.848
>            trtt2/TR1       0.057741 0.24029  0.990  0.905
>            trtt2/TR2 0.110075 0.33178  0.638  0.944  0.731
>   Residual                     0.021744 0.14746
> # of obs: 1437, groups: group1, 1088; group2, 31; group3, 3
> 
> Fixed effects:
>                         Estimate  Std. Error   DF t value  Pr(>|t|)
> (Intercept)            4.875320    0.102476 1433  47.575 < 2.2e-16 ***
> trtt1/TR2   -4.647211    0.149408 1433 -31.104 < 2.2e-16 ***
> trtt2/TR1          0.577186    0.052293 1433  11.037 < 2.2e-16 ***
> trtt2/TR2   -4.237753    0.166187 1433 -25.500 < 2.2e-16 ***
> ---
> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> 
> 
> 
> I am working with:
> 
> R 2.1.0
> lme4 0.96-1
> Matrix 0.96-3
> lattice 0.11-6
> latticeExtra 0.1-3
> 
> On Mac OS X 10.3.9
> 
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