[R] Extract random part of summary nlme

[Andrew Robinson]

Hi Rense,

Try:


> fm1 <- lme(distance ~ age, data = Orthodont)
> VarCorr(fm1)
Subject = pdSymm(age) 
            Variance   StdDev    Corr  
(Intercept) 5.41508675 2.3270339 (Intr)
age         0.05126947 0.2264276 -0.609
Residual    1.71620460 1.3100399       



I hope that this helps,

Andrew






On Mon, Jul 30, 2007 at 02:19:41PM +0200, Rense Nieuwenhuis wrote:
> Dear helpers,
> 
> I'm estimating multilevel regression models, using the lme-function  
> from the nlme-package. Let's say that I estimated a model and stored  
> it inside the object named 'model'. The summary of that model is  
> shown below:
> 
> Using summary(model)$tTable , I receive the following output:
> 
>  > summary(model)$tTable
>                      Value  Std.Error   DF     t-value       p-value
> (Intercept)    0.23268607 0.09350662 3990   2.4884449  1.287080e-02
> sexM          -0.15338225 0.03169762 3990  -4.8389206  1.354802e-06
> standLRT       0.38593558 0.01677195 3990  23.0107762 4.005182e-110
> vrmid 50%      0.07606394 0.09389376   61   0.8101064  4.210281e-01
> vrtop 25%      0.24561327 0.10483374   61   2.3428838  2.241317e-02
> intakemid 50% -0.41469716 0.03177240 3990 -13.0521199  3.698344e-38
> intaketop 25% -0.75920783 0.05357980 3990 -14.1696648  1.666780e-44
> typeSngl       0.15680532 0.07173835   61   2.1857949  3.267903e-02
> 
> 
> All looks fine to me. The output above is simply  a section from the  
> full summary shown below. Now, I want to extract from the summary (or  
> the full model) the part stating the random parameters. More  
> specifically, I want to extract from the summary the following:
> 
> (Intercept) 0.2869401 (Intr)
> typeSngl    0.2791040 -0.617
> Residual    0.7302233
> 
> How could this be done?
> 
> Thanks for the effort,
> 
> Rense Nieuwenhuis
> 
> 
> 
> 
> 
> 
> 
> 
> Linear mixed-effects model fit by REML
>   Data: Exam
>        AIC      BIC   logLik
>    9158.56 9234.241 -4567.28
> 
> Random effects:
>   Formula: ~type | school
>   Structure: General positive-definite, Log-Cholesky parametrization
>              StdDev    Corr
> (Intercept) 0.2869401 (Intr)
> typeSngl    0.2791040 -0.617
> Residual    0.7302233
> 
> Fixed effects: normexam ~ sex + standLRT + vr + intake + type
>                     Value  Std.Error   DF    t-value p-value
> (Intercept)    0.2326861 0.09350662 3990   2.488445  0.0129
> sexM          -0.1533822 0.03169762 3990  -4.838921  0.0000
> standLRT       0.3859356 0.01677195 3990  23.010776  0.0000
> vrmid 50%      0.0760639 0.09389376   61   0.810106  0.4210
> vrtop 25%      0.2456133 0.10483374   61   2.342884  0.0224
> intakemid 50% -0.4146972 0.03177240 3990 -13.052120  0.0000
> intaketop 25% -0.7592078 0.05357980 3990 -14.169665  0.0000
> typeSngl       0.1568053 0.07173835   61   2.185795  0.0327
>   Correlation:
>                (Intr) sexM   stnLRT vrm50% vrt25% int50% int25%
> sexM          -0.201
> standLRT      -0.125  0.028
> vrmid 50%     -0.742  0.028 -0.035
> vrtop 25%     -0.652  0.051 -0.065  0.649
> intakemid 50% -0.246 -0.011  0.541 -0.002  0.007
> intaketop 25% -0.218 -0.018  0.676  0.014  0.013  0.660
> typeSngl      -0.421  0.080  0.007  0.033 -0.027 -0.001  0.001
> 
> Standardized Within-Group Residuals:
>          Min          Q1         Med          Q3         Max
> -3.59074329 -0.63776965  0.03829878  0.67303837  3.33952680
> 
> Number of Observations: 4059
> Number of Groups: 65
> 
> ______________________________________________
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/