[R] 2 lme questions

[Chuck Cleland]

Spencer Graves wrote:
>      The "print" method and the "summary" command display the STANDARD 
> DEVIATIONS (not the variances) on the screen (or in a sink file).  
> However, when I do attributes(lme(...)) and 
> attributes(summary(lme(...))), I don't see anything I can use.  
> Fortunately, the "interval" function produces a list, from which the 
> variance estimates can be extracted.  Consider the following example:
> DF <- data.frame(group=c(1,1,2,2), y=c(1, 2, 11, 12))
> library(nlme)
> fit <- lme(y~1, random=~1|group, DF)
> 
> Linear mixed-effects model fit by REML
>  Data: DF
>  Log-restricted-likelihood: -6.559401
>  Fixed: y ~ 1
> (Intercept)
>        6.5
> 
> Random effects:
> Formula: ~1 | group
>        (Intercept)  Residual
> StdDev:    7.053597 0.7070954
> 
> Number of Observations: 4
> Number of Groups: 2
>  > lme.int <- intervals(fit)
>  > lme.int$reStruct^2
> Error in lme.int$reStruct^2 : non-numeric argument to binary operator
> 
>  > lme.int$reStruct$group^2
>                  lower     est.    upper
> sd((Intercept)) 3.06859 49.75323 806.6845
>  > lme.int$sigma^2
>    lower      est.     upper
> 0.0704255 0.4999839 3.5496217
> attr(,"label")
> [1] "Within-group standard error:"
> 
>      There may be a better way;  if there is, I hope someone will 
> enlighten us all.  If not, at least this works in R 1.8.1

   How about VarCorr(fit) ?

See ?VarCorr

-- 
Chuck Cleland, Ph.D.
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