R help - Mar 2009 - Extracting SD of random effects from lme object

Hello,
How do I get the standard deviations for the random effects out of the
lme object?  I feel like there's probably a simple way of doing this,
but I can't see it.  Using the first example from the documentation:
> fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
> fm1
Linear mixed-effects model fit by REML
  Data: Orthodont
  Log-restricted-likelihood: -221.3183
  Fixed: distance ~ age
(Intercept)         age
 16.7611111   0.6601852

Random effects:
 Formula: ~age | Subject
 Structure: General positive-definite
            StdDev    Corr
(Intercept) 2.3270339 (Intr)
age         0.2264276 -0.609
Residual    1.3100399

Number of Observations: 108
Number of Groups: 27

I want to extract the column vector (2.3270339, 0.2264276,
1.3100399)'.  Any thoughts?
Thanks,
Ben

On Mon, Mar 23, 2009 at 11:26 AM, Ben Domingue <ben.domingue at gmail.com>
wrote:
> Hello,
> How do I get the standard deviations for the random effects out of the
> lme object? ?I feel like there's probably a simple way of doing this,
> but I can't see it. ?Using the first example from the documentation:
>
>> fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age
>> fm1
> Linear mixed-effects model fit by REML
> ?Data: Orthodont
> ?Log-restricted-likelihood: -221.3183
> ?Fixed: distance ~ age
> (Intercept) ? ? ? ? age
> ?16.7611111 ? 0.6601852
>
> Random effects:
> ?Formula: ~age | Subject
> ?Structure: General positive-definite
> ? ? ? ? ? ?StdDev ? ?Corr
> (Intercept) 2.3270339 (Intr)
> age ? ? ? ? 0.2264276 -0.609
> Residual ? ?1.3100399
>
> Number of Observations: 108
> Number of Groups: 27
>
> I want to extract the column vector (2.3270339, 0.2264276,
> 1.3100399)'. ?Any thoughts?
To get the covariance matrix of the random effects:
> getVarCov(fm1)
Random effects variance covariance matrix
            (Intercept)       age
(Intercept)     5.41510 -0.321060
age            -0.32106  0.051269
  Standard Deviations: 2.327 0.22643


One way to extract the standard deviations shown by the print method above is:
> diag(sqrt(getVarCov(fm1)))
(Intercept)         age
  2.3270339   0.2264276
Warning message:
In sqrt(getVarCov(fm1)) : NaNs produced


And to get the estimate of the error standard deviation:
> fm1$sigma
[1] 1.31004


hth,

Kingsford Jones
> Thanks,
> Ben
>
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