R help - Jan 2010 - 'nlme' library - lme function results

Dear R-helpers

I am running a simple mixed effects model using lme(). The call looks 
like this:
fit <- lme(Analyte~Sample, data=Data, random=~1 | Run)

I am particularly interested in the estimated random effects. When I 
print the 'fit' object, it looks something like example below:

(...)
Random effects:
  Formula: ~1 | Run
         (Intercept) Residual
StdDev:    3.483794 3.637523
(...)

While I have no problem obtaining the 'Residual' value by calling 
fit$sigma, I have no idea how to obtain the '(Intercept)' value from the
'fit' object. Anyone can help with that?

Best regards,

-- 
Michal J. Figurski, PhD
HUP, Pathology & Laboratory Medicine
Biomarker Research Laboratory
3400 Spruce St. 7 Maloney
Philadelphia, PA 19104
tel. (215) 662-3413

Michal Figurski wrote:
> 
> I am running a simple mixed effects model using lme(). The call looks 
> like this:
> fit <- lme(Analyte~Sample, data=Data, random=~1 | Run)
> 
> I am particularly interested in the estimated random effects. When I 
> print the 'fit' object, it looks something like example below:
> 
> (...)
> Random effects:
>   Formula: ~1 | Run
>          (Intercept) Residual
> StdDev:    3.483794 3.637523
> (...)
> 
> While I have no problem obtaining the 'Residual' value by calling 
> fit$sigma, I have no idea how to obtain the '(Intercept)' value
from the
> 'fit' object. Anyone can help with that?
> 
> 
There might be an official way to get it, but I would use as a hack.

library(nlme)
fm2 <- summary(lme(distance ~ age + Sex, data = Orthodont, random = ~ 1))
sqrt(getVarCov(fm2)[1,1])

Dieter


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