Extracting SD of random effects from lme object
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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