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. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894
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