[R] variance estimates in lme biased?

[Pascal A. Niklaus]

Running lme on your data set results exactly in what you expect - or do 
you expect something different?

Pascal

 > L1<-factor(F1f)
 > L2<-factor(F2f)
 > L3<-factor(F3f)
 > lme(value ~ 1,random = ~ 1 | L1/L2/L3)
Linear mixed-effects model fit by REML
  Data: NULL
  Log-restricted-likelihood: 438.9476
  Fixed: value ~ 1
(Intercept)
  0.2955631

Random effects:
 Formula: ~1 | L1
        (Intercept)
StdDev:  0.02472988              <== level F1 which is 0

 Formula: ~1 | L2 %in% L1
        (Intercept)
StdDev:    1.140782                <== level F2 which is 1

 Formula: ~1 | L3 %in% L2 %in% L1
         (Intercept)  Residual
StdDev: 0.0005512791 0.1020479   <== F3 which is 0 , and F4 which is 0.1

Number of Observations: 625
Number of Groups:
                L1         L2 %in% L1 L3 %in% L2 %in% L1
                 5                 25                125