R Under development (unstable) (2024-06-05 r86695 ucrt) -- "Unsuffered Consequences"
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> ## PR#15678
> 
> library(nlme)
> set.seed(1)
> X1 <- gl(2,4)
> X2 <- gl(2,2,8)
> Y <- rnorm(8)
> mis.dat <- data.frame(Y = Y,X1 = X1,X2 = X2)
> mis.dat[3, "Y"] <- NA
> 
> ## Fit model -----------------------
> model <- lme(Y ~ 1, random = ~ 1 | X1/X2, data = mis.dat, na.action = na.omit)
> summary(model)
Linear mixed-effects model fit by REML
  Data: mis.dat 
       AIC      BIC    logLik
  24.16881 23.33585 -8.084405

Random effects:
 Formula: ~1 | X1
         (Intercept)
StdDev: 1.687736e-05

 Formula: ~1 | X2 %in% X1
        (Intercept)  Residual
StdDev:   0.6305232 0.6131974

Fixed effects:  Y ~ 1 
                Value Std.Error DF  t-value p-value
(Intercept) 0.3602806 0.3947926  3 0.912582  0.4288

Standardized Within-Group Residuals:
       Min         Q1        Med         Q3        Max 
-1.2548616 -0.5187205  0.3368379  0.4882496  0.9789656 

Number of Observations: 7
Number of Groups: 
        X1 X2 %in% X1 
         2          4 
> 
> labs <- with(na.omit(mis.dat), paste(X1, X2, sep = "/" ))
> fit <- fitted(model)
> stopifnot(identical(names(fit), labs))
> 
> 
> proc.time()
   user  system elapsed 
   0.17    0.07    0.23