lmer() with 'na.action=na.exclude'; error with summary()

John Maindonald <john.maindonald at ...> writes:

The following demonstrates the issue:

library(DAAG)
science.lmer <- lmer(like ~ sex + PrivPub + (1 | school) + 

+                      (1 | school:class), data = science,  
+                      na.action=na.exclude) 

summary(science.lmer)

Linear mixed model fit by REML ['lmerMod']

[snip]

Scaled residuals: 
Error in quantile.default(resids) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE

## Suppress details of residuals

summary(science.lmer, show.resids=FALSE)

This is a confusion between the arguments of the summary method
(summary.merMod) and the *print method* (print.summary.merMod).
We should add a warning to summary that says it is discarding
unused arguments (the ... in the model definition is only there
for compatibility with the summary() generic method).

  print(summary(science.lmer), show.resids=FALSE)

works fine.

I doubt that there is an intention for summary.merMod() to throw an error
lmer() has been called with 'na.action=na.exclude?.  
It should certainly not 
throw an error with the argument 'show.resids=FALSE?.

Now I'm wondering whether the correct behaviour when there are
NAs in the (extended) residuals is 

  1 omit NAs from the residual quantile calculation (easiest)
  2 return NA values for all quantiles of the residual
  3 return the quantiles plus a statement of the number of NAs.

Any good reason not to just do #1?