[R-sig-ME] Bug in lme4: attr(mod at frame, "na.action") is not re-initialized to NULL

[Ben Bolker]

  I think I agree that this is a bug; in our defense, there are *lots*
of possible permutations of when and how NAs can show up in data.
What surprises me slightly is that this doesn't show up in any of the
permutations tested at

https://github.com/lme4/lme4/blob/master/inst/tests/napredict2.R

...

On 14-03-11 04:26 PM, Alexandre Courtiol wrote:
> Yes, but it does not solve the problem for all function that use a direct
> call to refit, e.g. PBmodcomp...
> So it would be beter that the attributes of the model frame really
> correspond to the model frame, no?
> alex
> 
> 
> 2014-03-11 21:16 GMT+01:00 Steve Walker <steve.walker at utoronto.ca>:
> 
>> This seems to work:
>>
>> refit(mod, simulate(mod, na.action = na.exclude))
>>
>> Cheers,
>> Steve
>>
>>
>> On 3/11/2014, 3:51 PM, Alexandre Courtiol wrote:
>>
>>> I think I found a bug... and it may affect several versions of lmer (but I
>>> did not try the one before 1.0).
>>> The bug is that the attribute na.action of the model frame is not
>>> re-initialized to NULL (both in lmer and glmer).
>>>
>>> example:
>>>
>>> data <- data.frame(y=rnorm(100), K=factor(rep(1:10,10)))
>>> data[3, "y"] <- NA
>>> library(lme4)
>>> mod <- lmer(y~1+(1|K), data=data)
>>> dim(mod at frame) # 99 2 The model frame has excluded the line as it should
>>> attr(mod at frame, "na.action") # 3 The value 3 is still considered missing
>>> while it should not
>>>
>>> This feature is slightly annoying because it creates the function refit to
>>> crash and others using refit (I came to discover that from a crash in
>>> PBmodcomp from pbkrtest)...
>>>
>>> example:
>>>
>>> refit(mod, simulate(mod)) # CRASH
>>> attr(mod at frame,"na.action") <- NULL # fast and dirty patch...
>>> refit(mod, simulate(mod)) # works
>>>
>>> Thanks to the lmer team for your great work!
>>> PS: If you don't see that as a bug, please send an informative warning.
>>>
>>>
>>>
>>>  sessionInfo()
>>>>
>>> R version 3.0.2 (2013-09-25)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> attached base packages:
>>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] pbkrtest_0.3-8 MASS_7.3-29    lme4_1.1-4     Rcpp_0.11.0
>>> Matrix_1.1-2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] grid_3.0.2          lattice_0.20-27     minqa_1.2.3
>>> [4] nlme_3.1-113        RcppEigen_0.3.2.0.3 splines_3.0.2
>>> [7] tools_3.0.2
>>>
>>>
>>
> 
>