[Rd] model.matrix() may be misleading for "lme" models

[John Fox]

Thank you Ivan and Ben for your recent further comments.

I think that the current code for the unregistered model.matrix.lme() in 
the development version of the car package is pretty robust and 
certainly an improvement over what was there before (which returned 
incorrect results for non-default contrasts!).

I expect that if someone in R-core picks up the task of writing a 
model.matrix.lme() for the nlme package, they would do a better job than 
I did, and I'd then be able to retire the version in the car package.

Again, thanks,
  John

On 2024-09-23 4:25 p.m., Ben Bolker wrote:
> Caution: External email.
> 
> 
>>   I can't tell whether evaluating object$call$data in
> environment(object$formula) is a better or worse idea than parent.frame().
> 
> I have struggled with this a lot over the years. There is a bunch of
> wonky code in lme4, e.g. here
> <https://github.com/lme4/lme4/blob/master/R/lmer.R#L814-L838>, that
> tries to look for data in different possible locations, but I don't
> think anything works perfectly/robustly.
> 
> https://stackoverflow.com/questions/14945274/determine-whether-evaluation-of-an-argument-will-fail-due-to-non-existence
> 
> On Mon, Sep 23, 2024 at 3:54 PM Ivan Krylov via R-devel
> <r-devel using r-project.org> wrote:
>>
>> В Sun, 22 Sep 2024 10:23:50 -0400
>> John Fox <jfox using mcmaster.ca> пишет:
>>
>>>> Evaluating object$call$data in the environment of the suggested
>>>> nlme:::model.matrix.lme function may also not work right. Without an
>>>> explicit copy of the data, the best environment to evaluate it in
>>>> would be parent.frame().
>>>
>>> I'm afraid that I don't understand the suggestion. Isn't
>>> parent.frame() the default for the envir argument of eval()? Do you
>>> mean the parent frame of the call to model.matrix.lme()?
>>
>> Yes, I do mean the parent frame of the model.matrix.lme() function
>> call. While eval()'s default for the 'envir' argument is
>> parent.frame(), this default value is evaluated in the context of the
>> eval() call. Letting model.matrix.lme() call eval() results in the
>> 'envir' being the eval()'s parent, the model.matrix.lme() call frame.
>>
>> In most cases, model.matrix.lme() works as intended: either lme() has
>> been given the 'data' argument, so object$data is not NULL and the
>> branch to eval() is not taken, or 'data' has not been given, so both
>> object$data and object$call$data are NULL, and NULL doesn't cause any
>> harm when evaluated in any environment. In the latter case
>> model.matrix.default() can access the variables in the environment of
>> the formula.
>>
>> With keep.data = FALSE, the function may evaluate object$call$data in
>> the wrong environment:
>>
>> maybe_model_matrix <- function(X)
>>   model.matrix(lme(distance ~ Sex, random = ~ 1 | Subject, X,
>>                    contrasts=list(Sex=contr.sum), keep.data=FALSE))
>>
>> maybe_model_matrix(Orthodont)
>> # Error in eval(object$call$data) : object 'X' not found
>>
>> ...but then model.matrix.default doesn't work on such objects either,
>> and if the user wanted the data to be accessible, they could have set
>> keep.data = TRUE. I can't tell whether evaluating object$call$data in
>> environment(object$formula) is a better or worse idea than
>> parent.frame().
>>
>> --
>> Best regards,
>> Ivan
>>
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