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

[John Fox]

Dear Ivan,

Thank you for addressing my questions with your usual thoroughness. 
Please see below:

On 2024-09-21 2:51 p.m., Ivan Krylov wrote:
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> 
> Dear Prof. John Fox,
> 
> В Sat, 21 Sep 2024 12:47:49 -0400
> John Fox <jfox using mcmaster.ca> пишет:
> 
>>       NextMethod(formula(object),  data=eval(object$call$data),
>>                  contrasts.arg=object$contrasts)
> 
> The use of NextMethod worries me a bit. It will work as intended as
> long as everyone gives fully-named arguments to the generic, without
> relying on positional or partial matching, but may give unexpected
> results otherwise:

That's not an issue for car:::model.matrix.lme(), which isn't registered 
and so isn't accessible to users, but could be a problem if 
model.matrix.lme() is incorporated in the nlme package, as I suggested. 
An alternative that I think should work would be to call

     model.matrix(formula(object),  data=eval(object$call$data), 

                  contrasts.arg=object$contrasts, ...)

rather than NextMethod() from model.matrix.lme().

. . .

> 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()?

I tested car:::Anova.lme()/model.matrix.lme() with models fit to data in 
the global environment, in an attach()ed data frame, and within another 
function(), and didn't encounter any problems. For example:

------ snip -----

 > f <- function(){
+   OD <- Orthodont
+   m7 <- with(OD, lme(distance ~ Sex, random = ~ 1 | Subject,
+                      contrasts=list(Sex=contr.sum)))
+   Anova(m7, type=3)
+ }

 > f()
Analysis of Deviance Table (Type III tests)

Response: distance
                 Chisq Df Pr(>Chisq)
(Intercept) 3910.8377  1  < 2.2e-16
Sex            9.2921  1   0.002301

------ snip -----

Best,
  John

> 
> --
> Best regards,
> Ivan
> 
> [1] https://github.com/HenrikBengtsson/Wishlist-for-R/issues/44