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 <j...@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
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