>>>>> Fox, John
>>>>> on Fri, 22 Feb 2019 17:40:15 +0000 writes:
> Dear Martin and Ben, I agree that a warning is a good idea
> (and perhaps that wasn't clear in my response to Ben's
> post).
> Also, it would be nice to correct the omission in the help
> file, which as far as I could see doesn't mention that a
> contrast-generating function (as opposed to its quoted
> name) can be an element of the contrasts.arg list.
> Best, John
Thank you John for the clarification and the reminder about
filling the omission there!
Prepared to go (into the sources) now.
Martin
>> -----Original Message----- From: Martin Maechler
>> [mailto:maech...@stat.math.ethz.ch] Sent: Friday,
>> February 22, 2019 11:50 AM To: Ben Bolker
>> <bbol...@gmail.com> Cc: Fox, John <j...@mcmaster.ca>;
>> r-devel@r-project.org Subject: Re: [Rd]
>> model.matrix.default() silently ignores bad contrasts.arg
>>
>> >>>>> Ben Bolker >>>>> on Thu, 21 Feb 2019 08:18:51 -0500
>> writes:
>>
>> > On Thu, Feb 21, 2019 at 7:49 AM Fox, John
>> <j...@mcmaster.ca> wrote:
>> >>
>> >> Dear Ben,
>> >>
>> >> Perhaps I'm missing the point, but contrasts.arg is
>> documented to be a list. From ?model.matrix:
>> "contrasts.arg: A list, whose entries are values (numeric
>> matrices or character strings naming functions) to be
>> used as replacement values for the contrasts replacement
>> function and whose names are the names of columns of data
>> containing factors."
>>
>> > I absolutely agree that this is not a bug/behaves as
>> documented (I > could have said that more clearly). It's
>> just that (for reasons I > attempted to explain) this is
>> a really easy mistake to make.
>>
>> >> This isn't entirely accurate because a function also
>> works as a named element of the list (in addition to a
>> character string naming a function and a contrast
>> matrix), as your example demonstrates, but nowhere that
>> I'm aware of is it suggested that a non-list should work.
>> >>
>> >> It certainly would be an improvement if specifying
>> contrast.arg as a non- list generated an error or warning
>> message, and it at least arguably would be convenient to
>> allow a general contrast specification such as
>> contrasts.arg- "contr.sum", but I don't see a bug here.
>>
>> > I agree. That's what my patch does (throws a warning
>> message if > contrasts.arg is non-NULL and not a list).
>>
>> I currently do think this is a good idea... "even though"
>> I'm 99% sure that this will make work for package
>> maintainers and others whose code may suddenly show
>> warnings. I hope they would know better than
>> suppressWarnings(.) ...
>>
>> I see a version of the patch using old style indentation
>> which makes the diff even "considerably" smaller -- no
>> need to submit this different, though -- and I plan to
>> test that a bit, and commit eventually to R-devel,
>> possibly in a 5 days or so.
>>
>> Thank you Ben for the suggestion and patch ! Martin
>>
>> > cheers > Ben Bolker
>>
>> >> Best, >> John
>> >>
>> >> -------------------------------------------------
>> >> John Fox, Professor Emeritus >> McMaster University >>
>> Hamilton, Ontario, Canada >> Web:
>> http::/socserv.mcmaster.ca/jfox
>> >>
>> >> > On Feb 20, 2019, at 7:14 PM, Ben Bolker
>> <bbol...@gmail.com> wrote:
>> >> >
>> >> > An lme4 user pointed out
>> <https://github.com/lme4/lme4/issues/491> that >> >
>> passing contrasts as a string or symbol to [g]lmer (which
>> would work if >> > we were using `contrasts<-` to set
>> contrasts on a factor variable) is >> > *silently
>> ignored*. This goes back to model.matrix(), and seems bad
>> >> > (this is a very easy mistake to make, because of the
>> multitude of ways >> > to specify contrasts for factors
>> in R - e.g. options(contrasts=...); >> > setting
>> contrasts on the specific factors; passing contrasts as a
>> list >> > to the model function ... )
>> >> >
>> >> > The relevant code is here:
>> >> >
>> >> > https://github.com/wch/r-
>> source/blob/trunk/src/library/stats/R/models.R#L578-L603
>> >> >
>> >> > The following code shows the problem: a
>> plain-vanilla model.matrix() >> > call with no contrasts
>> argument, followed by two wrong contrasts >> > arguments,
>> followed by a correct contrasts argument.
>> >> >
>> >> > data(cbpp, package="lme4") >> > mf1 <-
>> model.matrix(~period, data=cbpp) >> > mf2 <-
>> model.matrix(~period, contrasts.arg="contr.sum",
>> data=cbpp) >> > all.equal(mf1,mf2) ## TRUE >> > mf3 <-
>> model.matrix(~period, contrasts.arg=contr.sum, data=cbpp)
>> >> > all.equal(mf1,mf3) ## TRUE >> > mf4 <-
>> model.matrix(~period,
>> contrasts.arg=list(period=contr.sum), >> > data=cbpp) >>
>> > isTRUE(all.equal(mf1,mf4)) ## FALSE
>> >> >
>> >> >
>> >> > I've attached a potential patch for this, which is
>> IMO the mildest >> > possible case (if contrasts.arg is
>> non-NULL and not a list, it produces >> > a warning). I
>> haven't been able to test it because of some mysterious
>> >> > issues I'm having with re-making R properly ...
>> >> >
>> >> > Thoughts? Should I submit this as a bug
>> report/patch?
>> >> >
>> >> > cheers >> > Ben Bolker
>> >>
>> >> >
>> <models.R.diff>______________________________________________
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
