From bbo|ker @end|ng |rom gm@||@com  Thu Feb 21 14:18:51 2019
From: bbo|ker @end|ng |rom gm@||@com (Ben Bolker)
Date: Thu, 21 Feb 2019 08:18:51 -0500
Subject: [Rd] model.matrix.default() silently ignores bad contrasts.arg
In-Reply-To: <D3DC2A5A-7AE7-4EAE-B6EA-853C85972368@mcmaster.ca>
References: <3553_1550708062_x1L0EMNQ028449_7bf65e6d-839d-9475-79fd-3a8ee341929a@gmail.com>
 <D3DC2A5A-7AE7-4EAE-B6EA-853C85972368@mcmaster.ca>
Message-ID: <CABghstS8qm9hgbz6Laj-juTu9ra02jPZqhuU41_GkoKKJbzFYw@mail.gmail.com>

On Thu, Feb 21, 2019 at 7:49 AM Fox, John <jfox at 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).

  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 <bbolker at 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 at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>



[Rd] model.matrix.default() silently ignores bad contrasts.arg
Ben Bolker