R devel - Feb 2019 - model.matrix.default() silently ignores bad contrasts.arg

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."

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.

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

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
>

>>>>> Ben Bolker 
>>>>>     on Thu, 21 Feb 2019 08:18:51 -0500 writes:
    > 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).

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 <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>______________________________________________