R help - Jun 2005 - Caution on the use of model.matrix.

I have just been bitten by a quirk in the behaviour of model.matrix.
I used model.matrix inside a function, and passed to it a formula
that was built elsewhere.

The formula was of the form ``y ~ x + w + z''.  Now, model.matrix
cheerfully accepts formulae of this form, although it only
***needs*** the right hand side, i.e. ``~ x + w + z'' --- the
``y''
can be dropped (but in general needn't be).

The quirk by which I was bitten was that if the y column of the data
frame being used contains missing values, then the corresponding rows
are dropped (silently) and the resulting design matrix has rows
corresponding only to the non-missing values of y.  This was not the
desired behaviour in my application.

Might I respectfully suggest to R Core that a WARNING be added to the
help for model.matrix to the effect that

		model.matrix(y~x + w + z,XXX)
and
		model.matrix(~x + w + z,XXX)

give DIFFERENT results if the column ``y'' of the data frame XXX
contains missing values?

					cheers,

						Rolf Turner
						rolf at math.unb.ca

I think you could bit that using (inside your function) something like 
this

old.o <- options(na.action = na.fail)
# old.o <- options(na.action = na.pass)
on.exit(old.o)


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/336899
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
     http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Rolf Turner" <rolf at math.unb.ca>
To: <r-help at stat.math.ethz.ch>
Sent: Thursday, June 02, 2005 4:14 PM
Subject: [R] Caution on the use of model.matrix.

>I have just been bitten by a quirk in the behaviour of model.matrix.
> I used model.matrix inside a function, and passed to it a formula
> that was built elsewhere.
>
> The formula was of the form ``y ~ x + w + z''.  Now, model.matrix
> cheerfully accepts formulae of this form, although it only
> ***needs*** the right hand side, i.e. ``~ x + w + z'' --- the
``y''
> can be dropped (but in general needn't be).
>
> The quirk by which I was bitten was that if the y column of the data
> frame being used contains missing values, then the corresponding 
> rows
> are dropped (silently) and the resulting design matrix has rows
> corresponding only to the non-missing values of y.  This was not the
> desired behaviour in my application.
>
> Might I respectfully suggest to R Core that a WARNING be added to 
> the
> help for model.matrix to the effect that
>
> model.matrix(y~x + w + z,XXX)
> and
> model.matrix(~x + w + z,XXX)
>
> give DIFFERENT results if the column ``y'' of the data frame XXX
> contains missing values?
>
> cheers,
>
> Rolf Turner
> rolf at math.unb.ca
>
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! 
> http://www.R-project.org/posting-guide.html
>

Brian Ripley wrote:
> <snip> But the real problem is more likely that Rolf has not passed 
> model.matrix a model frame, so it calls model.frame() internally.  The 
> help page is a bit confused in that it says
> 
>      data: a data frame created with 'model.frame'.
> 
> which the default for the argument is not.  So a better solution would 
> then be to call model.frame and pass a model frame to model.matrix.
> 
> delete.response() might also be useful.
> 
> The suggested warning only applies if `data' is not supplied.
	I don't grok this.  I ***did*** supply data (in the form
	of a data frame, not a model frame).  My call was of the form

		X <- model.matrix(fmla,XXX)

	where (originally) ``fmla'' was a formula with the structure
	``y ~ x + w + z'', and XXX was a data frame with columns
	``y'', ``x'', ``w'', and ``z''.  (The response
variable ``y''
	had NAs in it, which caused the problem.) The data frame XXX was
	``input data''; it was not created with model.frame, but it
	was data nonetheless.

	I replaced the forgoing call with

		X <- model.matrix(fmla[-2],XXX)

	(the ``-2'' causing the ``y'' part of the formula to
	be discarded) and got the results I wanted.

	There may be a better way of achieving my goal, but
	I'm happy with my method --- unless someone points out
	lurking hazzards that have so far not been apparent to me.

	I merely wanted to point out to others the somewhat
	unintuitive behaviour of model.matrix.

				cheers,

					Rolf Turner
					rolf at math.unb.ca