From wdunlap at tibco.com  Thu Jan  5 22:15:33 2012
From: wdunlap at tibco.com (William Dunlap)
Date: Thu, 5 Jan 2012 21:15:33 +0000
Subject: [Rd] delete.response leaves response in attribute dataClasses
In-Reply-To: <E66794E69CFDE04D9A70842786030B932574D6@PA-MBX03.na.tibco.com>
References: <CAErODj9Aibpb4M=xq9+hHKw6Qurphxb2O7nb4A8x=F3UxPZLgA@mail.gmail.com>
	<E66794E69CFDE04D9A70842786030B932574D6@PA-MBX03.na.tibco.com>
Message-ID: <E66794E69CFDE04D9A70842786030B932574F5@PA-MBX03.na.tibco.com>

My feeling that everyone would index dataClasses by name was
wrong.  I looked through the packages that used dataClasses
and saw code that would break if the first (response) entry
were omitted.  (I didn't check to see if passing the output
of delete.response to these functions would be appropriate.)
E.g.,
file: AICcmodavg/R/predictSE.mer.r
  ##matrix with info on factors
  fact.frame <- attr(attr(orig.frame, "terms"), "dataClasses")[-1]

  ##continue if factors
  if(any(fact.frame == "factor")) {
    id.factors <- which(fact.frame == "factor")
    fact.name <- names(fact.frame)[id.factors] #identify the rows for factors

Some packages create a dataClass attribute for a model.frame
(not its terms attribute) that does not have any names:
file: caper/R/macrocaic.R
   attr(mf, "dataClasses") <- rep("numeric", dim(termFactors)[2])
.checkMFClasses() does not throw an error for that, but it
doesn't do any real checking either.

Most users of dataClasses do pass it to .checkMFClasses() to
compare it with newdata and that doesn't care if you have extra
entries in dataClasses.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 

> -----Original Message-----
> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of William Dunlap
> Sent: Thursday, January 05, 2012 12:57 PM
> To: Paul Johnson; R Devel List
> Subject: Re: [Rd] delete.response leaves response in attribute dataClasses
> 
> I had noticed the same thing but figured that most
> people (writers of predict methods) would be looking
> up entries in dataClasses by name and not by position,
> since predict's newdata argument need not have entries
> in the same order as the data used to fit the model.
> Hence the extra entry would not noticed (nor would it be
> missed if it were omitted).
> 
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
> 
> > -----Original Message-----
> > From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-project.org] On Behalf Of Paul Johnson
> > Sent: Thursday, January 05, 2012 12:27 PM
> > To: R Devel List
> > Subject: [Rd] delete.response leaves response in attribute dataClasses
> >
> > I posted this one as an R bug
> > (https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=14767), but
> > Prof. Ripley says I'm premature, and I should raise the question here.
> >
> > Here's the behavior I assert is a bug:
> > The output from delete.response on a terms object alters the formula
> > by removing the dependent variable. It removes the response from the
> > "variables" attribute and it changes the response attribute from 1 to
> > 0.  The response is removed from "predvars"
> >
> > But it leaves the name of the dependent variable first in the in
> > "dataClasses".  It caused an unexpected behavior in my code, so (as
> > usual) the bug may be mine, but in my heart, I believe it belongs to
> > delete.response.
> >
> > To illustrate, here's a terms object from a regression.
> >
> > > tt
> > y ~ x1 * x2 + x3 + x4
> > attr(,"variables")
> > list(y, x1, x2, x3, x4)
> > attr(,"factors")
> >    x1 x2 x3 x4 x1:x2
> > y   0  0  0  0     0
> > x1  1  0  0  0     1
> > x2  0  1  0  0     1
> > x3  0  0  1  0     0
> > x4  0  0  0  1     0
> > attr(,"term.labels")
> > [1] "x1"    "x2"    "x3"    "x4"    "x1:x2"
> > attr(,"order")
> > [1] 1 1 1 1 2
> > attr(,"intercept")
> > [1] 1
> > attr(,"response")
> > [1] 1
> > attr(,".Environment")
> > <environment: R_GlobalEnv>
> > attr(,"predvars")
> > list(y, x1, x2, x3, x4)
> > attr(,"dataClasses")
> >         y        x1        x2        x3        x4
> > "numeric" "numeric" "numeric" "numeric" "numeric"
> >
> > Now observe that delete.response removes the response from all
> > attributes except dataClasses.
> >
> > > delete.response(tt)
> > ~x1 * x2 + x3 + x4
> > attr(,"variables")
> > list(x1, x2, x3, x4)
> > attr(,"factors")
> >    x1 x2 x3 x4 x1:x2
> > x1  1  0  0  0     1
> > x2  0  1  0  0     1
> > x3  0  0  1  0     0
> > x4  0  0  0  1     0
> > attr(,"term.labels")
> > [1] "x1"    "x2"    "x3"    "x4"    "x1:x2"
> > attr(,"order")
> > [1] 1 1 1 1 2
> > attr(,"intercept")
> > [1] 1
> > attr(,"response")
> > [1] 0
> > attr(,".Environment")
> > <environment: R_GlobalEnv>
> > attr(,"predvars")
> > list(x1, x2, x3, x4)
> > attr(,"dataClasses")
> >         y        x1        x2        x3        x4
> > "numeric" "numeric" "numeric" "numeric" "numeric"
> >
> >
> > pj
> >
> > --
> > Paul E. Johnson
> > Professor, Political Science
> > 1541 Lilac Lane, Room 504
> > University of Kansas
> >
> > ______________________________________________
> > R-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
> 
> ______________________________________________
> R-devel at r-project.org mailing list
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[Rd] delete.response leaves response in attribute dataClasses
William Dunlap