From friendly at yorku.ca  Wed Dec 29 14:33:07 2010
From: friendly at yorku.ca (Michael Friendly)
Date: Wed, 29 Dec 2010 08:33:07 -0500
Subject: [Rd] aperm() should retain class of input object
In-Reply-To: <yajf7heu9cvy.fsf@gmail.com>
References: <4D18BF9A.6040404@yorku.ca> <yajf7heu9cvy.fsf@gmail.com>
Message-ID: <4D1B3893.8040500@yorku.ca>

On 12/28/2010 9:43 AM, Tim Hesterberg wrote:
> Having aperm() return an object of the same class is dangerous, there
> are undoubtedly classes for which that is not appropriate, producing an
> illegal object for that class or quietly giving incorrect results.
OK.  I can see that my initial proposal would be dangerous for xtabs 
objects without further
modifications and that it is unwise to change default behavior in base 
functions without
very strong reasons.
> Three alternatives are to:
> * add the keep.class option but with default FALSE
This first option is the minimally invasive corrective surgery.
This would put the burden on the user (or package writer), but at least 
make it known
that keep.class=TRUE is an option.  This version is

## add keep.class, non-generic
aperm <- function (a, perm, resize = TRUE, keep.class=FALSE)
{
     if (missing(perm))
         perm <- integer(0L)
     result <- .Internal(aperm(a, perm, resize))
     if(keep.class) class(result) <- class(a)
     result
}

> * make aperm a generic function
>    - without a keep.class argument
>    - with a ... argument
>    - methods for classes like table could have keep.class = TRUE
This would be much better, as long as an aperm.table method was added to 
base, to complement table() itself,
and gives the desired behavior for table objects by default.
This version seems to be:

## make generic, with ...
aperm <- function(a, ...)
     UseMethod("aperm", ...)

aperm.default <- function (a, perm, resize = TRUE, ...)
{
     if (missing(perm))
         perm <- integer(0L)
     .Internal(aperm(a, perm, resize))
}

aperm.table <- function(a, perm, resize=TRUE, keep.class=TRUE, ...)
{
     result <- aperm.default(a, perm, resize=resize)
     if(keep.class) class(result) <- class(a)
     result
}

But it throws an error, maybe because I haven't redefined aperm as a 
generic:

 > UCB <- aperm(UCBAdmissions, c(2,1,3))
Error in aperm(UCBAdmissions, c(2, 1, 3)) :
   '...' used in an incorrect context

The .table method does work as desired:

 > UCB <- aperm.table(UCBAdmissions, c(2,1,3))
 > str(UCB)
  table [1:2, 1:2, 1:6] 512 89 313 19 353 17 207 8 120 202 ...
  - attr(*, "dimnames")=List of 3
   ..$ Gender: chr [1:2] "Male" "Female"
   ..$ Admit : chr [1:2] "Admitted" "Rejected"
   ..$ Dept  : chr [1:6] "A" "B" "C" "D" ...
 >

> * make aperm a generic function
>    - without a keep.class argument
>    - with a ... argument
>    - default method have keep.class = TRUE
>
> The third option would give the proposed behavior by default, but
> allow a way out for classes where the behavior is wrong.  This puts
> the burden on a class author to realize the potential problem with
> aperm, so my preference is one of the first two options.
>
>> aperm() was designed for multidimensional arrays, but is also useful for
>> table objects, particularly
>> with the lattice, vcd and vcdExtra packages.  But aperm() was designed
>> and implemented before other
>> related object classes were conceived, and I propose a small tune-up to
>> make it more generally useful.
>>
>> The problem is that  aperm() always returns an object of class 'array',
>> which causes problems for methods
>> designed for table objects. It also requires some package writers to
>> implement both .array and .table
>> methods for the same functionality, usually one in terms of the other.
>> Some examples of unexpected, and initially perplexing results (when only
>> methods for one class are implemented)
>> are shown below.
>>
>>
>>> library(vcd)
>>> pairs(UCBAdmissions, shade=TRUE)
>>> UCB<- aperm(UCBAdmissions, c(2, 1, 3))
>>>
>>> # UCB is now an array, not a table
>>> pairs(UCB, shade=TRUE)
>> There were 50 or more warnings (use warnings() to see the first 50)
>>> # fix it, to get pairs.table
>>> class(UCB)<- "table"
>>> pairs(UCB, shade=TRUE)
>>>
>>
>>
>> Of course, I can define a new function, tperm() that does what I think
>> should be the expected behavior:
>>
>> # aperm, for table objects
>>
>> tperm<- function(a, perm, resize = TRUE) {
>>      result<- aperm(a, per, resize)
>>      class(result)<- class(a)
>>      result
>> }
>>
>> But I think it is more natural to include this functionality in aperm()
>> itself.  Thus, I propose the following
>> revision of base::aperm(), at the R level:
>>
>> aperm<- function (a, perm, resize = TRUE, keep.class=TRUE)
>> {
>>      if (missing(perm))
>>          perm<- integer(0L)
>>      result<- .Internal(aperm(a, perm, resize))
>>      if(keep.class) class(result)<- class(a)
>>      result
>> }
>>
>>
>> I don't think this would break any existing code, except where someone
>> depended on coercion to an array.
>> The drop-in replacement for aperm would set keep.class=FALSE by default,
>> but I think TRUE is  more
>> natural.
>>
>> FWIW, here are the methods for table and array objects
> >from my current (non-representative) session.
>>> methods(class="table")
>>   [1] as.data.frame.table barchart.table*     cloud.table*
>> contourplot.table*  dotplot.table*
>>   [6] head.table*         levelplot.table*    pairs.table*
>> plot.table*         print.table
>> [11] summary.table       tail.table*
>>
>>     Non-visible functions are asterisked
>>> methods(class="array")
>> [1] anyDuplicated.array as.data.frame.array as.raster.array*
>> barchart.array*     contourplot.array*  dotplot.array*
>> [7] duplicated.array    levelplot.array*    unique.array
>>
>>
>> --
>> Michael Friendly     Email: friendly AT yorku DOT ca
>> Professor, Psychology Dept.
>> York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
>> 4700 Keele Street    Web:http://www.datavis.ca
>> Toronto, ONT  M3J 1P3 CANADA


-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA



[Rd] aperm() should retain class of input object
Michael Friendly