Re: [R] setMethod for "["

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Fri, 21 Mar 2008 10:05:07 -0700

Hi Musa --

Musa Parmaksiz wrote:
> Hi Martin,
>
> Thanks for the suggestions.
>
> If possible I would avoid defining several methods with different
> signatures. For the first solution,namely
>
> setMethod("[",
> signature=signature(x="myClass"),
> function(x, i, j, ..., drop=FALSE)
> {
> if (missing(i) && missing(j))
> callNextMethod(x=x_at_x,,, ..., drop=drop)
> else if (missing(j))
> callNextMethod(x=x_at_x, i=i, , ..., drop=drop)
> else if (missing(i))
> callNextMethod(x=x_at_x, , j=j, ..., drop=drop)
> else
> callNextMethod(x=x_at_x, i=i, j=j, ..., drop=drop)
> })
>
> one cannot distinguish between test[1] and test[1,] ! I suspect we could
> use nargs()...

I thought I had seen a cleaner solution to this; perhaps someone else will contribute. Here's what I think:

One could do something like nargs() - length(list(...)) - !missing(drop), but as a class designer a better decision might be to define [1] to be the same as [1,], and provide other ways for the user to convert a matrix-like object to a vector-like object.

To make this point a bit stronger, an interpretation of '[' is that it returns a subset of the original object (i.e., an object of the same class as the original). This is in contrast to '[[', which might be interpreted as returning the contents of (a subset of) the object. '[' returning a vector-like object when invoked on a matrix-like object violates this interpretation, and might therefore be avoided.

Also, it might seem good to 'mimic' the behavior of [ on matrices. But remember that the method defined above matches arguments by name rather than position, so already one is departing from the way in which subsets work with the primitive [. I would say that this departure is an improvement over the situation with primitive [, and it would be a mistake to implement [ for myClass in such a way as to restore position-matching.

These are my opinions, probably others arrive at different conclusions.

Martin

> On Fri, Mar 21, 2008 at 12:43 AM, Martin Morgan <mtmorgan@fhcrc.org
> <mailto:mtmorgan_at_fhcrc.org>> wrote:
>
> Hi Musa --
>
> Musa Parmaksiz wrote:
> > Hi R-Help,
> >
> > Please consider the following simple case: I have a class like
> >
> > setClass("myClass",
> > representation(x="matrix", y="character"))
> >
> > and I would like to use the method *"["* for a *myClass* objects (but
> > changing the default *drop* argument from TRUE to FALSE):
> >
> > setMethod("[","myClass",
> > function(x,i,j,...,drop=FALSE)
> > {
> > x <- x_at_x
> > callNextMethod()
>
> I think you are hoping that x_at_x will be subsetted, and it appears that
> it is. But I think this is a bug. 'callNextMethod' without any arguments
> should be using the 'x' in the signature. This should result in an error
> like the one seen here
>
> setMethod("[",
> signature=signature(x="myClass"),
> function(x, i, j, ..., drop=FALSE)
> {
> callNextMethod()
> })
>
> > test[1,]
> Error in x[i = i, j = , ...] : object is not subsettable
>
> Normally, to change the value of the variable 'seen' by the next method,
> one would expect to have to write something like
>
>
> setMethod("[",
> signature=signature(x="myClass"),
> function(x, i, j, ..., drop=FALSE)
> {
> callNextMethod(x=x_at_x, i=i, j=j, ..., drop=drop)
> })
>
> You can now see how this is a little more complicated -- if j is missing
> in the original function call, then it can't be used in an assignment in
> callNextMethod. You'd have to write something like
>
> setMethod("[",
> signature=signature(x="myClass"),
> function(x, i, j, ..., drop=FALSE)
> {
> if (missing(i) && missing(j))
> callNextMethod(x=x_at_x,,, ..., drop=drop)
> else if (missing(j))
> callNextMethod(x=x_at_x, i=i, , ..., drop=drop)
> else if (missing(i))
> callNextMethod(x=x_at_x, , j=j, ..., drop=drop)
> else
> callNextMethod(x=x_at_x, i=i, j=j, ..., drop=drop)
> })
>
> or, since this is really an implementation that dispatches on the
> 'misssing'-ness of i, j, a series of methods like
>
> setMethod("[",
> signature=signature(
> x="myClass",
> i="ANY',
> j="missing")
> function(x, i, j, ..., drop=FALSE)
> {
> callNextMethod(x_at_x, i=i, , ..., drop=drop)
> })
>
> Notice too how it is necessary to specify the argument list in quite an
> odd way, with a ',' for the 'missing' variable(s). This is because "["
> is a so-called 'Primitive' function, and primitive functions match by
> position rather than the usual matching by name:
>
> > matrix(1:20,5)[4,2]
> [1] 9
> > matrix(1:20,5)[j=4,i=2]
> [1] 9
>
> !
>
> I read somewhere that when faced with learning complicated systems,
> otherwise intelligent people will develop wildly inaccurate stories to
> explain why the system 'works'. The above is my story.
>
> Martin
>
>
> > x<-as.myClass(x)
> > }
> > )
> >
> > suppose that *as.myClass* method has been already defined.
> Actually, all I
> > want is to pass all the arguments to *"["* method for *matrix*,
> except
> > changing the default behaviour for *drop*.
> >
> > When I execute:
> >> test<-new("myClass",x=cbind(1:3,4:6),y="a")
> >> test[1,] # works as expected
> > [1] 1 4
> >
> >> test[1,drop=TRUE] # does not work
> > Error: argument "j" is missing, with no default
> > Error in callNextMethod() : error in evaluating a 'primitive'
> next method
> >
> > but with a matrix the two cases work:
> >> m<-cbind(1:3,4:6)
> >> m[1,]
> > [1] 1 4
> >> m[1,drop=TRUE]
> > [1] 1
> >
> > Can you please advise me a solution for this problem?
> > Thank you in advance for the help.
> >
> > Musa
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help_at_r-project.org <mailto:R-help_at_r-project.org> mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
>

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793

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