Re: [R] setMethod "[" - extract by names within Slot

[Martin Morgan]

On 10/22/2011 08:03 AM, Omphalodes Verna wrote:
Thanks Martin.
Here is my ''updated'' code.

setClass("myClass", representation(ID.r = "numeric", ID.c = "character", DAT = 
"matrix"))

to.myClass<- function(ID.r, ID.c, DAT) {
     out<- new("myClass", ID.r = ID.r, ID.c = ID.c, DAT = DAT)
     return(out)
       }

setMethod("[", "myClass", function(x, i, j, drop = TRUE) {
     x@ID.r<- x@ID.r[i]
     x@ID.c<- x@ID.c[j]
     out.0<- x@DAT[i,j]
     out.1<- to.myClass(x@ID.r, x@ID.c, as.matrix(out.0))
     return(out.1)
   })

setMethod("[", c("myClass", "ANY", "character"),
     function(x, i, j, ..., drop = TRUE) {
     if(missing(i)) {x@ID.r<- x@ID.r} else {x@ID.r<- x@ID.r[i]}
     j<- which(j == x@ID.c)
     x@ID.c<- x@ID.c[j]
     out.0<- x@DAT[i, j]
     out.1<- to.myClass(x@ID.r, x@ID.c, as.matrix(out.0))
     return(out.1)
       })

a<- to.myClass(seq(1,25), c("A","A","B","B"), matrix(rnorm(100), nrow = 25))
a

a[1:20, ] #works
a[, 1:3] #works
a[1:10, 1:3] #works
a[, "A"] #works
a[5:20, "B"] #works

It works, but Is it normal to write two codes for setMethod???

Hi --

I defined the class as

setClass("A",
         representation=representation(
           rid="integer",
           cid="character",
           elt="matrix"))

A common pattern is that the methods provide a 'facade' that make 
different user inputs conform to a particular signature, and then all 
invoke a common function where the complicated work is done; sometimes 
the function is one of the methods. Here's where I'd do the work

setMethod("[", c("A", "numeric", "character"),
    function(x, i, j, ..., drop=TRUE)
{
    cidx <- match(j, x@cid)
    if (any(is.na(cidx)))
        stop("invalid 'j'")
    initialize(x, rid=x@rid[i], cid=x@cid[cidx],
               elt=x@elt[i, cidx, drop=FALSE])
})

This uses 'initialize' as a copy constructor. Any complicated code for 
subsetting would be added to this method, and only in one place.

For "[" a minimal facade needs to handle the cases where i, j, or both 
are missing -- these are the facade, doing some minimal work to make it 
possible to invoke the underlying work-horse


setMethod("[", c("A", "missing", "character"),
    function(x, i, j, ..., drop=TRUE)
{
    x[x@rid, j, ..., drop=drop]
})

setMethod("[", c("A", "numeric", "missing"),
    function(x, i, j, ..., drop=TRUE)
{
    x[i, x@cid, ..., drop=drop]
})

setMethod("[", c("A", "missing", "missing"),
    function(x, i, j, ..., drop=TRUE)
{
    x[x@rid, x@cid, ..., drop=drop]
})

You also want to use a numeric (actually, integer) value for the second 
argument. This requires two more facade methods, distinguishing between 
a 'missing' first argument and an 'ANY' first argument

setMethod("[", c("A", "ANY", "numeric"),
    function(x, i, j, ..., drop=TRUE)
{
    x[i, x@cid[j], ..., drop=TRUE]
})

setMethod("[", c("A", "missing", "numeric"),
    function(x, i, j, ..., drop=TRUE)
{
    x[, x@cid[j], ..., drop=drop]
})

Here are some tests

a <- new("A", rid=1:5, cid=c("A", "B", "C"), elt=matrix(1:15, nrow=5))
a[1:2, "A"]

a[1:2,]
a[,"A"]
a[,]

a[1:2, 1:2]
a[,1:2]

The use of 'numeric' is a little loose, allowing a[1.1,] for instance, 
but a stricter 'integer' is probably too inconvenient for the user. 
'rid' is a bit weird -- is the user supposed to index it (x@rid[i], 
x@elt[i,]) or match it (ridx = match(i, x@rid); x@rid[ridx], x@elt[ridx,])?

Martin

Nice weekend, OV


________________________________
From: Martin Morgan<mtmor...@fhcrc.org>

Cc: "r-help@r-project.org"<r-help@r-project.org>
Sent: Saturday, October 22, 2011 3:50 PM
Subject: Re: [R] setMethod "[" - extract by names within Slot

On 10/22/2011 02:11 AM, Omphalodes Verna wrote:
Hi R-helper!

I have problem with setMethods for "[". Here is example :

setClass("myClass", representation(ID.r = "numeric", ID.c = "character", DAT = 
"matrix"))

to.myClass<- function(ID.r, ID.c, DAT) {
       out<- new("myClass", ID.r = ID.r, ID.c = ID.c, DAT = DAT)
       return(out)
         }

setMethod("[", "myClass", function(x, i, j, drop) {
       x@ID.r<- x@ID.r[i]
       x@ID.c<- x@ID.c[j]
       out.0<- x@DAT[i,j]
       out.1<- to.myClass(x@ID.r, x@ID.c, as.matrix(out.0))
       return(out.1)
     })

a<- to.myClass(seq(1,25), c("A","A","B","B"), matrix(rnorm(100), nrow = 25))
a


a[1:20, ] #works
a[, 1:3] #works
a[1:10, 1:3] #works

a[, "A"] #not works

thinking about your code, this is the same as

    ID.c = c("A","A","B","B")
    j = "A"
    ID.c[j]
[1] NA



What is solution to write "[" methods for extraction by names of Slot "ID.c"

Maybe (untested)

    setMethod("[", c("myClass", "ANY", "character"),
        function(x, i, j, ..., drop=TRUE) {
            j = match(j, x@ID.c)
            x[i, j, ..., drop=TRUE]
       })


Thanks all. OV

     [[alternative HTML version deleted]]




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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.