On Tue, 18 May 2010 10:22:03 +0200, Martin Maechler
<maech...@stat.math.ethz.ch> wrote:
>>>>>> Tony Plate <tpl...@acm.org>
>>>>>> on Mon, 17 May 2010 20:51:12 -0600 writes:
>
> > Jim, yes, I have dealt with that particular challenge that
list(...)
> > throws an error for a call like f(x,,,) where the empty args match
> > to a
> > ... formal argument. Here's some fragments of code that I used
to
> > cope
> > with this:
>
> > # to find the empty anon args, must work with the unevaluated dot
> > args
> > dot.args.uneval <- match.call(expand.dots=FALSE)$...
> > if (length(dot.args.uneval))
> > missing.dot.args <- sapply(dot.args.uneval, function(arg)
> > is.symbol(arg) && as.character(arg)=="")
> > else
> > missing.dot.args <- logical(0)
> > ...
> > # Now we can work with evaluated dot args.
> > # Can't do dot.args <- list(...) because that will
> > # stop with an error for missing args.
> > dot.args <- mapply(dot.args.uneval, missing.dot.args,
> > FUN=function(arg, m) if (!m) eval(arg) else NULL)
>
> I don't have much time at the moment, to delve into Jim's code,
> nor to analyze what exactly Tony's does.
>
> Some notes however which I deem important:
>
> 1) My experiece in writing many S4 methods for "[" -- with the
> Matrix package, but also for 'Rmpfr' -- is that you
> really need to work with nargs()
> rather than with things like length(list(...))
>
> 2) If you really want to be compatible to the very rich
> semantics of S and R subsetting, you need to spend more time
> than you anticipate.
>
> - negative subscripts, names, logicals
>
> - A[i] for an array A where i can be a vector and then the
> array is treated as if it had no dim() attribute
> - A[i] for an array A where i is a *matrix* with k columns
> where k <- length(dim(A)) --- (k = 2 for matrices)
> - A[]
> ....
>
I might not get all of the way, but random access and logical subsetting
seem very doable.
> Are you sure you would not try to use
> setClass('myExample', contains = "array", representation = ...)
> rather than your
> setClass('myExample', representation(x = "array", ...))
> ?
> You would get all the "[" (and other array methods) for free,
> and would only need to specify those methods where 'myExample'
> really differed from array-subsetting.
My example is completely contrived. My back end are hdf5 files and so the
'[' method calls C functions, which at the moment grab contiguous blocks.
>
> 3) Lots of well-tested setMethod("[", ....) examples
> are in the sources of the Matrix package.
>
> There, BTW, I found it useful to use
>
> ## for 'i' in x[i] or A[i,] : (numeric = {double, integer})
> setClassUnion("index", members = c("numeric", "logical",
"character"))
>
> and then, e.g., a simple example method ..
>
> setMethod("[", signature(x = "denseMatrix", i = "index", j =
"missing",
> drop = "logical"),
> function (x, i, j, ..., drop) {
> if((na <- nargs()) == 3)
> r <- as(x, "matrix")[i, drop=drop]
> else if(na == 4)
> r <- as(x, "matrix")[i, , drop=drop]
> else stop("invalid nargs()= ",na)
> if(is.null(dim(r))) r else as(r, geClass(x))
> })
>
> The examples in the "Rmpfr" package are much less and simpler.
>
> To find the methods, for both, use
> fgrep 'setMethod("["' R/*R
> if you are on a decent OS and in side the package source directory.
>
Thanks, I had briefly scanned the matrix package - and the pointer to
nargs is extremely helpful.
thanks again, jim
> --
> Martin Maechler, ETH Zurich
>
> > Let me know if you need any further explanation.
>
> > Several warnings:
> > * I was using this code with S3 generics and methods.
> > * There are quite possibly better ways of detecting empty
> > unevaluated
> > arguments than 'is.symbol(arg) && as.character(arg)==""'.
> > * You'll probably want to be careful that the eval() in the last
> > line is
> > using the appropriate environment for your application.
>
> > I didn't read your code in detail, so apologies if the above is
> > off-the-point, but your verbal description of the problem and the
> > coding
> > style and comments in the "[" method for "myExample" triggered my
> > memory.
>
> > -- Tony Plate
>
> > On 05/17/2010 07:48 PM, James Bullard wrote:
> >> Apologies if I am not understanding something about how things
are
> >> being
> >> handled when using S4 methods, but I have been unable to find an
> >> answer to
> >> my problem for some time now.
> >>
> >> Briefly, I am associating the generic '[' with a class which I
wrote
> >> (here: myExample). The underlying back-end allows me to read
> >> contiguous
> >> slabs, e.g., 1:10, but not c(1, 10). I want to shield the user
from
> >> this
> >> infelicity, so I grab the slab and then subset in memory. The
main
> >> problem
> >> is with datasets with dim(.)> 2. In this case, the '...'
argument
> >> doesn't
> >> seem to be in a reasonable state. When it is indeed missing then
it
> >> properly reports that fact, however, when it is not missing it
> >> reports
> >> that it is not missing, but then the call to: list(...) throws an
> >> argument
> >> is missing exception.
> >>
> >> I cannot imagine that this has not occurred before, so I am
> >> expecting
> >> someone might be able to point me to some example code. I have
> >> attached
> >> some code demonstrating my general problem ((A) and (B) below) as
> >> well as
> >> the outline of the sub-selection code. I have to say that coding
> >> this has
> >> proven non-trivial and any thoughts on cleaning up the mess are
> >> welcome.
> >>
> >> As always, thanks for the help.
> >>
> >> Jim
> >>
> >> require(methods)
> >>
> >> setClass('myExample', representation = representation(x =
"array"))
> >>
> >> myExample<- function(dims = c(1,2)) {
> >> a<- array(rnorm(prod(dims)))
> >> dim(a)<- dims
> >> obj<- new("myExample")
> >> o...@x<- a
> >> return(obj)
> >> }
> >>
> >> setMethod("dim", "myExample", function(x) return(dim(x...@x)))
> >>
> >> functionThatCanOnlyGrabContiguous<- function(x, m, kall) {
> >> kall$x<- x...@x
> >> for (i in 1:nrow(m)) {
> >> kall[[i+2]]<- seq.int(m[i,1], m[i,2])
> >> }
> >> print(as.list(kall))
> >> return(eval(kall))
> >> }
> >>
> >> setMethod("[", "myExample", function(x, i, j, ..., drop = TRUE) {
> >> if (missing(...)){
> >> print("Missing!")
> >> }
> >> e<- list(...)
> >> m<- matrix(nrow = length(dim(x)), ncol = 2)
> >>
> >> if (missing(i))
> >> m[1,]<- c(1, dim(x)[1])
> >> else
> >> m[1,]<- range(i)
> >>
> >> if (length(dim(x))> 1) {
> >> if (missing(j))
> >> m[2,]<- c(1, dim(x)[2])
> >> else
> >> m[2,]<- range(j)
> >>
> >> k<- 3
> >> while (k<= nrow(m)) {
> >> if (k-2<= length(e))
> >> m[k,]<- range(e[[k-2]])
> >> else
> >> m[k,]<- c(1, dim(x)[k])
> >> k<- k + 1
> >> }
> >> }
> >> kall<- match.call()
> >> d<- functionThatCanOnlyGrabContiguous(x, m, kall)
> >>
> >> kall$x<- d
> >> if (! missing(i)) {
> >> kall[[3]]<- i - min(i) + 1
> >> }
> >> if (! missing(j)) {
> >> kall[[4]]<- j - min(j) + 1
> >> } else {
> >> if (length(dim(x))> 1)
> >> kall[[4]]<- seq.int(1, dim(x)[2])
> >> }
> >> ## XXX: Have to handle remaining dimensions, but since I can't
> >> ## really get a clean '...' it is on hold.
> >>
> >> eval(kall)
> >> })
> >>
> >> ## ############### 1-D
> >> m<- myExample(10)
> >> m...@x[c(1,5)] == m[c(1, 5)]
> >>
> >> ## ############### 2-D
> >> m<- myExample(c(10, 10))
> >> m...@x[c(1,5), c(1,5)] == m[c(1,5), c(1,5)]
> >> m...@x[c(5, 2),] == m[c(5,2),]
> >>
> >> ## ############### 3-D
> >> m<- myExample(c(1,3,4))
> >>
> >> ## (A) doesn't work
> >> m...@x[1,1:2,] == m[1,1:2,]
> >>
> >> ## (B) nor does this for different reasons.
> >> m[1,,1]
> >> m...@x[1,,1]
> >>
> >>
> >>> sessionInfo()
> >>>
> >> R version 2.11.0 (2010-04-22)
> >> x86_64-pc-linux-gnu
> >>
> >> locale:
> >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
> >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> >> [9] LC_ADDRESS=C LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods
base
> >>
> >> loaded via a namespace (and not attached):
> >> [1] tools_2.11.0
> >>
> >> ______________________________________________
> >> R-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-devel
> >>
> >>
> >>
>
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
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