>>>>> 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[] .... 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. 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. -- 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 ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel