Diff of /pkg/R/Matrix.R

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	revision 1548, Mon Sep 11 22:13:07 2006 UTC	revision 2110, Sat Jan 26 20:59:26 2008 UTC
#	Line 3	Line 3
3
4	### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)	### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5
6	setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))	setAs("Matrix", "sparseMatrix", function(from) as(from, "CsparseMatrix"))
7		setAs("Matrix", "CsparseMatrix", function(from) as_Csparse(from))
8	setAs("Matrix", "denseMatrix",  function(from) as_dense(from))	setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
9
10		## Maybe TODO:
11		## setAs("Matrix", "nMatrix", function(from) ....)
12
13		## Most of these work; this is a last resort:
14	setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:	setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
15	function(from) .bail.out.2("coerce", class(from), class(to)))	function(from) .bail.out.2("coerce", class(from), class(to)))
16		setAs(from = "matrix", to = "Matrix", function(from) Matrix(from))
17
18	## ## probably not needed eventually:	## ## probably not needed eventually:
19	## setAs(from = "ddenseMatrix", to = "matrix",	## setAs(from = "ddenseMatrix", to = "matrix",
#	Line 25	Line 31
31	setMethod("head", signature(x = "Matrix"), utils::head.matrix)	setMethod("head", signature(x = "Matrix"), utils::head.matrix)
32	setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)	setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
33
34		setMethod("drop", signature(x = "Matrix"),
35		function(x) if(all(dim(x) != 1)) x else drop(as(x, "matrix")))
36
37	## slow "fall back" method {subclasses should have faster ones}:	## slow "fall back" method {subclasses should have faster ones}:
38	setMethod("as.vector", signature(x = "Matrix", mode = "missing"),	setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
39	function(x) as.vector(as(x, "matrix")))	function(x) as.vector(as(x, "matrix")))
#	Line 35	Line 44
44	setMethod("as.logical", signature(x = "Matrix"),	setMethod("as.logical", signature(x = "Matrix"),
45	function(x, ...) as.logical(as.vector(x)))	function(x, ...) as.logical(as.vector(x)))
46
47		setMethod("cov2cor", signature(V = "Matrix"),
48		function(V) as(cov2cor(as(V, "matrix")), "dpoMatrix"))
49
50	## "base" has an isSymmetric() S3-generic since R 2.3.0	## "base" has an isSymmetric() S3-generic since R 2.3.0
51	setMethod("isSymmetric", signature(object = "symmetricMatrix"),	setMethod("isSymmetric", signature(object = "symmetricMatrix"),
#	Line 54	Line 65
65
66	setMethod("dim", signature(x = "Matrix"),	setMethod("dim", signature(x = "Matrix"),
67	function(x) x@Dim, valueClass = "integer")	function(x) x@Dim, valueClass = "integer")
68
69		setMethod("length", "Matrix", function(x) prod(dim(x)))
70
71	setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)	setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
72
73
74	## not exported but used more than once for "dimnames<-" method :	## not exported but used more than once for "dimnames<-" method :
75	## -- or do only once for all "Matrix" classes ??	## -- or do only once for all "Matrix" classes ??
76	dimnamesGets <- function (x, value) {	dimnamesGets <- function (x, value) {
#	Line 73	Line 89
89	setMethod("unname", signature("Matrix", force="missing"),	setMethod("unname", signature("Matrix", force="missing"),
90	function(obj) { obj@Dimnames <- list(NULL,NULL); obj})	function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
91
92		setMethod("all", signature(x = "Matrix"),
93		function(x, ..., na.rm)
94		callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
95
96		setMethod("any", signature(x = "Matrix"),
97		function(x, ..., na.rm)
98		callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
99
100		## NOTE:  "&" and "|"  are now in group "Logic" c "Ops" --> ./Ops.R
101		##        "!" is in ./not.R
102
103
104	Matrix <-	Matrix <-
105	function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,	function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
106	sparse = NULL, forceCheck = FALSE)	sparse = NULL, forceCheck = FALSE)
107	{	{
108	sparseDefault <- function(m)	sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
	prod(dim(m)) > 2*sum(is.na(m <- as(m, "matrix")) | m != 0)
109
110	i.M <- is(data, "Matrix")	i.M <- is(data, "Matrix")
111	if(is.null(sparse) && (i.M || is(data, "matrix")))	if(!i.M && inherits(data, "table")) # special treatment
112		class(data) <- "matrix" # "matrix" first for S4 dispatch
113		if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
114	sparse <- sparseDefault(data)	sparse <- sparseDefault(data)
115
116	doDN <- TRUE	doDN <- TRUE
117	if (i.M && !forceCheck) {	if (i.M) {
118		if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
119		warning("'nrow', 'ncol', etc, are disregarded when 'data' is \"Matrix\" already")
120	sM <- is(data,"sparseMatrix")	sM <- is(data,"sparseMatrix")
121	if((sparse && sM) || (!sparse && !sM))	if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
122	return(data)	return(data)
123	## else : convert  dense <-> sparse -> at end	## else : convert  dense <-> sparse -> at end
124	}	}
#	Line 96	Line 127
127	nrow <- ceiling(length(data)/ncol)	nrow <- ceiling(length(data)/ncol)
128	else if (missing(ncol))	else if (missing(ncol))
129	ncol <- ceiling(length(data)/nrow)	ncol <- ceiling(length(data)/nrow)
130	if(length(data) == 1 && !is.na(data) && data == 0 &&	if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
131	!identical(sparse, FALSE)) {	## Matrix(0, ...) : always sparse unless "sparse = FALSE":
132		if(is.null(sparse)) sparse1 <- sparse <- TRUE
133	if(is.null(sparse)) sparse <- TRUE	i.M <- sM <- TRUE
134	## will be sparse: do NOT construct full matrix!	## will be sparse: do NOT construct full matrix!
135	data <- new(if(is.numeric(data)) "dgTMatrix" else	data <- new(if(is.numeric(data)) "dgTMatrix" else
136	if(is.logical(data)) "lgTMatrix" else	if(is.logical(data)) "lgTMatrix" else
#	Line 107	Line 138
138	Dim = as.integer(c(nrow,ncol)),	Dim = as.integer(c(nrow,ncol)),
139	Dimnames = if(is.null(dimnames)) list(NULL,NULL)	Dimnames = if(is.null(dimnames)) list(NULL,NULL)
140	else dimnames)	else dimnames)
141	} else { ## normal case	} else { ## normal case - using .Internal() to avoid more copying
142		if(getRversion() >= "2.7.0")
143		data <- .Internal(matrix(data, nrow, ncol, byrow, dimnames))
144		else {
145	data <- .Internal(matrix(data, nrow, ncol, byrow))	data <- .Internal(matrix(data, nrow, ncol, byrow))
146		dimnames(data) <- dimnames
147		}
148	if(is.null(sparse))	if(is.null(sparse))
149	sparse <- sparseDefault(data)	sparse <- sparseDefault(data)
	dimnames(data) <- dimnames
150	}	}
151	doDN <- FALSE	doDN <- FALSE
152	}	} else if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
153		warning("'nrow', 'ncol', etc, are disregarded for matrix 'data'")
154
155	## 'data' is now a "matrix" or "Matrix"	## 'data' is now a "matrix" or "Matrix"
156	if (doDN && !is.null(dimnames))	if (doDN && !is.null(dimnames))
157	dimnames(data) <- dimnames	dimnames(data) <- dimnames
#	Line 127	Line 164
164	if(isDiag)	if(isDiag)
165	isDiag <- isDiagonal(data)	isDiag <- isDiagonal(data)
166
	### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
167	## Find proper matrix class 'cl'	## Find proper matrix class 'cl'
168	cl <-	cl <-
169	if(isDiag)	if(isDiag && !isTRUE(sparse1))
170	"diagonalMatrix" # -> will automatically check for type	"diagonalMatrix" # -> will automatically check for type
171	else {	else {
172	## consider it's type	## consider it's type
#	Line 159	Line 194
194	}, sep="")	}, sep="")
195	}	}
196
197	## Now coerce and return	## Can we coerce and be done?
198		if(!canCoerce(data,cl)) { ## try to coerce ``via'' virtual classes
199		if(sparse && !sM)
200		data <- as(data, "sparseMatrix")
201		else if(!sparse && !is(data, "denseMatrix"))
202		data <- as(data, "denseMatrix")
203		if(isTri && !is(data, "triangularMatrix"))
204		data <- as(data, "triangularMatrix")
205		else if(isSym && !is(data, "symmetricMatrix"))
206		data <- as(data, "symmetricMatrix")
207		}
208		## now coerce in any case .. maybe producing sensible error message:
209	as(data, cl)	as(data, cl)
210	}	}
211
#	Line 170	Line 216
216
217	setMethod("%*%", signature(x = "Matrix", y = "numeric"),	setMethod("%*%", signature(x = "Matrix", y = "numeric"),
218	function(x, y) callGeneric(x, as.matrix(y)))	function(x, y) callGeneric(x, as.matrix(y)))
219	setMethod("%*%", signature(x = "numeric", y = "Matrix"),	setMethod("%*%", signature(x = "numeric", y = "Matrix"),
220	function(x, y) callGeneric(rbind(x), y))	function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
221
222		setMethod("%*%", signature(x = "Matrix", y = "matrix"),
223		function(x, y) callGeneric(x, Matrix(y)))
224		setMethod("%*%", signature(x = "matrix", y = "Matrix"),
225		function(x, y) callGeneric(Matrix(x), y))
226
227
228	setMethod("crossprod", signature(x = "Matrix", y = "numeric"),	setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
229	function(x, y = NULL) callGeneric(x, as.matrix(y)))	function(x, y = NULL) callGeneric(x, as.matrix(y)))
230	setMethod("crossprod", signature(x = "numeric", y = "Matrix"),	setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
231	function(x, y = NULL)  callGeneric(as.matrix(x), y))	function(x, y = NULL)  callGeneric(as.matrix(x), y))
232
233		setMethod("crossprod", signature(x = "Matrix", y = "matrix"),
234		function(x, y = NULL) callGeneric(x, Matrix(y)))
235		setMethod("crossprod", signature(x = "matrix", y = "Matrix"),
236		function(x, y = NULL) callGeneric(Matrix(x), y))
237
238	## The as.matrix() promotion seems illogical to MM,	## The as.matrix() promotion seems illogical to MM,
239	## but is according to help(tcrossprod, package = "base") :	## but is according to help(tcrossprod, package = "base") :
240	setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),	setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
241	function(x, y = NULL) callGeneric(x, as.matrix(y)))	function(x, y = NULL) callGeneric(x, as.matrix(y)))
242	setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),	setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
243	function(x, y = NULL)  callGeneric(as.matrix(x), y))	function(x, y = NULL)  callGeneric(as.matrix(x), y))
244		setMethod("tcrossprod", signature(x = "Matrix", y = "matrix"),
245		function(x, y = NULL) callGeneric(x, Matrix(y)))
246		setMethod("tcrossprod", signature(x = "matrix", y = "Matrix"),
247		function(x, y = NULL) callGeneric(Matrix(x), y))
248
249		## maybe not 100% optimal, but elegant:
250		setMethod("solve", signature(a = "Matrix", b = "missing"),
251		function(a, b, ...) solve(a, Diagonal(nrow(a))))
252
253	setMethod("solve", signature(a = "Matrix", b = "numeric"),	setMethod("solve", signature(a = "Matrix", b = "numeric"),
254	function(a, b, ...) callGeneric(a, as.matrix(b)))	function(a, b, ...) callGeneric(a, Matrix(b)))
255		setMethod("solve", signature(a = "Matrix", b = "matrix"),
256		function(a, b, ...) callGeneric(a, Matrix(b)))
257		setMethod("solve", signature(a = "matrix", b = "Matrix"),
258		function(a, b, ...) callGeneric(Matrix(a), b))
259
260		## when no sub-class method is found, bail out
261		setMethod("solve", signature(a = "Matrix", b = "Matrix"),
262		function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
263
264	## bail-out methods in order to get better error messages	## bail-out methods in order to get better error messages
265	setMethod("%*%", signature(x = "Matrix", y = "Matrix"),	setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
#	Line 214	Line 286
286	setMethod("kronecker", signature(X = "Matrix", Y = "ANY",	setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
287	FUN = "ANY", make.dimnames = "ANY"),	FUN = "ANY", make.dimnames = "ANY"),
288	function(X, Y, FUN, make.dimnames, ...) {	function(X, Y, FUN, make.dimnames, ...) {
289		if(is(X, "sparseMatrix"))
290		warning("using slow kronecker() method")
291	X <- as(X, "matrix") ; Matrix(callGeneric()) })	X <- as(X, "matrix") ; Matrix(callGeneric()) })
292
293	setMethod("kronecker", signature(X = "ANY", Y = "Matrix",	setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
294	FUN = "ANY", make.dimnames = "ANY"),	FUN = "ANY", make.dimnames = "ANY"),
295	function(X, Y, FUN, make.dimnames, ...) {	function(X, Y, FUN, make.dimnames, ...) {
296		if(is(Y, "sparseMatrix"))
297		warning("using slow kronecker() method")
298	Y <- as(Y, "matrix") ; Matrix(callGeneric()) })	Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
299
300
301		## FIXME: All of these should never be called
302		setMethod("chol", signature(x = "Matrix"),
303		function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
304		setMethod("determinant", signature(x = "Matrix"),
305		function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
306
307	setMethod("diag", signature(x = "Matrix"),	setMethod("diag", signature(x = "Matrix"),
308	function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))	function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
309	setMethod("t", signature(x = "Matrix"),	setMethod("t", signature(x = "Matrix"),
310	function(x) .bail.out.1(.Generic, class(x)))	function(x) .bail.out.1(.Generic, class(x)))
311
312	## Group Methods	setMethod("norm", signature(x = "Matrix", type = "character"),
313	setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)	function(x, type, ...) .bail.out.1(.Generic, class(x)))
314	## "fallback":	setMethod("rcond", signature(x = "Matrix", type = "character"),
315	setMethod("-", signature(e1 = "Matrix", e2 = "missing"),	function(x, type, ...) .bail.out.1(.Generic, class(x)))
316	function(e1) {
317	warning("inefficient method used for \"- e1\"")
318	0-e1	## for all :
319		setMethod("norm", signature(x = "ANY", type = "missing"),
320		function(x, type, ...) norm(x, type = "O", ...))
321		setMethod("rcond", signature(x = "ANY", type = "missing"),
322		function(x, type, ...) rcond(x, type = "O", ...))
323
324
325
326
327
328		## MM: More or less "Cut & paste" from
329		## --- diff.default() from  R/src/library/base/R/diff.R :
330		setMethod("diff", signature(x = "Matrix"),
331		function(x, lag = 1, differences = 1, ...) {
332		if (length(lag) > 1 || length(differences) > 1 ||
333		lag < 1 || differences < 1)
334		stop("'lag' and 'differences' must be integers >= 1")
335		xlen <- nrow(x)
336		if (lag * differences >= xlen)
337		return(x[,FALSE][0])  # empty of proper mode
338
339		i1 <- -1:-lag
340		for (i in 1:differences)
341		x <- x[i1, , drop = FALSE] -
342		x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
343		x
344	})	})
345
346	## bail-outs:	setMethod("image", "Matrix",
347	setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),	function(x, ...) { # coercing to sparse is not inefficient,
348	function(e1, e2) {	##               since we need 'i' and 'j' for levelplot()
349	d <- dimCheck(e1,e2)	x <- as(as(x, "sparseMatrix"), "dMatrix")
350	.bail.out.2(.Generic, class(e1), class(e2))	callGeneric()
351	})	})
	setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
	function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
	setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
	function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
352
353
354		## Group Methods
355
356		##-> see ./Ops.R
357		##         ~~~~~
358		## For all  non-dMatrix objects, and note that  "all" and "any" have their own
359		setMethod("Summary", signature(x = "Matrix", na.rm = "ANY"),
360		function(x, ..., na.rm)
361		callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
362
363
364	### --------------------------------------------------------------------------	### --------------------------------------------------------------------------
365	###	###
#	Line 259	Line 372
372	## "x[]":	## "x[]":
373	setMethod("[", signature(x = "Matrix",	setMethod("[", signature(x = "Matrix",
374	i = "missing", j = "missing", drop = "ANY"),	i = "missing", j = "missing", drop = "ANY"),
375	function (x, i, j, drop) x)	function (x, i, j, ..., drop) x)
376
377	## missing 'drop' --> 'drop = TRUE'	## missing 'drop' --> 'drop = TRUE'
378	##                     -----------	##                     -----------
379	## select rows	## select rows
380	setMethod("[", signature(x = "Matrix", i = "index", j = "missing",	setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
381	drop = "missing"),	drop = "missing"),
382	function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))	function(x,i,j, ..., drop) {
383		if(nargs() == 2) { ## e.g. M[0] , M[TRUE],  M[1:2]
384		if(any(i) || prod(dim(x)) == 0)
385		as.vector(x)[i]
386		else ## save memory
387		as.vector(x[1,1])[FALSE]
388		} else {
389		callGeneric(x, i=i, , drop=TRUE)
390		##                  ^^
391		}
392		})
393
394	## select columns	## select columns
395	setMethod("[", signature(x = "Matrix", i = "missing", j = "index",	setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
396	drop = "missing"),	drop = "missing"),
397	function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))	function(x,i,j, ..., drop) callGeneric(x, j=j, drop= TRUE))
398	setMethod("[", signature(x = "Matrix", i = "index", j = "index",	setMethod("[", signature(x = "Matrix", i = "index", j = "index",
399	drop = "missing"),	drop = "missing"),
400	function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))	function(x,i,j, ..., drop) callGeneric(x, i=i, j=j, drop= TRUE))
401
402	## bail out if any of (i,j,drop) is "non-sense"	## bail out if any of (i,j,drop) is "non-sense"
403	setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),	setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
404	function(x,i,j, drop)	function(x,i,j, ..., drop)
405	stop("invalid or not-yet-implemented 'Matrix' subsetting"))	stop("invalid or not-yet-implemented 'Matrix' subsetting"))
406
407	## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],	## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
408	## The following is *both* for    M [ <logical>   ]	## The following is *both* for    M [ <logical>   ]
409	##                 and also for   M [ <logical> , ]	##                 and also for   M [ <logical> , ]
410	.M.sub.i.logical <- function (x, i, j, drop)	.M.sub.i.logical <- function (x, i, j, ..., drop)
411	{	{
412	nA <- nargs()	nA <- nargs()
413	if(nA == 2) { ##  M [ M >= 7 ]	if(nA == 2) { ##  M [ M >= 7 ]
414		## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
415	as(x, geClass(x))@x[as.vector(i)]	as(x, geClass(x))@x[as.vector(i)]
416	## -> error when lengths don't match	## -> error when lengths don't match
417	} else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]	} else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
418	stop("not-yet-implemented 'Matrix' subsetting") ## FIXME	stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
419
420	} else stop("nargs() = ", nA,	} else stop("nargs() = ", nA,
421	" should never happen; please report.")	".  Extraneous illegal arguments inside '[ .. ]' (i.logical)?")
422	}	}
423	setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",	setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
424	drop = "ANY"),	drop = "ANY"),
#	Line 303	Line 428
428	.M.sub.i.logical)	.M.sub.i.logical)
429
430
431	## "FIXME:"	## A[ ij ]  where ij is (i,j) 2-column matrix -- but also when that is logical mat!
432	## ------ get at  A[ ij ]  where ij is (i,j) 2-column matrix?	.M.sub.i.2col <- function (x, i, j, ..., drop)
433		{
434		nA <- nargs()
435		if(nA == 2) { ##  M [ cbind(ii,jj) ] or M [ <logical matrix> ]
436		if(!is.integer(nc <- ncol(i)))
437		stop(".M.sub.i.2col(): 'i' has no integer column number;\n",
438		"should never happen; please report")
439		if(is.logical(i))
440		return(.M.sub.i.logical(x, i=i)) # call with 2 args!
441		else if(!is.numeric(i) || nc != 2)
442		stop("such indexing must be by logical or 2-column numeric matrix")
443		m <- nrow(i)
444		if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
445		## else
446		i1 <- i[,1]
447		i2 <- i[,2]
448		## potentially inefficient -- FIXME --
449		unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
450
451		} else stop("nargs() = ", nA,
452		".  Extraneous illegal arguments inside '[ .. ]' (i.2col)?")
453		}
454		setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
455		.M.sub.i.2col)
456
457
458	### "[<-" : -----------------	### "[<-" : -----------------
#	Line 314	Line 461
461	setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",	setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
462	value = "ANY"),## double/logical/...	value = "ANY"),## double/logical/...
463	function (x, value) {	function (x, value) {
464	x@x <- value	## Fails for 'nMatrix' ... FIXME : make sure have method there
465		x@x <- rep(value, length = length(x@x))
466	validObject(x)# check if type and lengths above match	validObject(x)# check if type and lengths above match
467	x	x
468	})	})
469
470	## Method for all 'Matrix' kinds (rather than incomprehensible error messages);	## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
471		## ----------------
472		## The cheap general method --- FIXME: provide special ones; done for Tsparse..
473		## NOTE:  need '...' below such that setMethod() does
474		##        not use .local() such that nargs() will work correctly:
475		.M.repl.i.2col <- function (x, i, j, ..., value)
476		{
477		nA <- nargs()
478		if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value  or M [ Lmat ] <- value
479		if(!is.integer(nc <- ncol(i)))
480		stop(".M.repl.i.2col(): 'i' has no integer column number;\n",
481		"should never happen; please report")
482		else if(!is.numeric(i) || nc != 2)
483		stop("such indexing must be by logical or 2-column numeric matrix")
484		if(is.logical(i)) {
485		message(".M.repl.i.2col(): drop 'matrix' case ...")
486		## c(i) : drop "matrix" to logical vector
487		return( callGeneric(x, i=c(i), value=value) )
488		}
489		if(!is.integer(i)) storage.mode(i) <- "integer"
490		if(any(i < 0))
491		stop("negative values are not allowed in a matrix subscript")
492		if(any(is.na(i)))
493		stop("NAs are not allowed in subscripted assignments")
494		if(any(i0 <- (i == 0))) # remove them
495		i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
496		## now have integer i >= 1
497		m <- nrow(i)
498		## mod.x <- .type.kind[.M.kind(x)]
499		if(length(value) > 0 && m %% length(value) != 0)
500		warning("number of items to replace is not a multiple of replacement length")
501		## recycle:
502		value <- rep(value, length = m)
503		i1 <- i[,1]
504		i2 <- i[,2]
505		## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
506		for(k in seq_len(m))
507		x[i1[k], i2[k]] <- value[k]
508
509		x
510		} else stop("nargs() = ", nA,
511		".  Extraneous illegal arguments inside '[ .. ]' ?")
512		}
513
514		setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
515		value = "replValue"),
516		.M.repl.i.2col)
517
518
519		setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
520		value = "Matrix"),
521		function (x, i, j, ..., value)
522		callGeneric(x=x, , j=j, value = as.vector(value)))
523
524		setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
525		value = "Matrix"),
526		function (x, i, j, ..., value)
527		callGeneric(x=x, i=i, , value = as.vector(value)))
528
529		setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
530		value = "Matrix"),
531		function (x, i, j, ..., value)
532		callGeneric(x=x, i=i, j=j, value = as.vector(value)))
533
534		setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
535		value = "matrix"),
536		function (x, i, j, ..., value)
537		callGeneric(x=x, , j=j, value = c(value)))
538
539		setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
540		value = "matrix"),
541		function (x, i, j, ..., value)
542		callGeneric(x=x, i=i, , value = c(value)))
543
544		setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
545		value = "matrix"),
546		function (x, i, j, value)
547		callGeneric(x=x, i=i, j=j, value = c(value)))
548
549	## (ANY,ANY,ANY) is used when no `real method' is implemented :	## (ANY,ANY,ANY) is used when no `real method' is implemented :
550	setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",	setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
551	value = "ANY"),	value = "ANY"),
552	function (x, i, j, value) {	function (x, i, j, value) {
553	if(!is.atomic(value))	if(!is.atomic(value))
554	stop("RHS 'value' must match matrix class ", class(x))	stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
555		class(value),class(x)))
556	else stop("not-yet-implemented 'Matrix[<-' method")	else stop("not-yet-implemented 'Matrix[<-' method")
557	})	})
	## The trivial methods :
	setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
	function(x, y) x)
	setMethod("cbind2", signature(x = "Matrix", y = "missing"),
	function(x, y) x)
	setMethod("cbind2", signature(x = "NULL", y="Matrix"),
	function(x, y) x)
	setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
	function(x, y) x)
	setMethod("rbind2", signature(x = "Matrix", y = "missing"),
	function(x, y) x)
	setMethod("rbind2", signature(x = "NULL", y="Matrix"),
	function(x, y) x)
	## Makes sure one gets x decent error message for the unimplemented cases:
	setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
	function(x, y) {
	rowCheck(x,y)
	stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
	class(x), class(y)))
	})
	## Use a working fall back {particularly useful for sparse}:
	## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
	setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
	function(x, y) {
	colCheck(x,y)
	t(cbind2(t(x), t(y)))
	})

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