Diff of /pkg/R/Matrix.R

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	revision 676, Sat Mar 26 15:59:18 2005 UTC	revision 2110, Sat Jan 26 20:59:26 2008 UTC
#	Line 1	Line 1
1	#### Toplevel ``virtual'' class "Matrix"	#### Toplevel ``virtual'' class "Matrix"
2
	## probably not needed eventually:
	setAs(from = "ddenseMatrix", to = "matrix",
	function(from) {
	if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
	array(from@x, dim = d, dimnames = dimnames(from))
	})
3
4	## private function to be used as show() method possibly more than once	### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
	prMatrix <- function(object) {
	d <- dim(object)
	cl <- class(object)
	cat(sprintf('%d x %d Matrix of class "%s"\n', d[1], d[2], cl))
	##- no longer needed: have no objects of virtual classes:
	##     if(cl == "Matrix") { ## have no data slot
	##         cat("Dim = ", d)
	##         if(any(sapply(object@Dimnames,length) > 0)) {
	##             cat("; Dimnames = ")
	##             str(object@Dimnames)
	##         }
	##         cat("\n")
	##     } else { # not "Matrix", hence have data 'x' slot
	m <- as(object, "matrix")
	maxp <- getOption("max.print")
	if(prod(d) <= maxp) print(m)
	else { ## d[1] > maxp / d[2] >= nr :
	nr <- maxp %/% d[2]
	n2 <- ceiling(nr / 2)
	print(head(m, max(1, n2)))
	cat("\n ..........\n\n")
	print(tail(m, max(1, nr - n2)))
	}
	## DEBUG: cat("str(.):\n") ; str(object)
	##    }
	invisible(object)# as print() S3 methods do
	}
	setMethod("show", signature(object = "ddenseMatrix"), prMatrix)
	setMethod("show", signature(object = "sparseMatrix"),
	function(object) {
	d <- dim(object)
	cl <- class(object)
	cat(sprintf('%d x %d sparse Matrix of class "%s"\n', d[1], d[2], cl))
	maxp <- getOption("max.print")
	if(prod(d) <= maxp) print(as(object, "matrix"))
	else { ## d[1] > maxp / d[2] >= nr :
	cat("\n Not printing large sparse matrix -- maybe increase options(max.print)\n")
	if(FALSE) { ### need storage economic "[,]" method for sparse!!
	nr <- maxp %/% d[2]
	n2 <- ceiling(nr / 2)
	print(head(m, max(1, n2)))
	cat("\n ..........\n\n")
	print(tail(m, max(1, nr - n2)))
	}
	}
	## DEBUG: cat("str(.):\n") ; str(object)
	invisible(object)
	})
5
6	## this may go away {since sparse matrices need something better!} :	setAs("Matrix", "sparseMatrix", function(from) as(from, "CsparseMatrix"))
7	setMethod("show", signature(object = "Matrix"), prMatrix)	setAs("Matrix", "CsparseMatrix", function(from) as_Csparse(from))
8		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:
15		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:
19		## setAs(from = "ddenseMatrix", to = "matrix",
20		##       function(from) {
21		##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
22		##        array(from@x, dim = d, dimnames = dimnames(from))
23		##       })
24
25	## should propagate to all subclasses:	## should propagate to all subclasses:
26	setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))	setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
27		## for 'Matrix' objects, as.array() should be equivalent:
28		setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
29
30		## head and tail apply to all Matrix objects for which subscripting is allowed:
31		setMethod("head", signature(x = "Matrix"), utils::head.matrix)
32		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}:
38		setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
39		function(x) as.vector(as(x, "matrix")))
40
41		## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
42		setMethod("as.numeric", signature(x = "Matrix"),
43		function(x, ...) as.numeric(as.vector(x)))
44		setMethod("as.logical", signature(x = "Matrix"),
45		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
51		setMethod("isSymmetric", signature(object = "symmetricMatrix"),
52		function(object,tol) TRUE)
53		setMethod("isSymmetric", signature(object = "triangularMatrix"),
54		## TRUE iff diagonal:
55		function(object,tol) isDiagonal(object))
56
57		setMethod("isTriangular", signature(object = "triangularMatrix"),
58		function(object, ...) TRUE)
59
60		setMethod("isTriangular", signature(object = "matrix"), isTriMat)
61
62		setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
63
64
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 87	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)
107	{	{
108	if (is(data, "Matrix")) return(data)	sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
109	if (is.matrix(data)) { val <- data }
110	else { ## cut & paste from "base::matrix" :	i.M <- is(data, "Matrix")
111		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)
115
116		doDN <- TRUE
117		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")
121		if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
122		return(data)
123		## else : convert  dense <-> sparse -> at end
124		}
125		else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
126	if (missing(nrow))	if (missing(nrow))
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	val <- .Internal(matrix(data, nrow, ncol, byrow))	if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
131	dimnames(val) <- dimnames	## Matrix(0, ...) : always sparse unless "sparse = FALSE":
132	}	if(is.null(sparse)) sparse1 <- sparse <- TRUE
133	as(val, "dgeMatrix")	i.M <- sM <- TRUE
134	}	## will be sparse: do NOT construct full matrix!
135		data <- new(if(is.numeric(data)) "dgTMatrix" else
136		if(is.logical(data)) "lgTMatrix" else
137		stop("invalid 'data'"),
138		Dim = as.integer(c(nrow,ncol)),
139		Dimnames = if(is.null(dimnames)) list(NULL,NULL)
140		else dimnames)
141		} 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))
146		dimnames(data) <- dimnames
147		}
148		if(is.null(sparse))
149		sparse <- sparseDefault(data)
150		}
151		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"
156		if (doDN && !is.null(dimnames))
157		dimnames(data) <- dimnames
158
159		## check for symmetric / triangular / diagonal :
160		isSym <- isSymmetric(data)
161		if((isTri <- !isSym))
162		isTri <- isTriangular(data)
163		isDiag <- isSym # cannot be diagonal if it isn't symmetric
164		if(isDiag)
165		isDiag <- isDiagonal(data)
166
167		## Find proper matrix class 'cl'
168		cl <-
169		if(isDiag && !isTRUE(sparse1))
170		"diagonalMatrix" # -> will automatically check for type
171		else {
172		## consider it's type
173		ctype <-
174		if(is(data,"Matrix")) class(data)
175		else {
176		if("complex" == (ctype <- typeof(data)))
177		"z" else ctype
178		}
179		ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
180		if(ctype == "z")
181		stop("complex matrices not yet implemented in Matrix package")
182		if(ctype == "i") {
183		warning("integer matrices not yet implemented in 'Matrix'; ",
184		"using 'double' ones'")
185		ctype <- "d"
186		}
187		paste(ctype,
188		if(sparse) {
189		if(isSym) "sCMatrix" else
190		if(isTri) "tCMatrix" else "gCMatrix"
191		} else { ## dense
192		if(isSym) "syMatrix" else
193		if(isTri) "trMatrix" else "geMatrix"
194		}, sep="")
195		}
196
197		## 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)
210		}
211
212		## Methods for operations where one argument is numeric
213
214		## Using as.matrix() and rbind()
215		## in order to get dimnames from names {at least potentially}:
216
217		setMethod("%*%", signature(x = "Matrix", y = "numeric"),
218		function(x, y) callGeneric(x, as.matrix(y)))
219		setMethod("%*%", signature(x = "numeric", y = "Matrix"),
220		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"),
229		function(x, y = NULL) callGeneric(x, as.matrix(y)))
230		setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
231		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,
239		## but is according to help(tcrossprod, package = "base") :
240		setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
241		function(x, y = NULL) callGeneric(x, as.matrix(y)))
242		setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
243		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"),
254		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
265		setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
266		function (x, y)
267		stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
268		class(x), class(y))))
269
270		setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
271		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
272		setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
273		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
274		setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
275		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
276		setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
277		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
278
279		## cheap fallbacks
280		setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
281		function(x, y = NULL) t(x) %*% y)
282		setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
283		function(x, y = NULL) x %*% t(y))
284
285		## There are special sparse methods; this is a "fall back":
286		setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
287		FUN = "ANY", make.dimnames = "ANY"),
288		function(X, Y, FUN, make.dimnames, ...) {
289		if(is(X, "sparseMatrix"))
290		warning("using slow kronecker() method")
291		X <- as(X, "matrix") ; Matrix(callGeneric()) })
292
293		setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
294		FUN = "ANY", make.dimnames = "ANY"),
295		function(X, Y, FUN, make.dimnames, ...) {
296		if(is(Y, "sparseMatrix"))
297		warning("using slow kronecker() method")
298		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"),
308		function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
309		setMethod("t", signature(x = "Matrix"),
310		function(x) .bail.out.1(.Generic, class(x)))
311
312		setMethod("norm", signature(x = "Matrix", type = "character"),
313		function(x, type, ...) .bail.out.1(.Generic, class(x)))
314		setMethod("rcond", signature(x = "Matrix", type = "character"),
315		function(x, type, ...) .bail.out.1(.Generic, class(x)))
316
317
318		## 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
	if(FALSE) { ##--- not-yet used -- {almost same code also in ./dgeMatrix.R }
325
326	## utility for as.Matrix() {which is currently invalid }
327	Matrix.class <- function(x, tol = 0, symmetry = TRUE, unit.diagonal = TRUE,
328	triangularity = c(TRUE, TRUE),	## MM: More or less "Cut & paste" from
329	orthogonality = c(TRUE, TRUE),	## --- diff.default() from  R/src/library/base/R/diff.R :
330	normality = c(TRUE, TRUE))	setMethod("diff", signature(x = "Matrix"),
331	{	function(x, lag = 1, differences = 1, ...) {
332	val <- "Matrix"	if (length(lag) > 1 || length(differences) > 1 ||
333	x <- as.matrix(x)	lag < 1 || differences < 1)
334	if (symmetry) {	stop("'lag' and 'differences' must be integers >= 1")
335	if (is.Hermitian(x, tol)) val <- c("Hermitian", val)	xlen <- nrow(x)
336	}	if (lag * differences >= xlen)
337	if (triangularity[1]) {	return(x[,FALSE][0])  # empty of proper mode
338	if (is.LowerTriangular(x, tol)) {
339	val <- c("LowerTriangular", val)	i1 <- -1:-lag
340	if (unit.diagonal)	for (i in 1:differences)
341	if (max(Mod(diag(x) - 1)) <= tol)	x <- x[i1, , drop = FALSE] -
342	val <- c("UnitLowerTriangular", val)	x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
343	}	x
344	}	})
345	if (triangularity[2]) {
346	if (is.UpperTriangular(x, tol)) {	setMethod("image", "Matrix",
347	val <- c("UpperTriangular", val)	function(x, ...) { # coercing to sparse is not inefficient,
348	if (unit.diagonal)	##               since we need 'i' and 'j' for levelplot()
349	if (max(Mod(diag(x) - 1)) <= tol)	x <- as(as(x, "sparseMatrix"), "dMatrix")
350	val <- c("UnitUpperTriangular", val)	callGeneric()
351	}	})
352	}
353	if (orthogonality[1]) {
354	if (is.ColOrthonormal(x, tol)) {	## Group Methods
355	val <- c("ColOrthoNormal", "ColOrthogonal", val)
356	} else {	##-> see ./Ops.R
357	if (Orthogonal.test(x, normal = FALSE) <= tol)	##         ~~~~~
358	val <- c("ColOrthogonal", val)	## 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	if (orthogonality[2]) {	callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
362	if (normality[2] && is.RowOrthonormal(x, tol)) {
363	val <- c("RowOrthoNormal", "RowOrthogonal", val)
364		### --------------------------------------------------------------------------
365		###
366		### Subsetting "["  and
367		### SubAssign  "[<-" : The "missing" cases can be dealt with here, "at the top":
368
369		## Using "index" for indices should allow
370		## integer (numeric), logical, or character (names!) indices :
371
372		## "x[]":
373		setMethod("[", signature(x = "Matrix",
374		i = "missing", j = "missing", drop = "ANY"),
375		function (x, i, j, ..., drop) x)
376
377		## missing 'drop' --> 'drop = TRUE'
378		##                     -----------
379		## select rows
380		setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
381		drop = "missing"),
382		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 {	} else {
389	if (Orthogonal.test(x, byrow = TRUE, normal = FALSE) <= tol)	callGeneric(x, i=i, , drop=TRUE)
390	val <- c("RowOrthogonal", val)	##                  ^^
	}
	}
	val
391	}	}
392		})
393
394		## select columns
395		setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
396		drop = "missing"),
397		function(x,i,j, ..., drop) callGeneric(x, j=j, drop= TRUE))
398		setMethod("[", signature(x = "Matrix", i = "index", j = "index",
399		drop = "missing"),
400		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"
403		setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
404		function(x,i,j, ..., drop)
405		stop("invalid or not-yet-implemented 'Matrix' subsetting"))
406
407		## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
408		## The following is *both* for    M [ <logical>   ]
409		##                 and also for   M [ <logical> , ]
410		.M.sub.i.logical <- function (x, i, j, ..., drop)
411		{
412		nA <- nargs()
413		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)]
416		## -> error when lengths don't match
417		} else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
418		stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
419
420		} else stop("nargs() = ", nA,
421		".  Extraneous illegal arguments inside '[ .. ]' (i.logical)?")
422		}
423		setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
424		drop = "ANY"),
425		.M.sub.i.logical)
426		setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
427		drop = "ANY"),
428		.M.sub.i.logical)
429
430	as.Matrix <- function(x, tol = .Machine$double.eps)
431		## A[ ij ]  where ij is (i,j) 2-column matrix -- but also when that is logical mat!
432		.M.sub.i.2col <- function (x, i, j, ..., drop)
433	{	{
434	asObject(if (inherits(x, "Matrix")) x else as.matrix(x),	nA <- nargs()
435	Matrix.class(x, tol = tol))	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		### "[<-" : -----------------
459
460		## x[] <- value :
461		setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
462		value = "ANY"),## double/logical/...
463		function (x, value) {
464		## 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
467		x
468		})
469
470		## 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	}## not-yet used	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 :
550		setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
551		value = "ANY"),
552		function (x, i, j, value) {
553		if(!is.atomic(value))
554		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")
557		})

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