Diff of /pkg/R/Matrix.R

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	revision 607, Fri Mar 4 17:33:03 2005 UTC	revision 1455, Mon Aug 28 15:35:44 2006 UTC
#	Line 1	Line 1
1	#### Toplevel ``virtual'' class "Matrix"	#### Toplevel ``virtual'' class "Matrix"
2
	## probably not needed eventually:
	setAs(from = "Matrix", to = "matrix",
	function(from) {
	if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
	array(as.numeric(NA), dim = d, dimnames = dimnames(from))
	})
3
4	prMatrix <-	### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5	## private function to be used as show() method possibly more than once
6	function(object) {	setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7		setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8
9		## ## probably not needed eventually:
10		## setAs(from = "ddenseMatrix", to = "matrix",
11		##       function(from) {
12		##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
13		##        array(from@x, dim = d, dimnames = dimnames(from))
14		##       })
15
16		## should propagate to all subclasses:
17		setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
18		## for 'Matrix' objects, as.array() should be equivalent:
19		setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
20
21		## head and tail apply to all Matrix objects for which subscripting is allowed:
22		## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {
23		setMethod("head", signature(x = "Matrix"), utils:::head.matrix)
24		setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)
25		## } else { # R 2.4.0 and newer
26		##     setMethod("head", signature(x = "Matrix"), utils::head.matrix)
27		##     setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
28		## }
29
30		## slow "fall back" method {subclasses should have faster ones}:
31		setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
32		function(x) as.vector(as(x, "matrix")))
33
34		## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
35		setMethod("as.numeric", signature(x = "Matrix"),
36		function(x, ...) as.numeric(as.vector(x)))
37		setMethod("as.logical", signature(x = "Matrix"),
38		function(x, ...) as.logical(as.vector(x)))
39
40
41		## Note that isSymmetric is *not* exported
42		## but that "base" has an isSymmetric() S3-generic since R 2.3.0
43		setMethod("isSymmetric", signature(object = "symmetricMatrix"),
44		function(object,tol) TRUE)
45		setMethod("isSymmetric", signature(object = "triangularMatrix"),
46		## TRUE iff diagonal:
47		function(object,tol) isDiagonal(object))
48
49		if(paste(R.version$major, R.version$minor, sep=".") < "2.3")
50		## need a "matrix" method as in R 2.3 and later
51		setMethod("isSymmetric", signature(object = "matrix"),
52		function(object, tol = 100*.Machine$double.eps, ...)
53		{
54		## pretest: is it square?
55	d <- dim(object)	d <- dim(object)
56	cat(paste(d, collapse= " x "), " Matrix of class ",	if(d[1] != d[2]) return(FALSE)
57	sQuote(class(object)),"\n", sep='')	## for `broken' all.equal in R <= 2.2.x:
58	m <- as(object, "matrix")	dn <- dimnames(object)
59	maxp <- getOption("max.print")	if(!identical(dn[1], dn[2])) return(FALSE)
60	if(prod(d) <= maxp) print(m)	test <-
61	else { ## d[1] > maxp / d[2] >= nr :	if(is.complex(object))
62	nr <- maxp %/% d[2]	all.equal.numeric(object, Conj(t(object)), tol = tol, ...)
63	n2 <- ceiling(nr / 2)	else              # numeric, character, ..
64	print(head(m, max(1, n2)))	all.equal(object, t(object), tol = tol, ...)
65	cat("\n ..........\n\n")	isTRUE(test)
66	print(tail(m, max(1, nr - n2)))	})
67	}
68	## DEBUG: cat("str(.):\n") ; str(object)
69	invisible()	setMethod("isTriangular", signature(object = "triangularMatrix"),
70	}	function(object, ...) TRUE)
71
72	setMethod("show", signature(object = "ddenseMatrix"), prMatrix)	setMethod("isTriangular", signature(object = "matrix"), isTriMat)
73	## this may go away {since sparse matrices need something better!} :
74	setMethod("show", signature(object = "Matrix"), prMatrix)	setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
75
76
77
78	setMethod("dim", signature(x = "Matrix"),	setMethod("dim", signature(x = "Matrix"),
79	function(x) x@Dim, valueClass = "integer")	function(x) x@Dim, valueClass = "integer")
#	Line 49	Line 93
93	setMethod("dimnames<-", signature(x = "Matrix", value = "list"),	setMethod("dimnames<-", signature(x = "Matrix", value = "list"),
94	dimnamesGets)	dimnamesGets)
95
96		setMethod("unname", signature("Matrix", force="missing"),
97		function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
98
99	Matrix <-	Matrix <-
100	function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL)	function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
101		sparse = NULL, forceCheck = FALSE)
102	{	{
103	if (is(data, "Matrix")) return(data)	sparseDefault <- function(m)
104	if (is.matrix(data)) { val <- data }	prod(dim(m)) > 2*sum(as(m, "matrix") != 0)
105	else { ## cut & paste from "base::matrix" :
106		i.M <- is(data, "Matrix")
107		if(is.null(sparse) && (i.M || is(data, "matrix")))
108		sparse <- sparseDefault(data)
109
110		doDN <- TRUE
111		if (i.M && !forceCheck) {
112		sM <- is(data,"sparseMatrix")
113		if((sparse && sM) || (!sparse && !sM))
114		return(data)
115		## else : convert  dense <-> sparse -> at end
116		}
117		else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
118	if (missing(nrow))	if (missing(nrow))
119	nrow <- ceiling(length(data)/ncol)	nrow <- ceiling(length(data)/ncol)
120	else if (missing(ncol))	else if (missing(ncol))
121	ncol <- ceiling(length(data)/nrow)	ncol <- ceiling(length(data)/nrow)
122	val <- .Internal(matrix(data, nrow, ncol, byrow))	if(length(data) == 1 && data == 0 && !identical(sparse,FALSE)) {
123	dimnames(val) <- dimnames	if(is.null(sparse)) sparse <- TRUE
124	}	## will be sparse: do NOT construct full matrix!
125	as(val, "dgeMatrix")	data <- new(if(is.numeric(data)) "dgTMatrix" else
126	}	if(is.logical(data)) "lgTMatrix" else
127		stop("invalid 'data'"),
128		Dim = as.integer(c(nrow,ncol)),
129		Dimnames = if(is.null(dimnames)) list(NULL,NULL)
130		else dimnames)
131		} else { ## normal case
132		data <- .Internal(matrix(data, nrow, ncol, byrow))
133		if(is.null(sparse))
134		sparse <- sparseDefault(data)
135		dimnames(data) <- dimnames
136		}
137		doDN <- FALSE
138		}
139		## 'data' is now a "matrix" or "Matrix"
140		if (doDN && !is.null(dimnames))
141		dimnames(data) <- dimnames
142
143		## check for symmetric / triangular / diagonal :
144		isSym <- isSymmetric(data)
145		if((isTri <- !isSym))
146		isTri <- isTriangular(data)
147		isDiag <- isSym # cannot be diagonal if it isn't symmetric
148		if(isDiag)
149		isDiag <- isDiagonal(data)
150
151		### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
152
153		## Find proper matrix class 'cl'
154		cl <-
155		if(isDiag)
156		"diagonalMatrix" # -> will automatically check for type
157		else {
158		## consider it's type
159		ctype <-
160		if(is(data,"Matrix")) class(data)
161		else {
162		if("complex" == (ctype <- typeof(data)))
163		"z" else ctype
164		}
165		ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
166		if(ctype == "z")
167		stop("complex matrices not yet implemented in Matrix package")
168		if(ctype == "i") {
169		warning("integer matrices not yet implemented in 'Matrix'; ",
170		"using 'double' ones'")
171		ctype <- "d"
172		}
173		paste(ctype,
174		if(sparse) {
175		if(isSym) "sCMatrix" else
176		if(isTri) "tCMatrix" else "gCMatrix"
177		} else { ## dense
178		if(isSym) "syMatrix" else
179		if(isTri) "trMatrix" else "geMatrix"
180		}, sep="")
181		}
182
183		## Now coerce and return
184		as(data, cl)
185		}
186
187		## Methods for operations where one argument is numeric
188
189		## Using as.matrix() and rbind()
190		## in order to get dimnames from names {at least potentially}:
191
192		setMethod("%*%", signature(x = "Matrix", y = "numeric"),
193		function(x, y) callGeneric(x, as.matrix(y)))
194
195		setMethod("%*%", signature(x = "numeric", y = "Matrix"),
196		function(x, y) callGeneric(rbind(x), y))
197
198		setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
199		function(x, y = NULL) callGeneric(x, as.matrix(y)))
200		setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
201		function(x, y = NULL)  callGeneric(as.matrix(x), y))
202
203		## The as.matrix() promotion seems illogical to MM,
204		## but is according to help(tcrossprod, package = "base") :
205		setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
206		function(x, y = NULL) callGeneric(x, as.matrix(y)))
207		setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
208		function(x, y = NULL)  callGeneric(as.matrix(x), y))
209
210		setMethod("solve", signature(a = "Matrix", b = "numeric"),
211		function(a, b, ...) callGeneric(a, as.matrix(b)))
212
213		## bail-out methods in order to get better error messages
214		setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
215		function (x, y)
216		stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
217		class(x), class(y))))
218
219		setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
220		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
221		setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
222		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
223		setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
224		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
225		setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
226		function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
227
228		## cheap fallbacks
229		setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
230		function(x, y = NULL) t(x) %*% y)
231		setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
232		function(x, y = NULL) x %*% t(y))
233
234		## There are special sparse methods; this is a "fall back":
235		setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
236		FUN = "ANY", make.dimnames = "ANY"),
237		function(X, Y, FUN, make.dimnames, ...) {
238		X <- as(X, "matrix") ; Matrix(callGeneric()) })
239		setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
240		FUN = "ANY", make.dimnames = "ANY"),
241		function(X, Y, FUN, make.dimnames, ...) {
242		Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
243
244
245		setMethod("diag", signature(x = "Matrix"),
246		function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
247		setMethod("t", signature(x = "Matrix"),
248		function(x) .bail.out.1(.Generic, class(x)))
249
250		## Group Methods
251		setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
252		## "fallback":
253		setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
254		function(e1) {
255		warning("inefficient method used for \"- e1\"")
256		0-e1
257		})
258
259		## bail-outs:
260		setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),
261		function(e1, e2) {
262		d <- dimCheck(e1,e2)
263		.bail.out.2(.Generic, class(e1), class(e2))
264		})
265		setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
266		function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
267		setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
268		function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
269
	if(FALSE) { ##--- not-yet used -- {almost same code also in ./dgeMatrix.R }
270
	## utility for as.Matrix() {which is currently invalid }
	Matrix.class <- function(x, tol = 0, symmetry = TRUE, unit.diagonal = TRUE,
	triangularity = c(TRUE, TRUE),
	orthogonality = c(TRUE, TRUE),
	normality = c(TRUE, TRUE))
	{
	val <- "Matrix"
	x <- as.matrix(x)
	if (symmetry) {
	if (is.Hermitian(x, tol)) val <- c("Hermitian", val)
	}
	if (triangularity[1]) {
	if (is.LowerTriangular(x, tol)) {
	val <- c("LowerTriangular", val)
	if (unit.diagonal)
	if (max(Mod(diag(x) - 1)) <= tol)
	val <- c("UnitLowerTriangular", val)
	}
	}
	if (triangularity[2]) {
	if (is.UpperTriangular(x, tol)) {
	val <- c("UpperTriangular", val)
	if (unit.diagonal)
	if (max(Mod(diag(x) - 1)) <= tol)
	val <- c("UnitUpperTriangular", val)
	}
	}
	if (orthogonality[1]) {
	if (is.ColOrthonormal(x, tol)) {
	val <- c("ColOrthoNormal", "ColOrthogonal", val)
	} else {
	if (Orthogonal.test(x, normal = FALSE) <= tol)
	val <- c("ColOrthogonal", val)
	}
	}
	if (orthogonality[2]) {
	if (normality[2] && is.RowOrthonormal(x, tol)) {
	val <- c("RowOrthoNormal", "RowOrthogonal", val)
	} else {
	if (Orthogonal.test(x, byrow = TRUE, normal = FALSE) <= tol)
	val <- c("RowOrthogonal", val)
	}
	}
	val
	}
271
272	as.Matrix <- function(x, tol = .Machine$double.eps)	### --------------------------------------------------------------------------
273	{	###
274	asObject(if (inherits(x, "Matrix")) x else as.matrix(x),	### Subsetting "["  and
275	Matrix.class(x, tol = tol))	### SubAssign  "[<-" : The "missing" cases can be dealt with here, "at the top":
276	}
277		## Using "index" for indices should allow
278		## integer (numeric), logical, or character (names!) indices :
279
280		## "x[]":
281		setMethod("[", signature(x = "Matrix",
282		i = "missing", j = "missing", drop = "ANY"),
283		function (x, i, j, drop) x)
284
285		## missing 'drop' --> 'drop = TRUE'
286		##                     -----------
287		## select rows
288		setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
289		drop = "missing"),
290		function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
291		## select columns
292		setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
293		drop = "missing"),
294		function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
295		setMethod("[", signature(x = "Matrix", i = "index", j = "index",
296		drop = "missing"),
297		function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))
298
299		## bail out if any of (i,j,drop) is "non-sense"
300		setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
301		function(x,i,j, drop)
302		stop("invalid or not-yet-implemented 'Matrix' subsetting"))
303
304		##  "logical *vector* indexing, such as  M [ M >= 10 ] :
305		setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
306		drop = "ANY"),
307		function (x, i, j, drop) {
308		as(x, geClass(x))@x[as.vector(i)]
309		## -> error when lengths don't match
310		})
311
312		## FIXME: The following is good for    M [ <logical>   ]
313		##        *BUT* it also triggers for   M [ <logical> , ] where it is *WRONG*
314		##       using nargs() does not help: it gives '3' for both cases
315		if(FALSE)
316		setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
317		drop = "ANY"),
318		function (x, i, j, drop) {
319		## DEBUG
320		cat("[(Matrix,i,..): nargs=", nargs(),"\n")
321		as(x, geClass(x))@x[i] })
322
323
324		## "FIXME:"
325		## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?
326		##  and                A[ LL ]  where LL is a logical *vector*
327		## -> [.data.frame uses nargs() - can we do this in the *generic* ?
328
329
330		### "[<-" : -----------------
331
332		## x[] <- value :
333		setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
334		value = "ANY"),## double/logical/...
335		function (x, value) {
336		x@x <- value
337		validObject(x)# check if type and lengths above match
338		x
339		})
340
341		## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
342		## (ANY,ANY,ANY) is used when no `real method' is implemented :
343		setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
344		value = "ANY"),
345		function (x, i, j, value) {
346		if(!is.atomic(value))
347		stop("RHS 'value' must match matrix class ", class(x))
348		else stop("not-yet-implemented 'Matrix[<-' method")
349		})
350
351
352	}## not-yet used	## The trivial methods :
353		setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
354		function(x, y) x)
355		setMethod("cbind2", signature(x = "Matrix", y = "missing"),
356		function(x, y) x)
357		setMethod("cbind2", signature(x = "NULL", y="Matrix"),
358		function(x, y) x)
359
360		setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
361		function(x, y) x)
362		setMethod("rbind2", signature(x = "Matrix", y = "missing"),
363		function(x, y) x)
364		setMethod("rbind2", signature(x = "NULL", y="Matrix"),
365		function(x, y) x)
366
367		## Makes sure one gets x decent error message for the unimplemented cases:
368		setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
369		function(x, y) {
370		rowCheck(x,y)
371		stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
372		class(x), class(y)))
373		})
374
375		## Use a working fall back {particularly useful for sparse}:
376		## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
377		setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
378		function(x, y) {
379		colCheck(x,y)
380		t(cbind2(t(x), t(y)))
381		})

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