Diff of /pkg/R/Matrix.R

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	revision 1329, Fri Jul 21 06:47:06 2006 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
3
4		### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5
6		setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7		setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8
9	## ## probably not needed eventually:	## ## probably not needed eventually:
10	## setAs(from = "ddenseMatrix", to = "matrix",	## setAs(from = "ddenseMatrix", to = "matrix",
11	##       function(from) {	##       function(from) {
#	Line 11	Line 17
17	setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))	setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
18	## for 'Matrix' objects, as.array() should be equivalent:	## for 'Matrix' objects, as.array() should be equivalent:
19	setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))	setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
20	## head and tail apply to all Matrix objects for which subscripting is allowed
21	setMethod("head", signature(x = "Matrix"),	## head and tail apply to all Matrix objects for which subscripting is allowed:
22	function(x, n = 6, ...)	## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {
23	x[seq(len = min(n, nrow(x))), , drop = FALSE])	setMethod("head", signature(x = "Matrix"), utils:::head.matrix)
24	setMethod("tail", signature(x = "Matrix"),	setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)
25	function (x, n = 6, addrownums = TRUE, ...)	## } else { # R 2.4.0 and newer
26	{	##     setMethod("head", signature(x = "Matrix"), utils::head.matrix)
27	nrx <- nrow(x)	##     setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
28	sel <- seq(to = nrx, length = min(n, nrx))	## }
	ans <- x[sel, , drop = FALSE]
	if (addrownums && is.null(rownames(x)))
	rownames(ans) <- paste("[", sel, ",]", sep = "")
	ans
	})
29
30	## slow "fall back" method {subclasses should have faster ones}:	## slow "fall back" method {subclasses should have faster ones}:
31	setMethod("as.vector", signature(x = "Matrix", mode = "missing"),	setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
32	function(x) as.vector(as(x, "matrix")))	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	## Note that isSymmetric is *not* exported
42	## but that "base" has an isSymmetric() S3-generic since R 2.3.0	## but that "base" has an isSymmetric() S3-generic since R 2.3.0
#	Line 91	Line 98
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)	sparse = NULL, forceCheck = FALSE)
102	{	{
103	sparseDefault <- function(m)	sparseDefault <- function(m)
104	prod(dim(m)) > 2*sum(as(m, "matrix") != 0)	prod(dim(m)) > 2*sum(as(m, "matrix") != 0)
#	Line 100	Line 107
107	if(is.null(sparse) && (i.M || is(data, "matrix")))	if(is.null(sparse) && (i.M || is(data, "matrix")))
108	sparse <- sparseDefault(data)	sparse <- sparseDefault(data)
109
110	if (i.M) {	doDN <- TRUE
111		if (i.M && !forceCheck) {
112	sM <- is(data,"sparseMatrix")	sM <- is(data,"sparseMatrix")
113	if((sparse && sM) || (!sparse && !sM))	if((sparse && sM) || (!sparse && !sM))
114	return(data)	return(data)
#	Line 118	Line 126
126	if(is.logical(data)) "lgTMatrix" else	if(is.logical(data)) "lgTMatrix" else
127	stop("invalid 'data'"),	stop("invalid 'data'"),
128	Dim = as.integer(c(nrow,ncol)),	Dim = as.integer(c(nrow,ncol)),
129	Dimnames = if(is.null(dimnames))	Dimnames = if(is.null(dimnames)) list(NULL,NULL)
130	list(NULL,NULL) else dimnames)	else dimnames)
131	} else { ## normal case	} else { ## normal case
132	data <- .Internal(matrix(data, nrow, ncol, byrow))	data <- .Internal(matrix(data, nrow, ncol, byrow))
133	if(is.null(sparse))	if(is.null(sparse))
134	sparse <- sparseDefault(data)	sparse <- sparseDefault(data)
135	dimnames(data) <- dimnames	dimnames(data) <- dimnames
136	}	}
137	} else if (!is.null(dimnames))	doDN <- FALSE
138	dimnames(data) <- dimnames	}
139	## 'data' is now a "matrix" or "Matrix"	## 'data' is now a "matrix" or "Matrix"
140		if (doDN && !is.null(dimnames))
141		dimnames(data) <- dimnames
142
143	## check for symmetric / triangular / diagonal :	## check for symmetric / triangular / diagonal :
144	isSym <- isSymmetric(data)	isSym <- isSymmetric(data)
#	Line 188	Line 197
197
198	setMethod("crossprod", signature(x = "Matrix", y = "numeric"),	setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
199	function(x, y = NULL) callGeneric(x, as.matrix(y)))	function(x, y = NULL) callGeneric(x, as.matrix(y)))
200	setMethod("crossprod", signature(x = "numeric", y = "Matrix"),	setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
201	function(x, y = NULL)  callGeneric(rbind(x), y))	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"),	setMethod("solve", signature(a = "Matrix", b = "numeric"),
211	function(a, b, ...) callGeneric(a, as.matrix(b)))	function(a, b, ...) callGeneric(a, as.matrix(b)))
#	Line 205	Line 220
220	function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))	function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
221	setMethod("crossprod", signature(x = "ANY", y = "Matrix"),	setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
222	function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))	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":	## There are special sparse methods; this is a "fall back":
235	setMethod("kronecker", signature(X = "Matrix", Y = "ANY",	setMethod("kronecker", signature(X = "Matrix", Y = "ANY",

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