Diff of /pkg/R/ddenseMatrix.R

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	revision 956, Fri Sep 30 17:28:00 2005 UTC	revision 1708, Fri Dec 22 19:53:37 2006 UTC
#	Line 1	Line 1
1	### Define Methods that can be inherited for all subclasses	### Define Methods that can be inherited for all subclasses
2
3		## This replaces many "d..Matrix" -> "dgeMatrix" ones
4		## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
5		##   -----  in  ../src/Mutils.c
6
7		## Should this method return 'from' without duplication when it has
8		## class dgeMatrix?
9		setAs("ddenseMatrix", "dgeMatrix",
10		function(from) {
11		if (class(from) != "dgeMatrix")
12		from <- .Call(dup_mMatrix_as_dgeMatrix, from)
13		from
14		})
15
16		## d(ouble) to l(ogical):
17	setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)	setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)
18	setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)	setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)
19	setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)	setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)
20	setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)	setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)
21	setAs("dspMatrix", "lspMatrix", d2l_Matrix)	setAs("dspMatrix", "lspMatrix", d2l_Matrix)
22
23		setAs("ddenseMatrix", "CsparseMatrix",
24		function(from) {
25		if (class(from) != "dgeMatrix")
26		from <- .Call(dup_mMatrix_as_dgeMatrix, from)
27		.Call(dense_to_Csparse, from)
28		})
29
30		## special case
31		setAs("dgeMatrix", "dgCMatrix",
32		function(from) .Call(dense_to_Csparse, from))
33
34		setAs("matrix", "CsparseMatrix",
35		function(from) {
36		if(is.numeric(from))
37		.Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
38		else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
39		as(Matrix(from, sparse=TRUE), "CsparseMatrix")
40		else stop('not-yet-implemented coercion to "CsparseMatrix"')
41		})
42
43
44		## special case needed in the Matrix function
45		setAs("matrix", "dgCMatrix",
46		function(from) {
47		storage.mode(from) <- "double"
48		.Call(dense_to_Csparse, from)
49		})
50
51		setAs("numeric", "CsparseMatrix",
52		function(from)
53		.Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
54
55		setMethod("as.numeric", signature(x = "ddenseMatrix"),
56		function(x, ...) as(x, "dgeMatrix")@x)
57
58	## -- see also ./Matrix.R  e.g., for a show() method	## -- see also ./Matrix.R  e.g., for a show() method
59
60	## These methods are the 'fallback' methods for all dense numeric	## These methods are the 'fallback' methods for all dense numeric
#	Line 28	Line 77
77	## setMethod("t", signature(x = "ddenseMatrix"),	## setMethod("t", signature(x = "ddenseMatrix"),
78	##        function(x) callGeneric(as(x, "dgeMatrix")))	##        function(x) callGeneric(as(x, "dgeMatrix")))
79
80	setMethod("tcrossprod", signature(x = "ddenseMatrix"),	setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
81	function(x) callGeneric(as(x, "dgeMatrix")))	function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
82
83	setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),	setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
84	function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))	function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
#	Line 37	Line 86
86	setMethod("diag", signature(x = "ddenseMatrix"),	setMethod("diag", signature(x = "ddenseMatrix"),
87	function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))	function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
88
89	setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),	## These methods cause an infinite loop in pre-2.4.0
90	function(a, b, ...) callGeneric(as(a, "dgeMatrix")))	## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
91		##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
92	setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
93	function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))	## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
94		##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
95
96		## General method for dense matrix multiplication in case specific methods
97		## have not been defined.
98		setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
99		function(x, y) .Call(dgeMatrix_matrix_mm,
100		.Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
101		valueClass = "dgeMatrix")
102
103	setMethod("lu", signature(x = "ddenseMatrix"),	setMethod("lu", signature(x = "ddenseMatrix"),
104	function(x, ...) callGeneric(as(x, "dgeMatrix")))	function(x, ...) callGeneric(as(x, "dgeMatrix")))
105
106		setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
107
108	setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),	setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
109	function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))	function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
110
#	Line 64	Line 123
123	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
124
125
126	### NAMESPACE must export this -- also only for R version 2.2.x:	## Cheap version: work via "dgeMatrix" and use the group methods there:
127	if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {	## FIXME(?): try to preserve "symmetric", "triangular", ...
128	## for R 2.2.x (and later):	setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
129		signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
130	### cbind2	function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
131	setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),	as(e2, "dgeMatrix")))
132	function(x, y) {	setMethod("Arith",
133	d <- dim(x); nr <- d[1]; nc <- d[2]	signature(e1 = "ddenseMatrix", e2 = "numeric"),
134	y <- rep(y, length.out = nr)# 'silent procrustes'	function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
135	## beware of (packed) triangular, symmetric, ...	setMethod("Arith",
136	x <- as(x, "dgeMatrix")	signature(e1 = "numeric", e2 = "ddenseMatrix"),
137	x@x <- c(x@x, as.double(y))	function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
	x@Dim[2] <- nc + 1:1
	if(is.character(dn <- x@Dimnames[[2]]))
	x@Dimnames[[2]] <- c(dn, "")
	x
	})
	## the same, (x,y) <-> (y,x):
	setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
	function(x, y) {
	d <- dim(y); nr <- d[1]; nc <- d[2]
	x <- rep(x, length.out = nr)
	y <- as(y, "dgeMatrix")
	y@x <- c(as.double(x), y@x)
	y@Dim[2] <- nc + 1:1
	if(is.character(dn <- y@Dimnames[[2]]))
	y@Dimnames[[2]] <- c("", dn)
	y
	})
	setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
	function(x, y) callGeneric(x, as(y, "dgeMatrix")))
	setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
	function(x, y) callGeneric(as(x, "dgeMatrix"), y))
	setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
	function(x, y) {
	nr <- rowCheck(x,y)
	ncx <- x@Dim[2]
	ncy <- y@Dim[2]
	## beware of (packed) triangular, symmetric, ...
	hasDN <- !is.null(dnx <- dimnames(x)) |
	!is.null(dny <- dimnames(y))
	x <- as(x, "dgeMatrix")
	y <- as(y, "dgeMatrix")
	x@x <- c(x@x, y@x)
	x@Dim[2] <- ncx + ncy
	if(hasDN) {
	## R and S+ are different in which names they take
	## if they differ -- but there's no warning in any case
	rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
	cx <- dnx[[2]] ; cy <- dny[[2]]
	cn <- if(is.null(cx) && is.null(cy)) NULL
	else c(if(!is.null(cx)) cx else rep.int("", ncx),
	if(!is.null(cy)) cy else rep.int("", ncy))
	x@Dimnames <- list(rn, cn)
	}
	x
	})
	### rbind2 -- analogous to cbind2 --- more to do for @x though:
	setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
	function(x, y) {
	if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
	new("dgeMatrix", Dim = x@Dim + 1:0,
	Dimnames = list(dn, x@Dimnames[[2]]),
	x = c(rbind2(as(x,"matrix"), y)))
	})
	## the same, (x,y) <-> (y,x):
	setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
	function(x, y) {
	if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
	new("dgeMatrix", Dim = y@Dim + 1:0,
	Dimnames = list(dn, y@Dimnames[[2]]),
	x = c(rbind2(x, as(y,"matrix"))))
	})
	setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
	function(x, y) callGeneric(x, as(y, "dgeMatrix")))
	setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
	function(x, y) callGeneric(as(x, "dgeMatrix"), y))
	setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
	function(x, y) {
	nc <- colCheck(x,y)
	nrx <- x@Dim[1]
	nry <- y@Dim[1]
	dn <-
	if(!is.null(dnx <- dimnames(x)) |
	!is.null(dny <- dimnames(y))) {
	## R and S+ are different in which names they take
	## if they differ -- but there's no warning in any case
	list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
	NULL else
	c(if(!is.null(rx)) rx else rep.int("", nrx),
	if(!is.null(ry)) ry else rep.int("", nry)),
	if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
	} else list(NULL, NULL)
	## beware of (packed) triangular, symmetric, ...
	new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
	x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
	})
138
139	}## R-2.2.x ff	setMethod("Math",
140		signature(x = "ddenseMatrix"),
141		function(x) callGeneric(as(x, "dgeMatrix")))
142
143
144		### FIXME: band() et al should be extended from "ddense" to "dense" !
145		###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
146
147		## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
148		##     for triangular ["dtr" and "dtp"]
149		setMethod("tril", "ddenseMatrix",
150		function(x, k = 0, ...) {
151		k <- as.integer(k[1])
152		dd <- dim(x); sqr <- dd[1] == dd[2]
153		stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
154		## returns "lower triangular" if k <= 0 && sqr
155		.Call(ddense_band, x, -dd[1], k)
156		})
157
158		setMethod("triu", "ddenseMatrix",
159		function(x, k = 0, ...) {
160		k <- as.integer(k[1])
161		dd <- dim(x); sqr <- dd[1] == dd[2]
162		stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
163		## returns "upper triangular" if k >= 0
164		.Call(ddense_band, x, k, dd[2])
165		})
166
167		setMethod("band", "ddenseMatrix",
168		function(x, k1, k2, ...) {
169		k1 <- as.integer(k1[1])
170		k2 <- as.integer(k2[1])
171		dd <- dim(x); sqr <- dd[1] == dd[2]
172		stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
173		r <- .Call(ddense_band, x, k1, k2)
174		if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
175		as(r, paste(.M.kind(x), "syMatrix", sep=''))
176		else
177		r
178		})

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