Diff of /pkg/R/ddenseMatrix.R

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	revision 856, Tue Aug 16 20:20:13 2005 UTC	revision 1575, Mon Sep 18 14:47:40 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)
18		setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)
19		setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)
20		setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)
21		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		.Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
37
38		## special case needed in the Matrix function
39		setAs("matrix", "dgCMatrix",
40		function(from) {
41		storage.mode(from) <- "double"
42		.Call(dense_to_Csparse, from)
43		})
44
45		setAs("numeric", "CsparseMatrix",
46		function(from)
47		.Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
48
49		setMethod("as.numeric", signature(x = "ddenseMatrix"),
50		function(x, ...) as(x, "dgeMatrix")@x)
51
52	## -- see also ./Matrix.R  e.g., for a show() method	## -- see also ./Matrix.R  e.g., for a show() method
53
54	## These methods are the 'fallback' methods for all dense numeric	## These methods are the 'fallback' methods for all dense numeric
#	Line 18	Line 67
67	setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),	setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
68	function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))	function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
69
70	setMethod("t", signature(x = "ddenseMatrix"),	## Not really useful; now require *identical* class for result:
71	function(x) callGeneric(as(x, "dgeMatrix")))	## setMethod("t", signature(x = "ddenseMatrix"),
72		##        function(x) callGeneric(as(x, "dgeMatrix")))
73
74	setMethod("tcrossprod", signature(x = "ddenseMatrix"),	setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
75	function(x) callGeneric(as(x, "dgeMatrix")))	function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
76
77	setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),	setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
78	function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))	function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
#	Line 30	Line 80
80	setMethod("diag", signature(x = "ddenseMatrix"),	setMethod("diag", signature(x = "ddenseMatrix"),
81	function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))	function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
82
83	setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),	## These methods cause an infinite loop in pre-2.4.0
84	function(a, b, ...) callGeneric(as(a, "dgeMatrix")))	## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
85		##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
86	setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
87	function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))	## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
88		##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
89
90		## General method for dense matrix multiplication in case specific methods
91		## have not been defined.
92		setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
93		function(x, y) .Call(dgeMatrix_matrix_mm,
94		.Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
95		valueClass = "dgeMatrix")
96
97	setMethod("lu", signature(x = "ddenseMatrix"),	setMethod("lu", signature(x = "ddenseMatrix"),
98	function(x, ...) callGeneric(as(x, "dgeMatrix")))	function(x, ...) callGeneric(as(x, "dgeMatrix")))
#	Line 46	Line 104
104	function(x, logarithm, ...)	function(x, logarithm, ...)
105	callGeneric(as(x, "dgeMatrix"), logarithm))	callGeneric(as(x, "dgeMatrix"), logarithm))
106
107	setMethod("expm", signature(x = "ddenseMatrix"),	## now done for "dMatrix":
108	function(x) callGeneric(as(x, "dgeMatrix")))	## setMethod("expm", signature(x = "ddenseMatrix"),
109		##           function(x) callGeneric(as(x, "dgeMatrix")))
110
111	setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),	setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
112	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
#	Line 56	Line 115
115	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
116
117
118		## Cheap version: work via "dgeMatrix" and use the group methods there:
119		## FIXME(?): try to preserve "symmetric", "triangular", ...
120		setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
121		signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
122		function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
123		as(e2, "dgeMatrix")))
124		setMethod("Arith",
125		signature(e1 = "ddenseMatrix", e2 = "numeric"),
126		function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
127		setMethod("Arith",
128		signature(e1 = "numeric", e2 = "ddenseMatrix"),
129		function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
130
131		setMethod("Math",
132		signature(x = "ddenseMatrix"),
133		function(x) callGeneric(as(x, "dgeMatrix")))
134
135
136
137		### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
138
139		### cbind2
140		setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
141		function(x, y) {
142		d <- dim(x); nr <- d[1]; nc <- d[2]
143		y <- rep(y, length.out = nr) # 'silent procrustes'
144		## beware of (packed) triangular, symmetric, ...
145		x <- as(x, "dgeMatrix")
146		x@x <- c(x@x, as.double(y))
147		x@Dim[2] <- nc + 1:1
148		if(is.character(dn <- x@Dimnames[[2]]))
149		x@Dimnames[[2]] <- c(dn, "")
150		x
151		})
152		## the same, (x,y) <-> (y,x):
153		setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
154		function(x, y) {
155		d <- dim(y); nr <- d[1]; nc <- d[2]
156		x <- rep(x, length.out = nr)
157		y <- as(y, "dgeMatrix")
158		y@x <- c(as.double(x), y@x)
159		y@Dim[2] <- nc + 1:1
160		if(is.character(dn <- y@Dimnames[[2]]))
161		y@Dimnames[[2]] <- c("", dn)
162		y
163		})
164
165		setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
166		function(x, y) callGeneric(x, as(y, "dgeMatrix")))
167		setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
168		function(x, y) callGeneric(as(x, "dgeMatrix"), y))
169
170		setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
171		function(x, y) {
172		nr <- rowCheck(x,y)
173		ncx <- x@Dim[2]
174		ncy <- y@Dim[2]
175		## beware of (packed) triangular, symmetric, ...
176		hasDN <- !is.null(dnx <- dimnames(x)) |
177		!is.null(dny <- dimnames(y))
178		x <- as(x, "dgeMatrix")
179		y <- as(y, "dgeMatrix")
180		x@x <- c(x@x, y@x)
181		x@Dim[2] <- ncx + ncy
182		if(hasDN) {
183		## R and S+ are different in which names they take
184		## if they differ -- but there's no warning in any case
185		rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
186		cx <- dnx[[2]] ; cy <- dny[[2]]
187		cn <- if(is.null(cx) && is.null(cy)) NULL
188		else c(if(!is.null(cx)) cx else rep.int("", ncx),
189		if(!is.null(cy)) cy else rep.int("", ncy))
190		x@Dimnames <- list(rn, cn)
191		}
192		x
193		})
194
195		### rbind2 -- analogous to cbind2 --- more to do for @x though:
196
197		setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
198		function(x, y) {
199		if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
200		new("dgeMatrix", Dim = x@Dim + 1:0,
201		Dimnames = list(dn, x@Dimnames[[2]]),
202		x = c(rbind2(as(x,"matrix"), y)))
203		})
204		## the same, (x,y) <-> (y,x):
205		setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
206		function(x, y) {
207		if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
208		new("dgeMatrix", Dim = y@Dim + 1:0,
209		Dimnames = list(dn, y@Dimnames[[2]]),
210		x = c(rbind2(x, as(y,"matrix"))))
211		})
212
213		setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
214		function(x, y) callGeneric(x, as(y, "dgeMatrix")))
215		setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
216		function(x, y) callGeneric(as(x, "dgeMatrix"), y))
217
218		setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
219		function(x, y) {
220		nc <- colCheck(x,y)
221		nrx <- x@Dim[1]
222		nry <- y@Dim[1]
223		dn <-
224		if(!is.null(dnx <- dimnames(x)) |
225		!is.null(dny <- dimnames(y))) {
226		## R and S+ are different in which names they take
227		## if they differ -- but there's no warning in any case
228		list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
229		NULL else
230		c(if(!is.null(rx)) rx else rep.int("", nrx),
231		if(!is.null(ry)) ry else rep.int("", nry)),
232		if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
233
234		} else list(NULL, NULL)
235		## beware of (packed) triangular, symmetric, ...
236		new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
237		x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
238		})
239
240		### FIXME: band() et al should be extended from "ddense" to "dense" !
241		###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
242
243		## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
244		##     for triangular ["dtr" and "dtp"]
245		setMethod("tril", "ddenseMatrix",
246		function(x, k = 0, ...) {
247		k <- as.integer(k[1])
248		dd <- dim(x); sqr <- dd[1] == dd[2]
249		stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
250		## returns "lower triangular" if k <= 0 && sqr
251		.Call(ddense_band, x, -dd[1], k)
252		})
253
254		setMethod("triu", "ddenseMatrix",
255		function(x, k = 0, ...) {
256		k <- as.integer(k[1])
257		dd <- dim(x); sqr <- dd[1] == dd[2]
258		stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
259		## returns "upper triangular" if k >= 0
260		.Call(ddense_band, x, k, dd[2])
261		})
262
263		setMethod("band", "ddenseMatrix",
264		function(x, k1, k2, ...) {
265		k1 <- as.integer(k1[1])
266		k2 <- as.integer(k2[1])
267		dd <- dim(x); sqr <- dd[1] == dd[2]
268		stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
269		r <- .Call(ddense_band, x, k1, k2)
270		if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
271		as(r, paste(.M.kind(x), "syMatrix", sep=''))
272		else
273		r
274		})

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