Diff of /pkg/R/ddenseMatrix.R

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	revision 856, Tue Aug 16 20:20:13 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)
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		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 18	Line 73
73	setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),	setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
74	function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))	function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
75
76	setMethod("t", signature(x = "ddenseMatrix"),	## Not really useful; now require *identical* class for result:
77	function(x) callGeneric(as(x, "dgeMatrix")))	## setMethod("t", signature(x = "ddenseMatrix"),
78		##        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 30	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 46	Line 112
112	function(x, logarithm, ...)	function(x, logarithm, ...)
113	callGeneric(as(x, "dgeMatrix"), logarithm))	callGeneric(as(x, "dgeMatrix"), logarithm))
114
115	setMethod("expm", signature(x = "ddenseMatrix"),	## now done for "dMatrix":
116	function(x) callGeneric(as(x, "dgeMatrix")))	## setMethod("expm", signature(x = "ddenseMatrix"),
117		##           function(x) callGeneric(as(x, "dgeMatrix")))
118
119	setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),	setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
120	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
#	Line 56	Line 123
123	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))	function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
124
125
126		## Cheap version: work via "dgeMatrix" and use the group methods there:
127		## FIXME(?): try to preserve "symmetric", "triangular", ...
128		setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
129		signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
130		function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
131		as(e2, "dgeMatrix")))
132		setMethod("Arith",
133		signature(e1 = "ddenseMatrix", e2 = "numeric"),
134		function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
135		setMethod("Arith",
136		signature(e1 = "numeric", e2 = "ddenseMatrix"),
137		function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
138
139		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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