Diff of /pkg/R/diagMatrix.R

Parent Directory | Revision Log | Patch

	revision 1331, Sat Jul 22 17:59:53 2006 UTC	revision 1655, Mon Oct 30 17:16:27 2006 UTC
#	Line 1	Line 1
1		#### All methods for "diagonalMatrix" and its subclasses,
2		####  currently "ddiMatrix", "ldiMatrix"
3
4	## Purpose: Constructor of diagonal matrices -- ~= diag() ,	## Purpose: Constructor of diagonal matrices -- ~= diag() ,
5	##          but *not* diag() extractor!	##          but *not* diag() extractor!
6	Diagonal <- function(n, x = NULL)	Diagonal <- function(n, x = NULL)
#	Line 10	Line 13
13	n <- as.integer(n)	n <- as.integer(n)
14	}	}
15
16	if(missing(x)) # unit diagonal matrix	if(missing(x)) ## unit diagonal matrix
17	new("ddiMatrix", Dim = c(n,n), diag = "U")	new("ddiMatrix", Dim = c(n,n), diag = "U")
18	else {	else {
19	stopifnot(length(x) == n)	stopifnot(length(x) == n)
20	if(is.logical(x))	if(is.logical(x))
21	cl <- "ldiMatrix"	cl <- "ldiMatrix"
22	else {	else if(is.numeric(x)) {
23	cl <- "ddiMatrix"	cl <- "ddiMatrix"
24	x <- as.numeric(x)	x <- as.numeric(x)
25	}	}
26		else if(is.complex(x)) {
27		cl <- "zdiMatrix"  # will not yet work
28		} else stop("'x' has invalid data type")
29	new(cl, Dim = c(n,n), diag = "N", x = x)	new(cl, Dim = c(n,n), diag = "N", x = x)
30	}	}
31	}	}
32
33	setAs("diagonalMatrix", "triangularMatrix",	### This is modified from a post of Bert Gunter to R-help on  1 Sep 2005.
34	function(from) {	### Bert's code built on a post by Andy Liaw who most probably was influenced
35	n <- from@Dim[1]	### by earlier posts, notably one by Scott Chasalow on S-news, 16 Jan 2002
36	i <- seq(length = n)	### who posted his bdiag() function written in December 1995.
37	x <- from@x
38	new(if(is.numeric(x)) "dtTMatrix" else "ltTMatrix",	bdiag <- function(...) {
39		if(nargs() == 0) return(new("dgCMatrix"))
40		## else :
41		mlist <- if (nargs() == 1) as.list(...) else list(...)
42		dims <- sapply(mlist, dim)
43		## make sure we had all matrices:
44		if(!(is.matrix(dims) && nrow(dims) == 2))
45		stop("some arguments are not matrices")
46		csdim <- rbind(rep.int(0:0, 2),
47		apply(sapply(mlist, dim), 1, cumsum))
48		ret <- new("dgTMatrix", Dim = as.integer(csdim[nrow(csdim),]))
49		add1 <- matrix(1:0, 2,2)
50		for(i in seq_along(mlist)) {
51		indx <- apply(csdim[i:(i+1),] + add1, 2, function(n) n[1]:n[2])
52		if(is.null(dim(indx))) ## non-square matrix
53		ret[indx[[1]],indx[[2]]] <- mlist[[i]]
54		else ## square matrix
55		ret[indx[,1],indx[,2]] <- mlist[[i]]
56		}
57		## slightly debatable if we really should return Csparse.. :
58		as(ret, "CsparseMatrix")
59		}
60
61		diag2T <- function(from) {
62		i <- if(from@diag == "U") integer(0) else seq_len(from@Dim[1]) - 1:1
63		new(paste(.M.kind(from), "tTMatrix", sep=''),
64	diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,	diag = from@diag, Dim = from@Dim, Dimnames = from@Dimnames,
65	x = x, i = i, j = i)	x = from@x, # <- ok for diag = "U" and "N" (!)
66	})	i = i, j = i)
67		}
68
69		setAs("diagonalMatrix", "triangularMatrix", diag2T)
70		setAs("diagonalMatrix", "sparseMatrix", diag2T)
71		## is better than this:
72		## setAs("diagonalMatrix", "sparseMatrix",
73		##       function(from)
74		##        as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))
75		setAs("diagonalMatrix", "CsparseMatrix",
76		function(from) as(diag2T(from), "CsparseMatrix"))
77
78	setAs("diagonalMatrix", "matrix",	setAs("diagonalMatrix", "matrix",
79	function(from) {	function(from) {
#	Line 42	Line 83
83	nrow = n, ncol = n)	nrow = n, ncol = n)
84	})	})
85
86	setAs("diagonalMatrix", "generalMatrix",	setAs("diagonalMatrix", "generalMatrix", # prefer sparse:
87	function(from) {	function(from) as(from, paste(.M.kind(from), "gCMatrix", sep='')))
	x <- as(from, "matrix")
	as(x,
	if(is.logical(x)) "lgeMatrix"
	## Not yet:
	##              else if(is.complex(x)) "zgeMatrix"
	##              else if(is.integer(x)) "igeMatrix"
	else "dgeMatrix")
	})
88
89		.diag.x <- function(m) {
90		if(m@diag == "U")
91		rep.int(if(is.numeric(m@x)) 1. else TRUE,
92		m@Dim[1])
93		else m@x
94		}
95
96		.diag.2N <- function(m) {
97		if(m@diag == "U") m@diag <- "N"
98		m
99		}
100
101		## given the above, the following  4  coercions should be all unneeded;
102		## we prefer triangular to general:
103	setAs("ddiMatrix", "dgTMatrix",	setAs("ddiMatrix", "dgTMatrix",
104	function(from) {	function(from) {
105		.Deprecated("as(, \"sparseMatrix\")")
106	n <- from@Dim[1]	n <- from@Dim[1]
107	i <- seq(length = n) - 1:1	i <- seq_len(n) - 1:1
108	new("dgTMatrix", i = i, j = i,	new("dgTMatrix", i = i, j = i, x = .diag.x(from),
	x = if(from@diag == "U") rep(1,n) else from@x,
109	Dim = c(n,n), Dimnames = from@Dimnames) })	Dim = c(n,n), Dimnames = from@Dimnames) })
110
111	setAs("ddiMatrix", "dgCMatrix",	setAs("ddiMatrix", "dgCMatrix",
112	function(from) as(as(from, "dgTMatrix"), "dgCMatrix"))	function(from) as(as(from, "sparseMatrix"), "dgCMatrix"))
113
114	setAs("ldiMatrix", "lgTMatrix",	setAs("ldiMatrix", "lgTMatrix",
115	function(from) {	function(from) {
116		.Deprecated("as(, \"sparseMatrix\")")
117	n <- from@Dim[1]	n <- from@Dim[1]
118	i <- (if(from@diag == "U") seq(length = n) else which(from@x)) - 1:1	if(from@diag == "U") { # unit-diagonal
119	new("lgTMatrix", i = i, j = i,	x <- rep.int(TRUE, n)
120		i <- seq_len(n) - 1:1
121		} else { # "normal"
122		nz <- nz.NA(from@x, na. = TRUE)
123		x <- from@x[nz]
124		i <- which(nz) - 1:1
125		}
126		new("lgTMatrix", i = i, j = i, x = x,
127	Dim = c(n,n), Dimnames = from@Dimnames) })	Dim = c(n,n), Dimnames = from@Dimnames) })
128
129	setAs("ldiMatrix", "lgCMatrix",	setAs("ldiMatrix", "lgCMatrix",
130	function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))	function(from) as(as(from, "lgTMatrix"), "lgCMatrix"))
131
	setAs("diagonalMatrix", "sparseMatrix",
	function(from)
	as(from, if(is(from, "dMatrix")) "dgCMatrix" else "lgCMatrix"))
132
133		if(FALSE) # now have faster  "ddense" -> "dge"
134	setAs("ddiMatrix", "dgeMatrix",	setAs("ddiMatrix", "dgeMatrix",
135	function(from) as(as(from, "matrix"), "dgeMatrix"))	function(from) as(as(from, "matrix"), "dgeMatrix"))
136
#	Line 95	Line 148
148	cl <- "ddiMatrix"	cl <- "ddiMatrix"
149	uni <- all(x == 1)	uni <- all(x == 1)
150	storage.mode(x) <- "double"	storage.mode(x) <- "double"
151	}	} ## TODO: complex
152	new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",	new(cl, Dim = c(n,n), diag = if(uni) "U" else "N",
153	x = if(uni) x[FALSE] else x)	x = if(uni) x[FALSE] else x)
154	})	})
#	Line 120	Line 173
173	x = if(uni) x[FALSE] else x)	x = if(uni) x[FALSE] else x)
174	})	})
175
176		## When you assign to a diagonalMatrix, the result should be
177		## diagonal or sparse
178		setReplaceMethod("[", signature(x = "diagonalMatrix",
179		i = "ANY", j = "ANY", value = "ANY"),
180		function(x, i, j, value) {
181		r <- callGeneric(x = as(x,"sparseMatrix"),
182		i=i, j=j, value=value)
183		if(isDiagonal(r)) as(r, "diagonalMatrix") else r
184		})
185
186
187	setMethod("t", signature(x = "diagonalMatrix"),	setMethod("t", signature(x = "diagonalMatrix"),
188	function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })	function(x) { x@Dimnames <- x@Dimnames[2:1] ; x })
189
#	Line 130	Line 194
194	setMethod("isSymmetric", signature(object = "diagonalMatrix"),	setMethod("isSymmetric", signature(object = "diagonalMatrix"),
195	function(object) TRUE)	function(object) TRUE)
196
197		setMethod("chol", signature(x = "ddiMatrix"),# pivot = "ANY"
198		function(x, pivot) {
199		if(any(x@x < 0)) stop("chol() is undefined for diagonal matrix with negative entries")
200		x@x <- sqrt(x@x)
201		x
202		})
203		## chol(L) is L for logical diagonal:
204		setMethod("chol", signature(x = "ldiMatrix"), function(x, pivot) x)
205
206
207	setMethod("diag", signature(x = "diagonalMatrix"),	setMethod("diag", signature(x = "diagonalMatrix"),
208	function(x = 1, nrow, ncol = n) {	function(x = 1, nrow, ncol = n) {
209	if(x@diag == "U")	if(x@diag == "U")
#	Line 148	Line 222
222	})	})
223
224	## Basic Matrix Multiplication {many more to add}	## Basic Matrix Multiplication {many more to add}
225		##       ---------------------
226	## FIXME: extend this for 'ldi', i.e. do "diagonalMatrix"	## Note that "ldi" logical are treated as numeric
227	diagdiagprod <- function(x, y) {	diagdiagprod <- function(x, y) {
228	if(any(dim(x) != dim(y))) stop("non-matching dimensions")	if(any(dim(x) != dim(y))) stop("non-matching dimensions")
229	if(x@diag != "U") {	if(x@diag != "U") {
230	if(y@diag != "U") x@x <- x@x * y@x	if(y@diag != "U") {
231		nx <- x@x * y@x
232		if(is.numeric(nx) && !is.numeric(x@x))
233		x <- as(x, "dMatrix")
234		x@x <- as.numeric(nx)
235		}
236	return(x)	return(x)
237	} else ## x is unit diagonal	} else ## x is unit diagonal
238	return(y)	return(y)
239	}	}
240
241	setMethod("%*%", signature(x = "ddiMatrix", y = "ddiMatrix"),	setMethod("%*%", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
242	diagdiagprod, valueClass = "ddiMatrix")	diagdiagprod, valueClass = "ddiMatrix")
243
244	formals(diagdiagprod) <- alist(x=, y=NULL)	formals(diagdiagprod) <- alist(x=, y=x)
245	setMethod("crossprod", signature(x = "ddiMatrix", y = "ddiMatrix"),	setMethod("crossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
246		diagdiagprod, valueClass = "ddiMatrix")
247		setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "diagonalMatrix"),
248	diagdiagprod, valueClass = "ddiMatrix")	diagdiagprod, valueClass = "ddiMatrix")
249	setMethod("tcrossprod", signature(x = "ddiMatrix", y = "ddiMatrix"),	setMethod("crossprod", signature(x = "diagonalMatrix", y = "missing"),
250		diagdiagprod, valueClass = "ddiMatrix")
251		setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "missing"),
252	diagdiagprod, valueClass = "ddiMatrix")	diagdiagprod, valueClass = "ddiMatrix")
253
254
#	Line 182	Line 265
265	formals(diagmatprod) <- alist(x=, y=NULL)	formals(diagmatprod) <- alist(x=, y=NULL)
266	setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),	setMethod("crossprod", signature(x = "diagonalMatrix", y = "matrix"),
267	diagmatprod)	diagmatprod)
268		setMethod("tcrossprod", signature(x = "diagonalMatrix", y = "matrix"),
269		diagmatprod)
270
271	diagdgeprod <- function(x, y) {	diagdgeprod <- function(x, y) {
272	dx <- dim(x)	dx <- dim(x)
#	Line 202	Line 287
287	dx <- dim(x)	dx <- dim(x)
288	dy <- dim(y)	dy <- dim(y)
289	if(dx[2] != dy[1]) stop("non-matching dimensions")	if(dx[2] != dy[1]) stop("non-matching dimensions")
290	as(if(y@diag == "U") x else x * rep.int(y@x, dx[1]), "Matrix")	as(if(y@diag == "U") x else x * rep(y@x, each = dx[1]), "Matrix")
291	})	})
292
293	setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),	setMethod("%*%", signature(x = "dgeMatrix", y = "diagonalMatrix"),
#	Line 211	Line 296
296	dy <- dim(y)	dy <- dim(y)
297	if(dx[2] != dy[1]) stop("non-matching dimensions")	if(dx[2] != dy[1]) stop("non-matching dimensions")
298	if(y@diag == "N")	if(y@diag == "N")
299	x@x <- x@x * rep.int(y@x, dx[1])	x@x <- x@x * rep(y@x, each = dx[1])
300	x	x
301	})	})
302
#	Line 231	Line 316
316
317	### ---------------- diagonal  o   sparse  -----------------------------	### ---------------- diagonal  o   sparse  -----------------------------
318
319
320		## Use function for several signatures, in order to evade
321		## ambiguous dispatch for "ddi", since there's also Arith(ddense., ddense.)
322		diagOdiag <- function(e1,e2) { # result should also be diagonal
323		r <- callGeneric(.diag.x(e1), .diag.x(e2)) # error if not "compatible"
324		if(is.numeric(r)) {
325		if(is.numeric(e2@x)) {
326		e2@x <- r; return(.diag.2N(e2)) }
327		if(!is.numeric(e1@x))
328		## e.g. e1, e2 are logical;
329		e1 <- as(e1, "dMatrix")
330		}
331		else if(is.logical(r))
332		e1 <- as(e1, "lMatrix")
333		else stop("intermediate 'r' is of type", typeof(r))
334		e1@x <- r
335		.diag.2N(e1)
336		}
337
338		setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "diagonalMatrix"),
339		diagOdiag)
340		## These two are just for method disambiguation:
341		setMethod("Ops", signature(e1 = "ddiMatrix", e2 = "diagonalMatrix"),
342		diagOdiag)
343		setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ddiMatrix"),
344		diagOdiag)
345
346		## For almost everything else, diag* shall be treated "as sparse" :
347	## These are cheap implementations via coercion	## These are cheap implementations via coercion
348
349		## for disambiguation
350		setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "sparseMatrix"),
351		function(e1,e2) callGeneric(as(e1, "sparseMatrix"), e2))
352		setMethod("Ops", signature(e1 = "sparseMatrix", e2 = "diagonalMatrix"),
353		function(e1,e2) callGeneric(e1, as(e2, "sparseMatrix")))
354		## in general:
355		setMethod("Ops", signature(e1 = "diagonalMatrix", e2 = "ANY"),
356		function(e1,e2) callGeneric(as(e1,"sparseMatrix"), e2))
357		setMethod("Ops", signature(e1 = "ANY", e2 = "diagonalMatrix"),
358		function(e1,e2) callGeneric(e1, as(e2,"sparseMatrix")))
359
360
361
362	## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()	## FIXME?: In theory, this can be done *FASTER*, in some cases, via tapply1()
363
364	setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),	setMethod("%*%", signature(x = "diagonalMatrix", y = "sparseMatrix"),
#	Line 268	Line 394
394	}	}
395
396	setMethod("show", signature(object = "diagonalMatrix"),	setMethod("show", signature(object = "diagonalMatrix"),
397	function(object) prDiag(object))	function(object) {
398		d <- dim(object)
399		cl <- class(object)
400		cat(sprintf('%d x %d diagonal matrix of class "%s"\n',
401		d[1], d[2], cl))
402		prDiag(object)
403		})

---

Colored Diff Long Colored Diff Unidiff Context Diff Side by Side

Legend: Removed from v.1331   changed lines   Added in v.1655

---

root@r-forge.r-project.org	ViewVC Help
Powered by ViewVC 1.0.0