Diff of /pkg/R/Matrix.R

Parent Directory | Revision Log | Patch

	revision 973, Fri Oct 7 20:15:08 2005 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 12	Line 18
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
21		## head and tail apply to all Matrix objects for which subscripting is allowed:
22		## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {
23		setMethod("head", signature(x = "Matrix"), utils:::head.matrix)
24		setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)
25		## } else { # R 2.4.0 and newer
26		##     setMethod("head", signature(x = "Matrix"), utils::head.matrix)
27		##     setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
28		## }
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 also note that "base" eigen may get an isSymmetric() that *would* be exported!	## but that "base" has an isSymmetric() S3-generic since R 2.3.0
43	setMethod("isSymmetric", signature(object = "symmetricMatrix", tol="ANY"),	setMethod("isSymmetric", signature(object = "symmetricMatrix"),
44	function(object,tol) TRUE)	function(object,tol) TRUE)
45	setMethod("isSymmetric", signature(object = "triangularMatrix", tol="ANY"),	setMethod("isSymmetric", signature(object = "triangularMatrix"),
46	## FIXME: 'TRUE' if *diagonal*, i.e. return(isDiagonal(object))	## TRUE iff diagonal:
47	function(object,tol) FALSE)	function(object,tol) isDiagonal(object))
48
49	setMethod("isDiagonal", signature(object = "sparseMatrix"),	if(paste(R.version$major, R.version$minor, sep=".") < "2.3")
50	function(object) {	## need a "matrix" method as in R 2.3 and later
51	gT <- as(object, "TsparseMatrix")	setMethod("isSymmetric", signature(object = "matrix"),
52	all(gT@i == gT@j)	function(object, tol = 100*.Machine$double.eps, ...)
53		{
54		## pretest: is it square?
55		d <- dim(object)
56		if(d[1] != d[2]) return(FALSE)
57		## for `broken' all.equal in R <= 2.2.x:
58		dn <- dimnames(object)
59		if(!identical(dn[1], dn[2])) return(FALSE)
60		test <-
61		if(is.complex(object))
62		all.equal.numeric(object, Conj(t(object)), tol = tol, ...)
63		else              # numeric, character, ..
64		all.equal(object, t(object), tol = tol, ...)
65		isTRUE(test)
66	})	})
67
68
69		setMethod("isTriangular", signature(object = "triangularMatrix"),
70		function(object, ...) TRUE)
71
72		setMethod("isTriangular", signature(object = "matrix"), isTriMat)
73
74		setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
75
76
77
78	setMethod("dim", signature(x = "Matrix"),	setMethod("dim", signature(x = "Matrix"),
79	function(x) x@Dim, valueClass = "integer")	function(x) x@Dim, valueClass = "integer")
80	setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)	setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
#	Line 54	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 63	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 74	Line 119
119	nrow <- ceiling(length(data)/ncol)	nrow <- ceiling(length(data)/ncol)
120	else if (missing(ncol))	else if (missing(ncol))
121	ncol <- ceiling(length(data)/nrow)	ncol <- ceiling(length(data)/nrow)
122		if(length(data) == 1 && data == 0 && !identical(sparse,FALSE)) {
123		if(is.null(sparse)) sparse <- TRUE
124		## will be sparse: do NOT construct full matrix!
125		data <- new(if(is.numeric(data)) "dgTMatrix" else
126		if(is.logical(data)) "lgTMatrix" else
127		stop("invalid 'data'"),
128		Dim = as.integer(c(nrow,ncol)),
129		Dimnames = if(is.null(dimnames)) list(NULL,NULL)
130		else dimnames)
131		} 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		doDN <- FALSE
138		}
139	## 'data' is now a "matrix" or "Matrix"	## 'data' is now a "matrix" or "Matrix"
140	## FIXME: consider it's type (logical,....)	if (doDN && !is.null(dimnames))
141	## ctype <- substr(class(data), 1,1) # "d", "l", ...	dimnames(data) <- dimnames
142	## FIXME(2): check for symmetric / triangular / ...
143		## check for symmetric / triangular / diagonal :
144		isSym <- isSymmetric(data)
145		if((isTri <- !isSym))
146		isTri <- isTriangular(data)
147		isDiag <- isSym # cannot be diagonal if it isn't symmetric
148		if(isDiag)
149		isDiag <- isDiagonal(data)
150
151	### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R	### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
152	if(sparse)
153	as(data, "dgCMatrix")	## Find proper matrix class 'cl'
154	else	cl <-
155	as(data, "dgeMatrix")	if(isDiag)
156		"diagonalMatrix" # -> will automatically check for type
157		else {
158		## consider it's type
159		ctype <-
160		if(is(data,"Matrix")) class(data)
161		else {
162		if("complex" == (ctype <- typeof(data)))
163		"z" else ctype
164		}
165		ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
166		if(ctype == "z")
167		stop("complex matrices not yet implemented in Matrix package")
168		if(ctype == "i") {
169		warning("integer matrices not yet implemented in 'Matrix'; ",
170		"using 'double' ones'")
171		ctype <- "d"
172		}
173		paste(ctype,
174		if(sparse) {
175		if(isSym) "sCMatrix" else
176		if(isTri) "tCMatrix" else "gCMatrix"
177		} else { ## dense
178		if(isSym) "syMatrix" else
179		if(isTri) "trMatrix" else "geMatrix"
180		}, sep="")
181		}
182
183		## Now coerce and return
184		as(data, cl)
185	}	}
186
187	## Methods for operations where one argument is numeric	## Methods for operations where one argument is numeric
#	Line 104	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 121	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",
#	Line 133	Line 242
242	Y <- as(Y, "matrix") ; Matrix(callGeneric()) })	Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
243
244
245		setMethod("diag", signature(x = "Matrix"),
246		function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
247	setMethod("t", signature(x = "Matrix"),	setMethod("t", signature(x = "Matrix"),
248	function(x) .bail.out.1(.Generic, class(x)))	function(x) .bail.out.1(.Generic, class(x)))
249
#	Line 170	Line 281
281	setMethod("[", signature(x = "Matrix",	setMethod("[", signature(x = "Matrix",
282	i = "missing", j = "missing", drop = "ANY"),	i = "missing", j = "missing", drop = "ANY"),
283	function (x, i, j, drop) x)	function (x, i, j, drop) x)
284
285	## missing 'drop' --> 'drop = TRUE'	## missing 'drop' --> 'drop = TRUE'
286	##                     -----------	##                     -----------
287	## select rows	## select rows
#	Line 189	Line 301
301	function(x,i,j, drop)	function(x,i,j, drop)
302	stop("invalid or not-yet-implemented 'Matrix' subsetting"))	stop("invalid or not-yet-implemented 'Matrix' subsetting"))
303
304		##  "logical *vector* indexing, such as  M [ M >= 10 ] :
305		setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
306		drop = "ANY"),
307		function (x, i, j, drop) {
308		as(x, geClass(x))@x[as.vector(i)]
309		## -> error when lengths don't match
310		})
311
312		## FIXME: The following is good for    M [ <logical>   ]
313		##        *BUT* it also triggers for   M [ <logical> , ] where it is *WRONG*
314		##       using nargs() does not help: it gives '3' for both cases
315		if(FALSE)
316		setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
317		drop = "ANY"),
318		function (x, i, j, drop) {
319		## DEBUG
320		cat("[(Matrix,i,..): nargs=", nargs(),"\n")
321		as(x, geClass(x))@x[i] })
322
323
324	## "FIXME:"	## "FIXME:"
325	## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?	## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?
326	##  and                A[ LL ]  where LL is a logical *vector*	##  and                A[ LL ]  where LL is a logical *vector*
#	Line 199	Line 331
331
332	## x[] <- value :	## x[] <- value :
333	setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",	setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
334	value = "index"),##  double/logical/...	value = "ANY"),## double/logical/...
335	function (x, value) { x@x <- value ; validObject(x); x })	function (x, value) {
336		x@x <- value
337		validObject(x)# check if type and lengths above match
338		x
339		})
340
341	## Otherwise (value is not "index"): bail out	## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
342		## (ANY,ANY,ANY) is used when no `real method' is implemented :
343	setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",	setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
344	value = "ANY"),	value = "ANY"),
345	function (x, i, j, value)	function (x, i, j, value) {
346	if(!is(value,"index"))	if(!is.atomic(value))
347	stop("RHS 'value' must be of class \"index\"")	stop("RHS 'value' must match matrix class ", class(x))
348	else stop("not-yet-implemented 'Matrix[<-' method"))	else stop("not-yet-implemented 'Matrix[<-' method")
349		})
	## NOTE: the following only works for R 2.2.x (and later) ---
	## ----  *and* 'Matrix' must have been *installed* by R >= 2.2.x
350
	if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {
351
352	## The trivial methods :	## The trivial methods :
353	setMethod("cbind2", signature(x = "Matrix", y = "NULL"),	setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
#	Line 247	Line 379
379	colCheck(x,y)	colCheck(x,y)
380	t(cbind2(t(x), t(y)))	t(cbind2(t(x), t(y)))
381	})	})
	}## R-2.2.x and newer

---

Colored Diff Long Colored Diff Unidiff Context Diff Side by Side

Legend: Removed from v.973   changed lines   Added in v.1455

---

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