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### Simple fallback methods for all dense matrices
### These are "cheap" to program, but potentially far from efficient;
### Methods for specific subclasses will overwrite these:
setAs("ANY", "denseMatrix", function(from) Matrix(from, sparse=FALSE, doDiag=FALSE))
## Conceivably, could write
## setAs("matrix", "denseMatrix", ....) which was slightly more efficient than
## Matrix(.) but would have many things in common
setAs("denseMatrix", "generalMatrix", as_geSimpl)
## dense to sparse:
## : if we do this, do it "right", i.e. preserve symmetric/triangular!
## setAs("denseMatrix", "dsparseMatrix",
## ## MM thought that as() will take the ``closest'' match; but that fails!
## ## function(from) as(as(from, "dgeMatrix"), "dsparseMatrix"))
## function(from) as(as(from, "dgeMatrix"), "dgCMatrix"))
.dense2C <- function(from, kind = NA, uplo = "U", symDimnames = FALSE) {
useK <- is.character(kind) && length(kind) == 1 &&
kind %in% c("gen", "sym", "tri")
if(!useK) {
cl <- class(from)
cld <- getClassDef(cl) ## get it once (speedup)
}
r <- .Call(dense_to_Csparse, from)# goes via "generalMatrix"
## FIXME: for symmetric / triangular matrices, this is a waste, notably if packed
if (useK && kind == "gen" || !useK && extends(cld, "generalMatrix"))
r
else if(useK && kind == "sym" || !useK && extends(cld, "symmetricMatrix"))
forceCspSymmetric(r, uplo, isTri = FALSE, symDimnames=symDimnames)
else if(!useK && extends(cld, "diagonalMatrix"))
stop("diagonalMatrix in .dense2C() -- should never happen, please report!")
else { ## we have "triangular" :
if(useK) {
cl <- class(from)
cld <- getClassDef(cl) ## get it once (speedup)
}
if (extends(cld,"dMatrix")) as(r, "dtCMatrix")
else if (extends(cld,"lMatrix")) as(r, "ltCMatrix")
else if (extends(cld,"nMatrix")) as(r, "ntCMatrix")
else if (extends(cld,"zMatrix")) as(r, "ztCMatrix")
else stop(gettextf("undefined method for class %s", dQuote(cl)), domain=NA)
}
}
setAs("denseMatrix", "CsparseMatrix", function(from) .dense2C(from))
## This sometimes fails (eg. for "lsyMatrix"), and we really want to
## use the generic ``go via Csparse'' (top of ./sparseMatrix.R) instead
## setAs("denseMatrix", "sparseMatrix",
## function(from) {
## cl <- class(from)
## cld <- getClassDef(cl)
## if (extends(cld, "generalMatrix"))
## .Call(dense_to_Csparse, from)
## else ## i.e. triangular | symmetric
## as_Csparse(from, cld)
## })
setAs("denseMatrix", "TsparseMatrix",
function(from) as(.dense2C(from), "TsparseMatrix"))
setMethod("show", signature(object = "denseMatrix"),
function(object) prMatrix(object))
##- ## FIXME: The following is only for the "dMatrix" objects that are not
##- ## "dense" nor "sparse" -- i.e. "packed" ones :
##- ## But these could be printed better -- "." for structural zeros.
##- setMethod("show", signature(object = "dMatrix"), prMatrix)
##- ## and improve this as well:
##- setMethod("show", signature(object = "pMatrix"), prMatrix)
##- ## this should now be superfluous [keep for safety for the moment]:
setMethod("dim<-", signature(x = "denseMatrix", value = "ANY"),
function(x, value) {
if(!is.numeric(value) || length(value) != 2)
stop("dim(.) value must be numeric of length 2")
if(prod(dim(x)) != prod(value <- as.integer(value)))
stop("dimensions don't match the number of cells")
clx <- as.character(MatrixClass(class(x))) # as.*(): drop attr
if(substring(clx,2) == "geMatrix") {
x@Dim <- value
if(length(x@factors) > 0)
x@factors <- list()
x
} else { ## other "denseMatrix"
x <- as_geSimpl2(x, clx)
dim(x) <- value
x
}
})
## Using "index" for indices should allow
## integer (numeric), logical, or character (names!) indices :
## use geClass() when 'i' or 'j' are missing:
## since symmetric, triangular, .. will not be preserved anyway:
setMethod("[", signature(x = "denseMatrix", i = "index", j = "missing",
drop = "logical"),
function (x, i, j, ..., drop) {
if((na <- nargs()) == 3)
r <- as(x, "matrix")[i, drop=drop]
else if(na == 4)
r <- as(x, "matrix")[i, , drop=drop]
else stop(gettextf("invalid nargs()= %d", na), domain=NA)
if(is.null(dim(r))) r else as(r, geClass(x))
})
setMethod("[", signature(x = "denseMatrix", i = "missing", j = "index",
drop = "logical"),
function (x, i, j, ..., drop) {
r <- as(x, "matrix")[, j, drop=drop]
if(is.null(dim(r))) r else as(r, geClass(x))
})
setMethod("[", signature(x = "denseMatrix", i = "index", j = "index",
drop = "logical"),
function (x, i, j, ..., drop) {
r <- callGeneric(x = as(x, "matrix"), i=i, j=j, drop=drop)
if(is.null(dim(r)))
r
else {
cld <- getClassDef(cl <- class(x))
if(extends(cld, "symmetricMatrix") &&
length(i) == length(j) && isTRUE(all(i == j)))
## keep original symmetric class (but not "dpo")
as(r, class2(cl, .M.kindC(cld)))
else as_smartClass(r, cl)
}
})
.dense.sub.i.2col <- function(x, i, j, ..., drop) {
r <- as(x, "matrix")[ i ]
if(is.null(dim(r))) r else as(r, geClass(x))
}
setMethod("[", signature(x = "denseMatrix", i = "matrix", j = "missing"),#drop="ANY"
.dense.sub.i.2col)
setMethod("[", signature(x = "denseMatrix", i = "matrix", j = "missing", drop="missing"),
.dense.sub.i.2col)
## Now the "[<-" ones --- see also those in ./Matrix.R
## It's recommended to use setReplaceMethod() rather than setMethod("[<-",.)
## even though the former is currently just a wrapper for the latter
## x[] <- value :
setReplaceMethod("[", signature(x = "denseMatrix", i = "missing", j = "missing",
value = "ANY"),## double/logical/...
function (x, value) {
x <- as(x, "generalMatrix")
x@x[] <- value
validObject(x)# check if type and lengths above match
x
})
## FIXME: 1) These are far from efficient
## -----
setReplaceMethod("[", signature(x = "denseMatrix", i = "index", j = "missing",
value = "replValue"),
function (x, i, j, ..., value) {
r <- as(x, "matrix")
## message("`[<-` with nargs()= ",nargs())
if((na <- nargs()) == 3)
r[i] <- value
else if(na == 4)
r[i, ] <- value
else stop(gettextf("invalid nargs()= %d", na), domain=NA)
as(r, geClass(x))
})
setReplaceMethod("[", signature(x = "denseMatrix", i = "missing", j = "index",
value = "replValue"),
function (x, i, j, ..., value) {
r <- as(x, "matrix")
r[, j] <- value
as(r, geClass(x))
})
setReplaceMethod("[", signature(x = "denseMatrix", i = "index", j = "index",
value = "replValue"),
function (x, i, j, ..., value) {
r <- as(x, "matrix")
r[i, j] <- value
as_smartClass(r, class(x)) ## was as(r, class(x))
})
setReplaceMethod("[", signature(x = "denseMatrix", i = "matrix", # 2-col.matrix
j = "missing", value = "replValue"),
function(x, i, j, ..., value) {
r <- as(x, "matrix")
r[ i ] <- value
as(r, geClass(x))
})
setMethod("isSymmetric", signature(object = "denseMatrix"),
function(object, tol = 100*.Machine$double.eps, tol1 = 8*tol, ...) {
## pretest: is it square?
d <- dim(object)
if((n <- d[1L]) != d[2L]) return(FALSE)
if(n <= 1L) return(TRUE)
## else: square (n x n) matrix, n >= 2 :
is.z <- is(object, "zMatrix")
## initial tests, fast for large non-symmetric:
if(length(tol1)) {
## initial pre-tests, fast for large non-symmetric:
Cj <- if(is.z) Conj else identity
for(i in unique(c(1L, 2L, n-1L, n)))
if(is.character(all.equal(object[i, ], Cj(object[, i]),
tolerance = tol1, ...))) return(FALSE)
}
## else slower test
if (is(object,"dMatrix"))
isTRUE(all.equal(as( object, "dgeMatrix"),
as(t(object), "dgeMatrix"), tolerance = tol, ...))
else if (is(object, "nMatrix"))
identical(as( object, "ngeMatrix"),
as(t(object), "ngeMatrix"))
else if (is(object, "lMatrix"))# not possible currently
## test for exact equality; FIXME(?): identical() too strict?
identical(as( object, "lgeMatrix"),
as(t(object), "lgeMatrix"))
else if (is.z) ## will error out here
isTRUE(all.equal(as( object, "zgeMatrix"),
as(Conj(t(object)), "zgeMatrix"),
tolerance = tol, ...))
else if (is(object, "iMatrix")) ## will error out here
identical(as(object, "igeMatrix"),
as(t(object), "igeMatrix"))
})
## rather methods in ./triangularMatrix.R
## setMethod("isTriangular", signature(object = "triangularMatrix"),
## function(object, ...) TRUE)
setMethod("isTriangular", signature(object = "denseMatrix"), isTriMat)
setMethod("isDiagonal", signature(object = "denseMatrix"), .is.diagonal)
setMethod("rcond", signature(x = "denseMatrix", norm = "character"),
function(x, norm, ...)
rcond(as(as(x, "dMatrix"), "dgeMatrix"), norm=norm, ...))
setMethod("symmpart", signature(x = "denseMatrix"),
function(x) symmpart(as(x, "dMatrix")))
setMethod("skewpart", signature(x = "denseMatrix"),
function(x) skewpart(as(x, "dMatrix")))
setMethod("is.na", signature(x = "denseMatrix"),
function(x) {
if(any((inax <- is.na(x@x)))) {
r <- as(x, "lMatrix")#-> logical x-slot
r@x <- inax
as(r, "nMatrix")
} else {
d <- x@Dim
new("ngCMatrix", Dim = d, Dimnames = dimnames(x),
i = integer(0), p = rep.int(0L, d[2]+1L))
}
})
if(.Matrix.avoiding.as.matrix) {
setMethod("qr", signature(x = "ddenseMatrix"),
function(x, ...) qr.default(ge2mat(..2dge(x)), ...))
setMethod("qr", signature(x = "denseMatrix"),
function(x, ...) qr(as(x, "ddenseMatrix"), ...))
}
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