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### Define Methods that can be inherited for all subclasses
## This replaces many "d..Matrix" -> "dgeMatrix" ones
## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
## ----- in ../src/Mutils.c
## Should this method return 'from' without duplication when it has
## class dgeMatrix?
setAs("ddenseMatrix", "dgeMatrix",
function(from) {
if (class(from) != "dgeMatrix")
from <- .Call(dup_mMatrix_as_dgeMatrix, from)
from
})
## d(ouble) to l(ogical):
setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)
setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)
setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)
setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)
setAs("dspMatrix", "lspMatrix", d2l_Matrix)
setAs("ddenseMatrix", "CsparseMatrix",
function(from) {
if (class(from) != "dgeMatrix")
from <- .Call(dup_mMatrix_as_dgeMatrix, from)
.Call(dense_to_Csparse, from)
})
## special case
setAs("dgeMatrix", "dgCMatrix",
function(from) .Call(dense_to_Csparse, from))
setAs("matrix", "CsparseMatrix",
function(from) {
if(is.numeric(from))
.Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
as(Matrix(from, sparse=TRUE), "CsparseMatrix")
else stop('not-yet-implemented coercion to "CsparseMatrix"')
})
## special case needed in the Matrix function
setAs("matrix", "dgCMatrix",
function(from) {
storage.mode(from) <- "double"
.Call(dense_to_Csparse, from)
})
setAs("numeric", "CsparseMatrix",
function(from)
.Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
setMethod("as.numeric", signature(x = "ddenseMatrix"),
function(x, ...) as(x, "dgeMatrix")@x)
## -- see also ./Matrix.R e.g., for a show() method
## These methods are the 'fallback' methods for all dense numeric
## matrices in that they simply coerce the ddenseMatrix to a
## dgeMatrix. Methods for special forms override these.
setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
function(x, type, ...) callGeneric(as(x, "dgeMatrix")))
setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),
function(x, type, ...) callGeneric(as(x, "dgeMatrix")))
setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
## Not really useful; now require *identical* class for result:
## setMethod("t", signature(x = "ddenseMatrix"),
## function(x) callGeneric(as(x, "dgeMatrix")))
setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
setMethod("diag", signature(x = "ddenseMatrix"),
function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
## These methods cause an infinite loop in pre-2.4.0
## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
## function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
## function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
## General method for dense matrix multiplication in case specific methods
## have not been defined.
setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
function(x, y) .Call(dgeMatrix_matrix_mm,
.Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
valueClass = "dgeMatrix")
setMethod("lu", signature(x = "ddenseMatrix"),
function(x, ...) callGeneric(as(x, "dgeMatrix")))
setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
function(x, logarithm, ...)
callGeneric(as(x, "dgeMatrix"), logarithm))
## now done for "dMatrix":
## setMethod("expm", signature(x = "ddenseMatrix"),
## function(x) callGeneric(as(x, "dgeMatrix")))
setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
setMethod("Schur", signature(x = "ddenseMatrix", vectors = "logical"),
function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
## Cheap version: work via "dgeMatrix" and use the group methods there:
## FIXME(?): try to preserve "symmetric", "triangular", ...
setMethod("Arith", ## "+", "-", "*", "^", "%%", "%/%", "/"
signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
as(e2, "dgeMatrix")))
setMethod("Arith",
signature(e1 = "ddenseMatrix", e2 = "numeric"),
function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
setMethod("Arith",
signature(e1 = "numeric", e2 = "ddenseMatrix"),
function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
setMethod("Math",
signature(x = "ddenseMatrix"),
function(x) callGeneric(as(x, "dgeMatrix")))
### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
### cbind2
setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
function(x, y) {
d <- dim(x); nr <- d[1]; nc <- d[2]
y <- rep(y, length.out = nr) # 'silent procrustes'
## beware of (packed) triangular, symmetric, ...
x <- as(x, "dgeMatrix")
x@x <- c(x@x, as.double(y))
x@Dim[2] <- nc + 1:1
if(is.character(dn <- x@Dimnames[[2]]))
x@Dimnames[[2]] <- c(dn, "")
x
})
## the same, (x,y) <-> (y,x):
setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
function(x, y) {
d <- dim(y); nr <- d[1]; nc <- d[2]
x <- rep(x, length.out = nr)
y <- as(y, "dgeMatrix")
y@x <- c(as.double(x), y@x)
y@Dim[2] <- nc + 1:1
if(is.character(dn <- y@Dimnames[[2]]))
y@Dimnames[[2]] <- c("", dn)
y
})
setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
function(x, y) callGeneric(x, as(y, "dgeMatrix")))
setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
function(x, y) callGeneric(as(x, "dgeMatrix"), y))
setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
function(x, y) {
nr <- rowCheck(x,y)
ncx <- x@Dim[2]
ncy <- y@Dim[2]
## beware of (packed) triangular, symmetric, ...
hasDN <- !is.null(dnx <- dimnames(x)) |
!is.null(dny <- dimnames(y))
x <- as(x, "dgeMatrix")
y <- as(y, "dgeMatrix")
x@x <- c(x@x, y@x)
x@Dim[2] <- ncx + ncy
if(hasDN) {
## R and S+ are different in which names they take
## if they differ -- but there's no warning in any case
rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
cx <- dnx[[2]] ; cy <- dny[[2]]
cn <- if(is.null(cx) && is.null(cy)) NULL
else c(if(!is.null(cx)) cx else rep.int("", ncx),
if(!is.null(cy)) cy else rep.int("", ncy))
x@Dimnames <- list(rn, cn)
}
x
})
### rbind2 -- analogous to cbind2 --- more to do for @x though:
setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
function(x, y) {
if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
new("dgeMatrix", Dim = x@Dim + 1:0,
Dimnames = list(dn, x@Dimnames[[2]]),
x = c(rbind2(as(x,"matrix"), y)))
})
## the same, (x,y) <-> (y,x):
setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
function(x, y) {
if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
new("dgeMatrix", Dim = y@Dim + 1:0,
Dimnames = list(dn, y@Dimnames[[2]]),
x = c(rbind2(x, as(y,"matrix"))))
})
setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
function(x, y) callGeneric(x, as(y, "dgeMatrix")))
setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
function(x, y) callGeneric(as(x, "dgeMatrix"), y))
setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
function(x, y) {
nc <- colCheck(x,y)
nrx <- x@Dim[1]
nry <- y@Dim[1]
dn <-
if(!is.null(dnx <- dimnames(x)) |
!is.null(dny <- dimnames(y))) {
## R and S+ are different in which names they take
## if they differ -- but there's no warning in any case
list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
NULL else
c(if(!is.null(rx)) rx else rep.int("", nrx),
if(!is.null(ry)) ry else rep.int("", nry)),
if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
} else list(NULL, NULL)
## beware of (packed) triangular, symmetric, ...
new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
})
### FIXME: band() et al should be extended from "ddense" to "dense" !
### However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
## for triangular ["dtr" and "dtp"]
setMethod("tril", "ddenseMatrix",
function(x, k = 0, ...) {
k <- as.integer(k[1])
dd <- dim(x); sqr <- dd[1] == dd[2]
stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
## returns "lower triangular" if k <= 0 && sqr
.Call(ddense_band, x, -dd[1], k)
})
setMethod("triu", "ddenseMatrix",
function(x, k = 0, ...) {
k <- as.integer(k[1])
dd <- dim(x); sqr <- dd[1] == dd[2]
stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
## returns "upper triangular" if k >= 0
.Call(ddense_band, x, k, dd[2])
})
setMethod("band", "ddenseMatrix",
function(x, k1, k2, ...) {
k1 <- as.integer(k1[1])
k2 <- as.integer(k2[1])
dd <- dim(x); sqr <- dd[1] == dd[2]
stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
r <- .Call(ddense_band, x, k1, k2)
if (k1 < 0 && k1 == -k2 && isSymmetric(x)) ## symmetric
as(r, paste(.M.kind(x), "syMatrix", sep=''))
else
r
})
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