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#### Containing all cbind2() and rbind2() methods for all our Matrices
###-- General -----------------------------------------------------------
###-- Dense, incl Diagonal ----------------------------------------------
###-- Sparse ------------------------------------------------------------
setMethod("cbind2", signature(x = "sparseMatrix", y = "matrix"),
function(x, y, ...) cbind2(x, .Call(dense_to_Csparse, y)))
setMethod("cbind2", signature(x = "matrix", y = "sparseMatrix"),
function(x, y, ...) cbind2(.Call(dense_to_Csparse, x), y))
setMethod("rbind2", signature(x = "sparseMatrix", y = "matrix"),
function(x, y, ...) rbind2(x, .Call(dense_to_Csparse, y)))
setMethod("rbind2", signature(x = "matrix", y = "sparseMatrix"),
function(x, y, ...) rbind2(.Call(dense_to_Csparse, x), y))
## originally from ./Matrix.R : -------------------------------
## The trivial methods :
setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
function(x, y, ...) x)
setMethod("cbind2", signature(x = "Matrix", y = "missing"),
function(x, y, ...) x)
setMethod("cbind2", signature(x = "NULL", y="Matrix"),
function(x, y, ...) y)
## using "atomicVector" not just "numeric"
setMethod("cbind2", signature(x = "Matrix", y = "atomicVector"),
function(x, y, ...) cbind2(x, matrix(y, nrow = nrow(x))))
setMethod("cbind2", signature(x = "atomicVector", y = "Matrix"),
function(x, y, ...) cbind2(matrix(x, nrow = nrow(y)), y))
setMethod("cbind2", signature(x = "ANY", y = "Matrix"),
function(x, y, ...) .bail.out.2(.Generic, class(x), class(y)))
setMethod("cbind2", signature(x = "Matrix", y = "ANY"),
function(x, y, ...) .bail.out.2(.Generic, class(x), class(y)))
setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
function(x, y, ...) x)
setMethod("rbind2", signature(x = "Matrix", y = "missing"),
function(x, y, ...) x)
setMethod("rbind2", signature(x = "NULL", y="Matrix"),
function(x, y, ...) y)
setMethod("rbind2", signature(x = "Matrix", y = "atomicVector"),
function(x, y, ...) rbind2(x, matrix(y, ncol = ncol(x))))
setMethod("rbind2", signature(x = "atomicVector", y = "Matrix"),
function(x, y, ...) rbind2(matrix(x, ncol = ncol(y)), y))
setMethod("rbind2", signature(x = "ANY", y = "Matrix"),
function(x, y, ...) .bail.out.2(.Generic, class(x), class(y)))
setMethod("rbind2", signature(x = "Matrix", y = "ANY"),
function(x, y, ...) .bail.out.2(.Generic, class(x), class(y)))
## Makes sure one gets x decent error message for the unimplemented cases:
setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
function(x, y, ...) {
rowCheck(x,y)
.bail.out.2("cbind2", class(x), class(y))
})
## Use a working fall back {particularly useful for sparse}:
## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
function(x, y, ...) {
colCheck(x,y)
t(cbind2(t(x), t(y)))
})
## originally from ./denseMatrix.R : -------------------------------
### cbind2
setMethod("cbind2", signature(x = "denseMatrix", y = "numeric"),
function(x, y, ...) {
d <- dim(x); nr <- d[1]; nc <- d[2]
y <- rep_len(y, nr) # 'silent procrustes'
## beware of (packed) triangular, symmetric, ...
x <- as(x, geClass(x))
x@x <- c(x@x, as.double(y))
x@Dim[2] <- nc + 1L
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 = "denseMatrix"),
function(x, y, ...) {
d <- dim(y); nr <- d[1]; nc <- d[2]
x <- rep_len(x, nr)
y <- as(y, geClass(y))
y@x <- c(as.double(x), y@x)
y@Dim[2] <- nc + 1L
if(is.character(dn <- y@Dimnames[[2]]))
y@Dimnames[[2]] <- c("", dn)
y
})
setMethod("cbind2", signature(x = "denseMatrix", y = "matrix"),
function(x, y, ...) cbind2(x, as_geSimpl(y)))
setMethod("cbind2", signature(x = "matrix", y = "denseMatrix"),
function(x, y, ...) cbind2(as_geSimpl(x), y))
cbind2DN <- function(dnx,dny, ncx,ncy) {
## 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 character(ncx),
if(!is.null(cy)) cy else character(ncy))
list(rn, cn)
}
setMethod("cbind2", signature(x = "denseMatrix", y = "denseMatrix"),
function(x, y, ...) {
rowCheck(x,y)
ncx <- x@Dim[2]
ncy <- y@Dim[2]
## beware of (packed) triangular, symmetric, ...
hasDN <- !is.null.DN(dnx <- dimnames(x)) | !is.null.DN(dny <- dimnames(y))
x <- as(x, geClass(x))
y <- as(y, geClass(y))
xx <- c(x@x, y@x)
## be careful, e.g., if we have an 'n' and 'd'
if(identical((tr <- typeof(xx)), typeof(x@x))) {
x@x <- xx
x@Dim[2] <- ncx + ncy
if(hasDN) x@Dimnames <- cbind2DN(dnx,dny, ncx,ncy)
x
} else if(identical(tr, typeof(y@x))) {
y@x <- xx
y@Dim[2] <- ncx + ncy
if(hasDN) y@Dimnames <- cbind2DN(dnx,dny, ncx,ncy)
y
} else stop("resulting x-slot has different type than x's or y's")
})
### rbind2 -- analogous to cbind2 --- more to do for @x though:
setMethod("rbind2", signature(x = "denseMatrix", y = "numeric"),
function(x, y, ...) {
if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
y <- rbind2(as(x,"matrix"), y)
new(paste0(.M.kind(y), "geMatrix"), x = c(y),
Dim = x@Dim + 1:0, Dimnames = list(dn, x@Dimnames[[2]]))
})
## the same, (x,y) <-> (y,x):
setMethod("rbind2", signature(x = "numeric", y = "denseMatrix"),
function(x, y, ...) {
if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
x <- rbind2(x, as(y,"matrix"))
new(paste0(.M.kind(x), "geMatrix"), x = c(x),
Dim = y@Dim + 1:0, Dimnames = list(dn, y@Dimnames[[2]]))
})
setMethod("rbind2", signature(x = "denseMatrix", y = "matrix"),
function(x, y, ...) rbind2(x, as_geSimpl(y)))
setMethod("rbind2", signature(x = "matrix", y = "denseMatrix"),
function(x, y, ...) rbind2(as_geSimpl(x), y))
rbind2DN <- function(dnx, dny, nrx,nry) {
if(!is.null.DN(dnx) || !is.null.DN(dny)) {
## 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 character(nrx),
if(!is.null(ry)) ry else character(nry)),
if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
} else list(NULL, NULL)
}
setMethod("rbind2", signature(x = "denseMatrix", y = "denseMatrix"),
function(x, y, ...) {
colCheck(x,y)
nrx <- x@Dim[1]
nry <- y@Dim[1]
## beware of (packed) triangular, symmetric, ...
hasDN <- !is.null.DN(dnx <- dimnames(x)) | !is.null.DN(dny <- dimnames(y))
x <- as(x, geClass(x))
y <- as(y, geClass(y))
xx <- .Call(R_rbind2_vector, x, y)
## be careful, e.g., if we have an 'n' and 'd'
if(identical((tr <- typeof(xx)), typeof(x@x))) {
x@x <- xx
x@Dim[1] <- nrx + nry
if(hasDN) x@Dimnames <- rbind2DN(dnx,dny, nrx,nry)
x
} else if(identical(tr, typeof(y@x))) {
y@x <- xx
y@Dim[1] <- nrx + nry
if(hasDN) y@Dimnames <- rbind2DN(dnx,dny, nrx,nry)
y
} else stop("resulting x-slot has different type than x's or y's")
})
## originally from ./diagMatrix.R : --------------------------------------
## For diagonalMatrix: preserve sparseness {not always optimal, but "the law"}
## hack to suppress the obnoxious dispatch ambiguity warnings:
diag2Sp <- function(x) suppressWarnings(as(x, "CsparseMatrix"))
setMethod("cbind2", signature(x = "diagonalMatrix", y = "sparseMatrix"),
function(x, y, ...) cbind2(diag2Sp(x), as(y,"CsparseMatrix")))
setMethod("cbind2", signature(x = "sparseMatrix", y = "diagonalMatrix"),
function(x, y, ...) cbind2(as(x,"CsparseMatrix"), diag2Sp(y)))
setMethod("rbind2", signature(x = "diagonalMatrix", y = "sparseMatrix"),
function(x, y, ...) rbind2(diag2Sp(x), as(y,"CsparseMatrix")))
setMethod("rbind2", signature(x = "sparseMatrix", y = "diagonalMatrix"),
function(x, y, ...) rbind2(as(x,"CsparseMatrix"), diag2Sp(y)))
## in order to evade method dispatch ambiguity, but still remain "general"
## we use this hack instead of signature x = "diagonalMatrix"
for(cls in names(getClass("diagonalMatrix")@subclasses)) {
setMethod("cbind2", signature(x = cls, y = "matrix"),
function(x, y, ...) cbind2(diag2Sp(x), .Call(dense_to_Csparse, y)))
setMethod("cbind2", signature(x = "matrix", y = cls),
function(x, y, ...) cbind2(.Call(dense_to_Csparse, x), diag2Sp(y)))
setMethod("rbind2", signature(x = cls, y = "matrix"),
function(x, y, ...) rbind2(diag2Sp(x), .Call(dense_to_Csparse, y)))
setMethod("rbind2", signature(x = "matrix", y = cls),
function(x, y, ...) rbind2(.Call(dense_to_Csparse, x), diag2Sp(y)))
## These are already defined for "Matrix"
## -- repeated here for method dispatch disambiguation {"design-FIXME" ?}
setMethod("cbind2", signature(x = cls, y = "atomicVector"),
function(x, y, ...) cbind2(x, matrix(y, nrow = nrow(x))))
setMethod("cbind2", signature(x = "atomicVector", y = cls),
function(x, y, ...) cbind2(matrix(x, nrow = nrow(y)), y))
setMethod("rbind2", signature(x = cls, y = "atomicVector"),
function(x, y, ...) rbind2(x, matrix(y, ncol = ncol(x))))
setMethod("rbind2", signature(x = "atomicVector", y = cls),
function(x, y, ...) rbind2(matrix(x, ncol = ncol(y)), y))
}
## originally from ./dsparseMatrix.R : --------------------------------
## FIXME: dimnames() handling should happen in C code
## ------> ../src/Csparse.c
## Fast - almost non-checking methods
.cbind2Csp <- function(x,y) .Call(Csparse_horzcat, as_Csp2(x), as_Csp2(y))
.rbind2Csp <- function(x,y) .Call(Csparse_vertcat, as_Csp2(x), as_Csp2(y))
cbind2sparse <- function(x,y) {
## beware of (packed) triangular, symmetric, ...
if(identical(c(dnx <- dimnames(x),
dny <- dimnames(y)),
list(NULL,NULL,NULL,NULL)))
## keep empty dimnames
.cbind2Csp(x,y)
else {
## 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 character(ncol(x)),
if(!is.null(cy)) cy else character(ncol(y)))
ans <- .cbind2Csp(x,y)
ans@Dimnames <- list(rn, cn)
ans
}
}
setMethod("cbind2", signature(x = "sparseMatrix", y = "sparseMatrix"),
function(x, y, ...) {
rowCheck(x,y)
cbind2sparse(x,y)
})
rbind2sparse <- function(x,y) {
## beware of (packed) triangular, symmetric, ...
if(identical(c(dnx <- dimnames(x),
dny <- dimnames(y)),
list(NULL,NULL,NULL,NULL)))
## keep empty dimnames
.rbind2Csp(x,y)
else {
## R and S+ are different in which names they take
## if they differ -- but there's no warning in any case
cn <- if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]]
rx <- dnx[[1]] ; ry <- dny[[1]]
rn <- if(is.null(rx) && is.null(ry)) NULL
else c(if(!is.null(rx)) rx else character(nrow(x)),
if(!is.null(ry)) ry else character(nrow(y)))
ans <- .rbind2Csp(x,y)
ans@Dimnames <- list(rn, cn)
ans
}
}
setMethod("rbind2", signature(x = "sparseMatrix", y = "sparseMatrix"),
function(x, y, ...) {
colCheck(x,y)
rbind2sparse(x,y)
})
if(length(formals(cbind2)) >= 3) { ## newer R -- can use optional 'sparse = NA'
setMethod("cbind2", signature(x = "sparseMatrix", y = "denseMatrix"),
function(x, y, sparse = NA, ...) {
nr <- rowCheck(x,y)
if(is.na(sparse)) # result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
as.double(nr) * (ncol(x)+ncol(y)) # as.double(): avoid integer overflow in '*'
if(sparse) cbind2sparse(x,y) else cbind2(as(x, "denseMatrix"), y)
})
setMethod("cbind2", signature(x = "denseMatrix", y = "sparseMatrix"),
function(x, y, sparse = NA, ...) {
nr <- rowCheck(x,y)
if(is.na(sparse)) # result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
as.double(nr) * (ncol(x)+ncol(y))
if(sparse) cbind2sparse(x,y) else cbind2(x, as(y, "denseMatrix"))
})
setMethod("rbind2", signature(x = "sparseMatrix", y = "denseMatrix"),
function(x, y, sparse = NA, ...) {
nc <- colCheck(x,y)
if(is.na(sparse)) # result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
(nrow(x)+nrow(y)) * as.double(nc)
if(sparse) rbind2sparse(x,y) else rbind2(as(x, "denseMatrix"), y)
})
setMethod("rbind2", signature(x = "denseMatrix", y = "sparseMatrix"),
function(x, y, sparse = NA, ...) {
nc <- colCheck(x,y)
if(is.na(sparse)) # result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
(nrow(x)+nrow(y)) * as.double(nc)
if(sparse) rbind2sparse(x,y) else rbind2(x, as(y, "denseMatrix"))
})
} else { ## older version of R -- cbind2() has no "..."
setMethod("cbind2", signature(x = "sparseMatrix", y = "denseMatrix"),
function(x, y, ...) {
nr <- rowCheck(x,y)
## result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
as.double(nr) * (ncol(x)+ncol(y))
if(sparse) cbind2sparse(x,y) else cbind2(as(x, "denseMatrix"), y)
})
setMethod("cbind2", signature(x = "denseMatrix", y = "sparseMatrix"),
function(x, y, ...) {
nr <- rowCheck(x,y)
## result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
as.double(nr) * (ncol(x)+ncol(y))
if(sparse) cbind2sparse(x,y) else cbind2(x, as(y, "denseMatrix"))
})
setMethod("rbind2", signature(x = "sparseMatrix", y = "denseMatrix"),
function(x, y, ...) {
nc <- colCheck(x,y)
## result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
(nrow(x)+nrow(y)) * as.double(nc)
if(sparse) rbind2sparse(x,y) else rbind2(as(x, "denseMatrix"), y)
})
setMethod("rbind2", signature(x = "denseMatrix", y = "sparseMatrix"),
function(x, y, ...) {
nc <- colCheck(x,y)
## result is sparse if "enough zeros" <==> sparseDefault() in Matrix()
sparse <- (nnzero(x,na.counted=TRUE)+nnzero(y,na.counted=TRUE)) * 2 <
(nrow(x)+nrow(y)) * as.double(nc)
if(sparse) rbind2sparse(x,y) else rbind2(x, as(y, "denseMatrix"))
})
}# older R -- no "sparse = NA"
if(FALSE) {
## FIXME
##------------- maybe a bit faster --- but too much to maintain
## would have to be done for "rbind2" as well ...
setMethod("cbind2", signature(x = "sparseMatrix", y = "numeric"),
function(x, y, ...) {
d <- dim(x); nr <- d[1]; nc <- d[2]; cl <- class(x)
x <- as(x, "CsparseMatrix")
if(nr > 0) {
y <- rep_len(y, nr) # 'silent procrustes'
n0y <- y != 0
n.e <- length(x@i)
x@i <- c(x@i, (0:(nr-1))[n0y])
x@p <- c(x@p, n.e + sum(n0y))
x@x <- c(x@x, y[n0y])
} else { ## nr == 0
}
x@Dim[2] <- nc + 1L
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 = "sparseMatrix"),
function(x, y, ...) {
d <- dim(y); nr <- d[1]; nc <- d[2]; cl <- class(y)
y <- as(y, "CsparseMatrix")
if(nr > 0) {
x <- rep_len(x, nr) # 'silent procrustes'
n0x <- x != 0
y@i <- c((0:(nr-1))[n0x], y@i)
y@p <- c(0L, sum(n0x) + y@p)
y@x <- c(x[n0x], y@x)
} else { ## nr == 0
}
y@Dim[2] <- nc + 1L
if(is.character(dn <- y@Dimnames[[2]]))
y@Dimnames[[2]] <- c(dn, "")
y
})
}## -- no longer
## Can be made very efficient
setMethod("rbind2", signature(x = "indMatrix", y = "indMatrix"),
function(x, y, ...) {
dx <- x@Dim
dy <- y@Dim
if(dx[2] != dy[2])
stop(gettextf("Matrices must have same number of columns in %s",
deparse(sys.call(sys.parent()))),
call. = FALSE, domain=NA)
new("indMatrix", Dim = c(dx[1]+dy[1], dx[2]),
perm = c(x@perm,y@perm),
Dimnames = rbind2DN(dimnames(x), dimnames(y), dx[1],dy[1]))
})
|
