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## METHODS FOR CLASS: sparseMatrix, [CRT]sparseMatrix (virtual)
## sparse matrices, in some cases restricted to CSC, CSR, triplet
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.sparse.band <- function(x, k1, k2, ...)
.Call(R_sparse_band, x, k1, k2)
.sparse.triu <- function(x, k = 0L, ...)
.Call(R_sparse_band, x, k, NULL)
.sparse.tril <- function(x, k = 0L, ...)
.Call(R_sparse_band, x, NULL, k)
.sparse.diag.get <- function(x = 1, nrow, ncol, names = TRUE)
.Call(R_sparse_diag_get, x, names)
.sparse.diag.set <- function(x, value)
.Call(R_sparse_diag_set, x, value)
.sparse.t <- function(x)
.Call(R_sparse_transpose, x, FALSE)
.sparse.fS1 <- function(x, uplo)
.Call(R_sparse_force_symmetric, x, NULL)
.sparse.fS2 <- function(x, uplo)
.Call(R_sparse_force_symmetric, x, uplo)
.sparse.symmpart <- function(x)
.Call(R_sparse_symmpart, x)
.sparse.skewpart <- function(x)
.Call(R_sparse_skewpart, x)
.sparse.is.di <- function(object)
.Call(R_sparse_is_diagonal, object)
.sparse.is.tr <- function(object, upper = NA, ...)
.Call(R_sparse_is_triangular, object, upper)
.sparse.is.sy <- function(object, checkDN = TRUE, ...) {
if(checkDN) {
ca <- function(check.attributes = TRUE, ...) check.attributes
checkDN <- ca(...)
}
.Call(R_sparse_is_symmetric, object, checkDN)
}
.sparse.is.sy.dz <- function(object, checkDN = TRUE,
tol = 100 * .Machine$double.eps, ...) {
## backwards compatibility: don't check DN if check.attributes=FALSE
if(checkDN) {
ca <- function(check.attributes = TRUE, ...) check.attributes
checkDN <- ca(...)
}
## be very fast when requiring exact symmetry
if(tol <= 0)
return(.Call(R_sparse_is_symmetric, object, checkDN))
## pretest: is it square?
d <- object@Dim
if((n <- d[2L]) != d[1L])
return(FALSE)
## pretest: are DN symmetric in the sense of validObject(<symmetricMatrix>)?
if(checkDN && !isSymmetricDN(object@Dimnames))
return(FALSE)
if(n == 0L)
return(TRUE)
## now handling an n-by-n [dz]g[CRT]Matrix, n >= 1:
Cj <- if(is.complex(object@x)) Conj else identity
ae <- function(check.attributes, ...) {
## discarding possible user-supplied check.attributes
all.equal(..., check.attributes = FALSE)
}
isTRUE(ae(target = .M2V( object ),
current = .M2V(Cj(t(object))),
tolerance = tol, ...))
}
setMethod("diff", c(x = "sparseMatrix"),
## Mostly cut and paste of base::diff.default :
function(x, lag = 1L, differences = 1L, ...) {
if(length(lag) != 1L || length(differences) != 1L ||
lag < 1L || differences < 1L)
stop(gettextf("'%s' and '%s' must be positive integers",
"lag", "differences"),
domain = NA)
if(lag * differences >= x@Dim[1L])
return(x[0L])
i1 <- -seq_len(lag)
for(i in seq_len(differences)) {
m <- x@Dim[1L]
x <- x[i1, , drop = FALSE] -
x[-m:-(m - lag + 1L), , drop = FALSE]
}
x
})
setMethod("mean", c(x = "sparseMatrix"),
function(x, ...) mean(as(x, "sparseVector"), ...))
setMethod("rep", c(x = "sparseMatrix"),
function(x, ...) rep(as(x, "sparseVector"), ...))
for(.cl in paste0(c("C", "R", "T"), "sparseMatrix")) {
setMethod("band" , c(x = .cl), .sparse.band)
setMethod("triu" , c(x = .cl), .sparse.triu)
setMethod("tril" , c(x = .cl), .sparse.tril)
setMethod("diag" , c(x = .cl), .sparse.diag.get)
setMethod("diag<-", c(x = .cl), .sparse.diag.set)
setMethod("t" , c(x = .cl), .sparse.t)
setMethod("forceSymmetric", c(x = .cl, uplo = "missing"), .sparse.fS1)
setMethod("forceSymmetric", c(x = .cl, uplo = "character"), .sparse.fS2)
setMethod("symmpart", c(x = .cl), .sparse.symmpart)
setMethod("skewpart", c(x = .cl), .sparse.skewpart)
setMethod("isSymmetric" , c(object = .cl), .sparse.is.sy)
setMethod("isTriangular", c(object = .cl), .sparse.is.tr)
setMethod("isDiagonal" , c(object = .cl), .sparse.is.di)
}
.sparse.subclasses <- names(getClassDef("sparseMatrix")@subclasses)
for(.cl in grep("^[dz][gt][CRT]Matrix$", .sparse.subclasses, value = TRUE))
setMethod("isSymmetric" , c(object = .cl), .sparse.is.sy.dz)
rm(.cl, .sparse.subclasses)
rm(list = c(grep("^[.]sparse[.](band|tri[ul]|diag[.](get|set)|t|fS[12]|symmpart|skewpart|is[.](sy|tr|di)([.]dz)?)$",
ls(all.names = TRUE), value = TRUE)))
if(FALSE) ### FIXME: This would *NOT* be needed, if as.matrix(<sparseMatrix>) was a no-op ;
### ----- and then, base::scale() -> base::scale.default() would work "magically" already..
scale.sparseMatrix <- function(x, center = FALSE, scale = TRUE) {
if(center) warning("a sparseMatrix should rarely be centered: will not be sparse anymore")
## x <- as.matrix(x)
## This rest is *identically* == base :: scale.default :
nc <- ncol(x)
if (is.logical(center)) {
if (center) {
center <- colMeans(x, na.rm=TRUE)
x <- sweep(x, 2L, center, check.margin=FALSE)
}
}
else if (is.numeric(center) && (length(center) == nc))
x <- sweep(x, 2L, center, check.margin=FALSE)
else
stop("length of 'center' must equal the number of columns of 'x'")
if (is.logical(scale)) {
if (scale) {
f <- function(v) {
v <- v[!is.na(v)]
sqrt(sum(v^2) / max(1, length(v) - 1L))
}
scale <- apply(x, 2L, f)
x <- sweep(x, 2L, scale, "/", check.margin=FALSE)
}
}
else if (is.numeric(scale) && length(scale) == nc)
x <- sweep(x, 2L, scale, "/", check.margin=FALSE)
else
stop("length of 'scale' must equal the number of columns of 'x'")
if(is.numeric(center)) attr(x, "scaled:center") <- center
if(is.numeric(scale)) attr(x, "scaled:scale") <- scale
x
}
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