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#### Permutation Matrices -- Coercion and Methods
## The typical 'constructor' : coerce from 'index'
setAs("integer", "pMatrix",
function(from) {
n <- length(from)
nn <- names(from)
new("pMatrix", Dim = rep.int(n, 2), Dimnames = list(nn,nn),
perm = from)
})
setAs("numeric", "pMatrix",
function(from)
if(all(from == (i <- as.integer(from)))) as(i, "pMatrix")
else stop("coercion to 'pMatrix' only works from integer numeric"))
setAs("pMatrix", "matrix",
function(from) {
fp <- from@perm
r <- ldiag(n = length(fp))[fp,]
if(.has.DN(from)) dimnames(r) <- from@Dimnames
r
})
## coerce to 0/1 sparse matrix, i.e. sparse pattern
setAs("pMatrix", "ngTMatrix",
function(from) {
d <- from@Dim
new("ngTMatrix", i = seq_len(d[1]) - 1L, j = from@perm - 1L,
Dim = d, Dimnames = from@Dimnames)
})
setAs("pMatrix", "TsparseMatrix", function(from) as(from, "ngTMatrix"))
setAs("pMatrix", "nMatrix", function(from) as(from, "ngTMatrix"))
setAs("pMatrix", "lMatrix", function(from) as(as(from, "nMatrix"), "lMatrix"))
setAs("pMatrix", "dMatrix", function(from) as(as(from, "nMatrix"), "dMatrix"))
setAs("pMatrix", "dsparseMatrix", function(from) as(from, "dMatrix"))
setAs("pMatrix", "nsparseMatrix", function(from) as(from, "nMatrix"))
setAs("pMatrix", "CsparseMatrix",
function(from) as(as(from, "ngTMatrix"), "CsparseMatrix"))
setAs("pMatrix", "ngeMatrix", function(from) as(as(from, "ngTMatrix"),"ngeMatrix"))
setAs("nMatrix", "pMatrix",
function(from) {
from <- as(as(from, "TsparseMatrix"), "ngTMatrix")
n <- (d <- from@Dim)[1]
if(n != d[2]) stop("not a square matrix")
if(length(i <- from@i) != n)
stop("the number of non-zero entries differs from nrow(.)")
if((need.sort <- is.unsorted(i))) {
ii <- sort.list(i)
i <- i[ii]
}
if(n >= 1 && !identical(i, 0:(n - 1)))
stop("must have exactly one non-zero entry per row")
new("pMatrix", ## validity checking checks the 'perm' slot:
perm = 1L + if(need.sort) from@j[ii] else from@j,
Dim = d, Dimnames = from@Dimnames)
})
setAs("matrix", "pMatrix", function(from) as(as(from, "nMatrix"), "pMatrix"))
setAs("sparseMatrix", "pMatrix", function(from)
as(as(from, "nsparseMatrix"), "pMatrix"))
setMethod("is.na", signature(x = "pMatrix"), is.na_nsp)
## how much faster would this be in C? -- less than a factor of two?
.inv.perm <- function(p) { p[p] <- seq_along(p) ; p }
setMethod("solve", signature(a = "pMatrix", b = "missing"),
function(a, b, ...) {
a@perm <- .inv.perm(a@perm)
a@Dimnames <- a@Dimnames[2:1]
a
})
setMethod("solve", signature(a = "Matrix", b = "pMatrix"),
function(a, b, ...)
## Or alternatively solve(a, as(b, "CsparseMatrix"))
solve(a)[, .inv.perm(b@perm)])
setMethod("determinant", signature(x = "pMatrix", logarithm = "logical"),
function(x, logarithm, ...)
mkDet(logarithm=logarithm, ldet = 0, sig = signPerm(x@perm)))
## t(pM) is == the inverse pM^(-1):
setMethod("t", signature(x = "pMatrix"), function(x) solve(x))
setMethod("%*%", signature(x = "matrix", y = "pMatrix"),
function(x, y) { mmultCheck(x,y); x[, .inv.perm(y@perm)] })
setMethod("%*%", signature(x = "Matrix", y = "pMatrix"),
function(x, y) { mmultCheck(x,y); x[, .inv.perm(y@perm)] })
setMethod("%*%", signature(x = "pMatrix", y = "matrix"),
function(x, y) { mmultCheck(x,y); y[x@perm ,] })
setMethod("%*%", signature(x = "pMatrix", y = "Matrix"),
function(x, y) { mmultCheck(x,y); y[x@perm ,] })
setMethod("%*%", signature(x = "pMatrix", y = "pMatrix"),
function(x, y) {
stopifnot(identical(d <- x@Dim, y@Dim))
## n <- d[1]
## FIXME: dimnames dealing: as with S3 matrix's %*%
x@perm <- x@perm[y@perm]
x
})
setMethod("crossprod", signature(x = "pMatrix", y = "matrix"),
function(x, y) { mmultCheck(x,y, 2L); y[.inv.perm(x@perm) ,]})
setMethod("crossprod", signature(x = "pMatrix", y = "Matrix"),
function(x, y) { mmultCheck(x,y, 2L); y[.inv.perm(x@perm) ,]})
setMethod("crossprod", signature(x = "pMatrix", y = "pMatrix"),
function(x, y) {
stopifnot(identical(x@Dim, y@Dim))
x@perm <- .inv.perm(x@perm)[y@perm]
x
})
setMethod("tcrossprod", signature(x = "matrix", y = "pMatrix"),
function(x, y) { mmultCheck(x,y, 3L); x[, y@perm] })
setMethod("tcrossprod", signature(x = "Matrix", y = "pMatrix"),
function(x, y) { mmultCheck(x,y, 3L); x[, y@perm] })
setMethod("tcrossprod", signature(x = "pMatrix", y = "pMatrix"),
function(x, y) {
stopifnot(identical(x@Dim, y@Dim))
x@perm <- x@perm[.inv.perm(y@perm)]
x
})
setMethod("crossprod", signature(x = "pMatrix", y = "missing"),
function(x, y=NULL) Diagonal(nrow(x)))
setMethod("tcrossprod", signature(x = "pMatrix", y = "missing"),
function(x, y=NULL) Diagonal(nrow(x)))
.pMat.nosense <- function (x, i, j, ..., value)
stop('replacing "pMatrix" entries is not allowed, as rarely sensible')
setReplaceMethod("[", signature(x = "pMatrix", i = "index"), .pMat.nosense)
setReplaceMethod("[", signature(x = "pMatrix", i = "missing", j = "index"),
.pMat.nosense) ## explicit ^^^^^^^^^^^^ for disambiguation
setReplaceMethod("[", signature(x = "pMatrix", i = "missing", j = "missing"),
.pMat.nosense)
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