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####--- All "Summary" group methods for all Matrix classes (incl sparseVector) ------
#### ======= but diagonalMatrix -> ./diagMatrix.R and abIndex.R
#### ~~~~~~~~~~~~ ~~~~~~~~~
## M-x grep -E -e 'Method\("(Summary|max|min|range|all|any|prod|sum)"' *.R
## ----
sG <- getGroupMembers("Summary")
if(FALSE)
sG ## "max" "min" "range" "prod" "sum" "any" "all"
## w/o "prod" & "sum":
summGener1 <- sG[match(sG, c("prod","sum"), 0) == 0]
rm(sG)
###---------- dMatrix
setMethod("Summary", "ddenseMatrix",
function(x, ..., na.rm) {
d <- x@Dim
if(any(d == 0)) return(callGeneric(numeric(0), ..., na.rm=na.rm))
clx <- getClassDef(class(x))
if(extends(clx, "generalMatrix"))
callGeneric(x@x, ..., na.rm = na.rm)
else if(extends(clx, "symmetricMatrix")) { # incl packed, pos.def.
if(.Generic %in% summGener1) {
callGeneric(if (length(x@x) < prod(d)) x@x
else x@x[indTri(d[1], upper= x@uplo == "U",
diag= TRUE)],
..., na.rm = na.rm)
} else callGeneric(..2dge(x)@x, ..., na.rm = na.rm)
}
else { ## triangular , possibly packed
if(.Generic %in% summGener1) {
if(.Generic %in% c("any","all")) {
Zero <- FALSE; One <- TRUE; xx <- as.logical(x@x)
} else {
Zero <- 0; One <- 1; xx <- x@x
}
callGeneric(if (length(xx) < prod(d)) xx ## <- 'packed'
else xx[indTri(d[1], upper= x@uplo == "U",
diag= TRUE)],
if(d[1] >= 2) Zero, if(x@diag == "U") One,
..., na.rm = na.rm)
} else callGeneric(..2dge(x)@x, ..., na.rm = na.rm)
}
})
setMethod("Summary", "dsparseMatrix",
function(x, ..., na.rm)
{
ne <- prod(d <- dim(x))
if(ne == 0) return(callGeneric(numeric(0), ..., na.rm=na.rm))
n <- d[1]
clx <- getClassDef(class(x))
isTri <- extends(clx, "triangularMatrix")
if(extends(clx, "TsparseMatrix") && anyDuplicatedT(x, di = d))
x <- .Call(Tsparse_to_Csparse, x, isTri)# = as(x, "Csparsematrix")
l.x <- length(x@x)
if(l.x == ne) ## fully non-zero (and "general") - very rare but quick
return( callGeneric(x@x, ..., na.rm = na.rm) )
## else l.x < ne
isSym <- !isTri && extends(clx, "symmetricMatrix")
isU.tri <- isTri && x@diag == "U"
## "full": has *no* structural zero : very rare, but need to catch :
full.x <- ((isSym && l.x == choose(n+1, 2)) ||
(n == 1 && (isU.tri || l.x == 1)))
isGener1 <- .Generic %in% summGener1
if(isGener1) { ## not prod() or sum() -> no need check for symmetric
## we rely on <generic>(x, NULL, y, ..) :== <generic>(x, y, ..):
if(any(.Generic == c("any","all"))) ## logic:
callGeneric(as.logical(x@x), if(!full.x) FALSE, if(isU.tri) TRUE,
..., na.rm = na.rm)
else
callGeneric(x@x, if(!full.x) 0, if(isU.tri) 1,
..., na.rm = na.rm)
}
else { ## prod() or sum() : care for "symmetric" and U2N
if(!full.x && .Generic == "prod") {
if(anyNA(x@x)) NaN else 0
}
else
callGeneric((if(isSym) as(x, "generalMatrix") else x)@x,
if(!full.x) 0, # one 0 <==> many 0's
if(isU.tri) rep.int(1, n),
..., na.rm = na.rm)
}
})
###---------- ldenseMatrix
if(FALSE) # not correct (@x may contain "wrong" in "other" triangel
setMethod("all", "lsyMatrix",
function(x, ..., na.rm = FALSE)
all(x@x, ..., na.rm = na.rm))
if(FALSE) # replaced by "Summary" below
## Note: the above "lsy*" method is needed [case below can be wrong]
setMethod("all", "ldenseMatrix",
function(x, ..., na.rm = FALSE) {
if(prod(dim(x)) >= 1)
(!is(x, "triangularMatrix") && !is(x, "diagonalMatrix") &&
all(x@x, ..., na.rm = na.rm))
else all(x@x, ..., na.rm = na.rm)
})
## almost copy_paste from "ddenseMatrix" above
Summ.ln.dense <- function(x, ..., na.rm) {
d <- x@Dim
if(any(d == 0)) return(callGeneric(logical(0), ..., na.rm=na.rm))
ext <- extends(getClassDef(class(x)))
if(any("generalMatrix" == ext))
callGeneric(x@x, ..., na.rm = na.rm)
else if(any("symmetricMatrix" == ext)) { # incl packed, pos.def.
if(.Generic != "sum") { ## i.e., %in% summGener1
callGeneric(if (length(x@x) < prod(d)) x@x
else x@x[indTri(d[1], upper= x@uplo == "U",
diag= TRUE)],
..., na.rm = na.rm)
} else ## sum() -- FIXME-faster: use x@x[indTri(...)] similar to above
callGeneric(as(x, paste0(if(any("ldenseMatrix" == ext)) "l" else "n", "geMatrix"))@x,
..., na.rm = na.rm)
}
else { ## triangular , possibly packed
if(.Generic != "sum") ## incl. prod() !
callGeneric(x@x, if(d[1] >= 2) FALSE, if(x@diag == "U") TRUE, ..., na.rm = na.rm)
else ## sum() -- FIXME-faster: using indTri()..; in unit-diag. case: plus n x TRUE = d[1]
## if packed: sum(x@x, if(x@diag == "U") d[1], ..., na.rm = na.rm)
callGeneric(as(x, paste0(if(any("ldenseMatrix" == ext)) "l" else "n", "geMatrix"))@x,
..., na.rm = na.rm)
}
}
setMethod("Summary", "ldenseMatrix", Summ.ln.dense)
setMethod("Summary", "ndenseMatrix", Summ.ln.dense)
###---------- lMatrix
setMethod("any", "lMatrix",
function(x, ..., na.rm = FALSE)
## logical unit-triangular has TRUE diagonal:
(prod(dim(x)) >= 1 && is(x, "triangularMatrix") && x@diag == "U") ||
any(x@x, ..., na.rm = na.rm))
###---------- lsparseMatrix
##------- Work via as(*, lgC) : ------------
setMethod("all", "lsparseMatrix",
function(x, ..., na.rm = FALSE) {
d <- x@Dim
l.x <- length(x@x)
if(l.x == prod(d)) ## fully non-zero
all(x@x, ..., na.rm = na.rm)
else if(is(x, "symmetricMatrix") && l.x == choose(d[1]+1, 2)) {
if(.Generic %in% summGener1)
all(x@x, ..., na.rm = na.rm)
else all(as(x, "generalMatrix")@x, ..., na.rm = na.rm)
}
else FALSE ## has at least one structural 0
})
###---------- Matrix
## For all other Matrix objects {and note that "all" and "any" have their own}:
setMethod("all", "Matrix",
function(x, ..., na.rm)
callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
setMethod("any", "Matrix",
function(x, ..., na.rm)
callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
setMethod("Summary", "Matrix", ## FIXME (too cheap): all(<lMatrix>) should not go via dMatrix!!
function(x, ..., na.rm)
callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
## Try to make min(1, <Matrix>) work, i.e., not dispatch on first arg to .Primitive
## This for(..) gives {during installation}
## Error in setGeneric(F, signature = "...") :
## ‘max’ is a primitive function; methods can be defined, but the generic function is implicit, and cannot be changed.
if(FALSE)
for(F in c("max", "min", "range", "prod", "sum", "any", "all")) {
setGeneric(F, signature = "...")
}
## try on "min" for now --- ~/R/Pkgs/Rmpfr/R/mpfr.R is the example (for "pmin")
if(FALSE)## This gives error message that the "ANY" is method is sealed ...
setMethod("min", "ANY",
function(..., na.rm = FALSE) {
args <- list(...)
if(all(isAtm <- vapply(args, is.atomic, NA)))
return( base::min(..., na.rm = na.rm) )
## else try to dispatch on an argument which is a Matrix.. or in a
if(any(isM <- vapply(args, is, NA, class2="Matrix"))) {
## swap the Matrix with the first argument
i <- which.max(isM)# the first "Matrix"
if(i == 1)
stop("programming error: min() should have dispatched w/ 1st arg much earlier")
} else { ## if no "Matrix", take the first non-atomic argument
## (FIXME: should take the first for which there is a method !)
i <- which.max(!isAtm)
}
ii <- seq_along(args)
ii[c(1,i)] <- c(i,1)
do.call(min, c(args[ii], list(na.rm=na.rm)))
})
if(FALSE) { ## FIXME: it does *not* solve the problem anyway ..
##
## (m <- Matrix(c(0,0,2:0), 3,5))
## min(1,m)
##-> error, as it calls the .Primitive min() and that does *not* dispatch on 2nd arg
##
setMethod("Summary", "ANY",
function(x, ..., na.rm) {
if(!length(a <- list(...))) (get(.Generic, envir=baseenv()))(x, na.rm=na.rm)
else {
if(!is.null(v <- getOption("Matrix.verbose")) && v >= 1)
if(length(a) > 1)
message(gettextf("in Summary(<ANY>, .): %s(<%s>, <%s>,...)\n",
.Generic, class(x), class(a[[1]])), domain = NA)
else
message(gettextf("in Summary(<ANY>, .): %s(<%s>, <%s>)\n",
.Generic, class(x), class(a[[1]])), domain = NA)
do.call(.Generic, c(x, a, list(na.rm=na.rm)))
}})
}## {does not help --> not used}
Summary.l <- function(x, ..., na.rm) { ## must be method directly
if(.Generic %in% c("all", "any"))
callGeneric(x@x, ..., na.rm = na.rm)
else {
r <- callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm)
if(.Generic != "prod" && !any(is.infinite(r))) as.integer(r) else r
}
}
## almost identical:
Summary.np <- function(x, ..., na.rm) {
if(.Generic %in% c("all", "any"))
callGeneric(as(x, "lMatrix"), ..., na.rm = na.rm)
else {
r <- callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm)
if(.Generic != "prod" && !any(is.infinite(r))) as.integer(r) else r
}
}
##
setMethod("Summary", "lMatrix", Summary.l)
setMethod("Summary", "nMatrix", Summary.np)
setMethod("Summary", "indMatrix", Summary.np)
###---------- nsparseMatrix
setMethod("all", "nsparseMatrix",
function(x, ..., na.rm = FALSE) {
pd <- prod(d <- dim(x))
if(pd == 0) return(TRUE)
cld <- getClassDef(class(x))
if(extends(cld, "triangularMatrix"))
return(FALSE)
## else
if(extends(cld, "TsparseMatrix"))
cld <- getClassDef(class(x <- as(x, "CsparseMatrix")))
## now have Csparse or Rsparse: length of index slot = no.{TRUE}
l.x <- length(if(extends(cld, "CsparseMatrix")) x@i else x@j)
(l.x == pd) || ## fully non-zero
(extends(cld, "symmetricMatrix") && l.x == choose(d[1]+1, 2))
## else FALSE
})
setMethod("any", "nsparseMatrix",
function(x, ..., na.rm = FALSE) {
if(any(dim(x) == 0)) return(FALSE)
cld <- getClassDef(class(x))
if(extends(cld, "triangularMatrix") && x@diag == "U")
TRUE # unit-diagonal
else if(extends1of(cld, c("CsparseMatrix", "TsparseMatrix")))
length(x@i) > 0
else # RsparseMatrix
length(x@j) > 0
})
###---------- sparseVector
setMethod("Summary", "nsparseVector",
function(x, ..., na.rm) { ## no 'x' slot, no NA's ..
n <- x@length
l.x <- length(x@i)
if(l.x == n)
callGeneric(rep.int(TRUE, n), ..., na.rm = na.rm)
else ## l.x < n : has some FALSE entries
switch(.Generic,
"prod" = 0,
"min" = 0L,
"all" = FALSE,
"any" = l.x > 0,
"sum" = l.x,
"max" = as.integer(l.x > 0),
"range" = c(0L, as.integer(l.x > 0)))
})
## The "other" "sparseVector"s ("d", "l", "i" ..): all have an 'x' slot :
setMethod("Summary", "sparseVector",
function(x, ..., na.rm) {
n <- x@length
l.x <- length(x@x)
if(l.x == n) ## fully non-zero (and "general") - very rare but quick
callGeneric(x@x, ..., na.rm = na.rm)
else if(.Generic != "prod") {
## we rely on <generic>(x, NULL, y, ..) :== <generic>(x, y, ..):
if(any(.Generic == c("any","all"))) ## logic:
callGeneric(as.logical(x@x), FALSE, ..., na.rm = na.rm)
else # "numeric"
callGeneric(x@x, 0, ..., na.rm = na.rm)
}
else { ## prod()
if(anyNA(x@x)) NaN else 0
}
})
## help( pmin ) in R :
## -----
## ‘pmax’ and ‘pmin’ will also work on classed objects with appropriate methods
## for comparison, ‘is.na’ and ‘rep’ (if recycling of arguments is needed).
##
##--> and that now *does* work, in 'R 3.3.1 patched' and newer
|
