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## METHODS FOR GENERIC: Math (group)
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## > getGroupMembers("Math")
## [1] "abs" "sign" "sqrt" "ceiling" "floor" "trunc"
## [7] "cummax" "cummin" "cumprod" "cumsum" "exp" "expm1"
## [13] "log" "log10" "log2" "log1p" "cos" "cosh"
## [19] "sin" "sinh" "tan" "tanh" "acos" "acosh"
## [25] "asin" "asinh" "atan" "atanh" "cospi" "sinpi"
## [31] "tanpi" "gamma" "lgamma" "digamma" "trigamma"
setMethod("Math", c(x = "denseMatrix"),
function(x) {
g <- get(.Generic, mode = "function")
if(startsWith(.Generic, "cum"))
return(g(.M2v(x)))
cl <- .M.class(x)
kind <- substr(cl, 1L, 1L)
shape <- substr(cl, 2L, 2L)
if (kind == "z") {
zero <- 0+0i; one <- 1+0i; a <- as.complex
} else {
zero <- 0 ; one <- 1 ; a <- as.double
substr(cl, 1L, 1L) <- "d"
}
if(shape == "t") {
stay0 <- is0(a(g(zero)))
if(!stay0) {
x <- .M2gen(x)
substr(cl, 2L, 3L) <- "ge"
}
}
r <- new(cl)
r@Dim <- x@Dim
r@Dimnames <- x@Dimnames
if(shape == "s" || (shape == "t" && stay0))
r@uplo <- x@uplo
r@x <- a(g({ y <- x@x; if(kind == "n") y | is.na(y) else y }))
if(shape == "t" && stay0 && x@diag != "N") {
if(is1(g1 <- a(g(one))))
r@diag <- "U"
else diag(r) <- g1
}
r
})
setMethod("log", c(x = "denseMatrix"),
function(x, ...) {
cl <- .M.class(x)
kind <- substr(cl, 1L, 1L)
shape <- substr(cl, 2L, 2L)
if(kind != "z")
substr(cl, 1L, 1L) <- "d"
if(shape == "t") {
x <- .M2gen(x)
substr(cl, 2L, 3L) <- "ge"
}
r <- new(cl)
r@Dim <- x@Dim
r@Dimnames <- x@Dimnames
if(shape == "s")
r@uplo <- x@uplo
r@x <- log({ y <- x@x; if(kind == "n") y | is.na(y) else y }, ...)
r
})
setMethod("Math", c(x = "sparseMatrix"),
function(x) {
g <- get(.Generic, mode = "function")
if(startsWith(.Generic, "cum"))
return(g(.M2v(x)))
cl <- .M.class(x)
kind <- substr(cl, 1L, 1L)
shape <- substr(cl, 2L, 2L)
repr <- substr(cl, 3L, 3L)
if (kind == "z") {
zero <- 0+0i; one <- 1+0i; a <- as.complex
} else {
zero <- 0 ; one <- 1 ; a <- as.double
substr(cl, 1L, 1L) <- "d"
}
stay0 <- is0(g0 <- a(g(zero)))
if(!stay0)
substr(cl, 2L, 3L) <- if(shape == "s") "sy" else "ge"
r <- new(cl)
r@Dim <- x@Dim
r@Dimnames <- x@Dimnames
if(shape == "s" || (shape == "t" && stay0))
r@uplo <- x@uplo
if(!stay0) {
y <- .M2V(x)
tmp <- rep.int(g0, y@length)
tmp[y@i] <- a(g(if(kind == "n") one else y@x))
r@x <- tmp
} else {
if(shape == "t" && x@diag != "N") {
if(is1(a(g(one))))
r@diag <- "U"
else diag(x) <- TRUE
}
nnz <- length(
switch(repr,
"C" = { r@p <- x@p; r@i <- x@i },
"R" = { r@p <- x@p; r@j <- x@j },
"T" = { r@i <- x@i; r@j <- x@j }))
r@x <- if(kind == "n") rep.int(a(g(one)), nnz) else a(g(x@x))
}
r
})
setMethod("log", c(x = "sparseMatrix"),
function(x, ...) {
cl <- .M.class(x)
kind <- substr(cl, 1L, 1L)
shape <- substr(cl, 2L, 2L)
repr <- substr(cl, 3L, 3L)
if(kind == "z") {
zero <- 0+0i; one <- 1+0i
} else {
zero <- 0 ; one <- 1
substr(cl, 1L, 1L) <- "d"
}
substr(cl, 2L, 3L) <- if(shape == "s") "sy" else "ge"
r <- new(cl)
r@Dim <- x@Dim
r@Dimnames <- x@Dimnames
if(shape == "s")
r@uplo <- x@uplo
y <- .M2V(x)
tmp <- rep.int(log(zero, ...), y@length)
tmp[y@i] <- log(if(kind == "n") one else y@x, ...)
r@x <- tmp
r
})
setMethod("Math", c(x = "diagonalMatrix"),
function(x) {
g <- get(.Generic, mode = "function")
if(startsWith(.Generic, "cum"))
return(g(.M2v(x)))
cl <- .M.class(x)
kind <- substr(cl, 1L, 1L)
if (kind == "z") {
zero <- 0+0i; one <- 1+0i; a <- as.complex
} else {
zero <- 0 ; one <- 1 ; a <- as.double
substr(cl, 1L, 1L) <- "d"
}
stay0 <- is0(g0 <- a(g(zero)))
if(!stay0)
substr(cl, 2L, 3L) <- "ge"
r <- new(cl)
r@Dim <- d <- x@Dim
r@Dimnames <- x@Dimnames
if(!stay0) {
if((n <- d[2L]) > 0L) {
tmp <- matrix(g0, n, n)
diag(tmp) <- a(g(if(x@diag != "N") one else { y <- x@x; if(kind == "n" && anyNA(y)) y | is.na(y) else y }))
dim(tmp) <- NULL
r@x <- tmp
}
} else {
if(x@diag != "N") {
if(is1(g1 <- a(g(one))))
r@diag <- "U"
else r@x <- rep.int(g1, d[1L])
} else r@x <- a(g({ y <- x@x; if(kind == "n" && anyNA(y)) y | is.na(y) else y }))
}
r
})
setMethod("log", c(x = "diagonalMatrix"),
function(x, ...) {
cl <- .M.class(x)
kind <- substr(cl, 1L, 1L)
if(kind == "z") {
zero <- 0+0i; one <- 1+0i
} else {
zero <- 0 ; one <- 1
substr(cl, 1L, 1L) <- "d"
}
substr(cl, 2L, 3L) <- "ge"
r <- new(cl)
r@Dim <- d <- x@Dim
r@Dimnames <- x@Dimnames
if((n <- d[2L]) > 0L) {
tmp <- matrix(log(zero, ...), n, n)
diag(tmp) <- log(if(x@diag != "N") one else { y <- x@x; if(kind == "n" && anyNA(y)) y | is.na(y) else y }, ...)
dim(tmp) <- NULL
r@x <- tmp
}
r
})
setMethod("Math", c(x = "indMatrix"),
function(x)
get(.Generic, mode = "function")(.M2kind(x, "n")))
setMethod("log", c(x = "indMatrix"),
function(x, ...)
log(.M2kind(x, "n"), ...))
setMethod("Math", c(x = "sparseVector"),
function(x) {
g <- get(.Generic, mode = "function")
if(startsWith(.Generic, "cum"))
return(g(.V2v(x)))
kind <- .M.kind(x)
if(kind == "z") {
zero <- 0+0i; one <- 1+0i; l <- "z"
} else if(kind == "d" || .Generic != "abs") {
zero <- 0 ; one <- 1 ; l <- "d"
} else {
zero <- 0L ; one <- 1L ; l <- "i"
}
if((g0 <- g(zero)) | is.na(g0)) {
r <- rep.int(g0, x@length)
if((nnz <- length(x@i)) > 0L)
r[x@i] <- if(kind == "n") rep.int(g(one), nnz) else g(x@x)
} else {
r <- new(paste0(l, "sparseVector"))
r@length <- x@length
r@i <- x@i
if((nnz <- length(x@i)) > 0L)
r@x <- if(kind == "n") rep.int(g(one), nnz) else g(x@x)
}
r
})
setMethod("log", c(x = "sparseVector"),
function(x, ...) {
kind <- .M.kind(x)
if(kind == "z") {
zero <- 0+0i; one <- 1+0i
} else {
zero <- 0 ; one <- 1
}
r <- rep.int(log(zero, ...), x@length)
if(length(x@i) > 0L)
r[x@i] <- log(if(kind == "n") one else x@x, ...)
r
})
## METHODS FOR GENERIC: Math2 (group)
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## > getGroupMembers("Math2")
## [1] "round" "signif"
setMethod("Math2", c(x = "Matrix"),
function(x, digits) {
x <- .indefinite(.M2kind(x, ","))
x@x <- get(.Generic, mode = "function")(x@x, digits = digits)
if(.hasSlot(x, "factors") && length(x@factors) > 0L)
x@factors <- list()
x
})
setMethod("Math2", c(x = "sparseVector"),
function(x, digits) {
x <- .V2kind(x, ",")
x@x <- get(.Generic, mode = "function")(x@x, digits = digits)
x
})
## METHODS FOR GENERIC: zapsmall
## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
setMethod("zapsmall", signature(x = "Matrix"),
function(x, digits = getOption("digits"),
mFUN = function(x, ina) max(abs(x[!ina])), min.d = 0L, ...) {
x <- .indefinite(.M2kind(x, ","))
x@x <- zapsmall(x@x, digits=digits, mFUN=mFUN, min.d=min.d, ...)
if(.hasSlot(x, "factors") && length(x@factors) > 0L)
x@factors <- list()
x
})
setMethod("zapsmall", signature(x = "sparseVector"),
function(x, digits = getOption("digits"),
mFUN = function(x, ina) max(abs(x[!ina])), min.d = 0L, ...) {
x <- .V2kind(x, ",")
x@x <- zapsmall(x@x, digits=digits, mFUN=mFUN, min.d=min.d, ...)
x
})
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