340 lines
13 KiB
R
340 lines
13 KiB
R
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## These are tests related to the replacement of many methods for the
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## proper subclasses of 'denseMatrix' with methods for the (new, more
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## general) virtual subclasses '(un)?packedMatrix'.
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## for R_DEFAULT_PACKAGES=NULL :
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library(stats)
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library(Matrix)
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set.seed(145206)
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if (interactive()) {
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options(Matrix.verbose = TRUE, warn = 1, error = recover)
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} else {
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options(Matrix.verbose = TRUE, warn = 1)
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}
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U <- function(x, diag = FALSE) x[upper.tri(x, diag)]
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L <- function(x, diag = FALSE) x[lower.tri(x, diag)]
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`U<-` <- function(x, diag = FALSE, value) { x[upper.tri(x, diag)] <- value; x }
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`L<-` <- function(x, diag = FALSE, value) { x[lower.tri(x, diag)] <- value; x }
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mkDN <- function(Dim) list(A = paste0("a", seq_len(Dim[1L])),
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B = paste0("b", seq_len(Dim[2L])))
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denseMatrix <- getClassDef("denseMatrix")
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packedMatrix <- getClassDef("packedMatrix")
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unpackedMatrix <- getClassDef("unpackedMatrix")
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generalMatrix <- getClassDef("generalMatrix")
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symmetricMatrix <- getClassDef("symmetricMatrix")
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triangularMatrix <- getClassDef("triangularMatrix")
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dMatrix <- getClassDef("dMatrix")
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lMatrix <- getClassDef("lMatrix")
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nMatrix <- getClassDef("nMatrix")
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## FIXME: Implement in C??
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unpackedClass <- function(packedClass) {
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getClassDef(c(dspMatrix = "dsyMatrix",
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lspMatrix = "lsyMatrix",
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nspMatrix = "nsyMatrix",
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dtpMatrix = "dtrMatrix",
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ltpMatrix = "ltrMatrix",
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ntpMatrix = "ntrMatrix",
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dppMatrix = "dpoMatrix",
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copMatrix = "corMatrix")[[packedClass@className]])
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}
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packedClass <- function(unpackedClass) {
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getClassDef(c(dgeMatrix = NA,
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lgeMatrix = NA,
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ngeMatrix = NA,
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dsyMatrix = "dspMatrix",
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lsyMatrix = "lspMatrix",
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nsyMatrix = "nspMatrix",
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dtrMatrix = "dtpMatrix",
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ltrMatrix = "ltpMatrix",
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ntrMatrix = "ntpMatrix",
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dpoMatrix = "dppMatrix",
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corMatrix = "copMatrix")[[unpackedClass@className]])
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}
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...Class <- function(denseClass) {
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cl <- "...Matrix"
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substr(cl, 1L, 1L) <-
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if (d <- extends(denseClass, dMatrix))
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"d"
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else if (extends(denseClass, lMatrix))
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"l"
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else
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"n"
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substr(cl, 2L, 3L) <-
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if (g <- extends(denseClass, generalMatrix))
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"ge"
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else if (extends(denseClass, symmetricMatrix))
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"sy"
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else
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"tr"
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if (!g && extends(denseClass, packedMatrix)) {
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substr(cl, 3L, 3L) <- "p"
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}
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getClassDef(cl)
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}
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## Tests methods for packed (unpacked) class 'Class'
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## using randomly generated matrices of size 'n'
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testDenseClass <- function(Class, n) {
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if (!is(Class, "classRepresentation")) {
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Class <- getClassDef(Class)
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}
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stopifnot(extends(Class, denseMatrix), !isVirtualClass(Class))
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is.p <- extends(Class, packedMatrix)
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is.ge <- extends(Class, generalMatrix)
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is.sy <- !is.ge && extends(Class, symmetricMatrix)
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is.tr <- !is.ge && !is.sy
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is.d <- extends(Class, dMatrix)
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is.l <- !is.d && extends(Class, lMatrix)
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is.n <- !is.d && !is.l
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## For randomly generating matrix data
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.mkX <- if (is.d)
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function(n) rlnorm(n) # not rnorm(n), for validObject(<dp[op]M>)
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else
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function(n) sample(c(NA, FALSE, TRUE), n, TRUE)
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mkX <- if (is.p)
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function(Dim) .mkX((Dim[1L] * (Dim[1L] + 1L)) %/% 2L)
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else
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function(Dim) .mkX(prod(Dim))
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## "Full factorial" design with varying 'Dim', 'uplo', 'diag' slots
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.Dim <- c(list(c(n, n)), if (is.ge) list(c(n+1L, n), c(n, n+1L)))
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.a <- c(list(Dim = seq_along(.Dim)),
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if (!is.ge) list(uplo = c("U", "L")),
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if ( is.tr) list(diag = c("N", "U")),
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list(stringsAsFactors = FALSE))
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newargs <- do.call(expand.grid, .a)
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newargs[["Dim"]] <- .Dim[.i <- newargs[["Dim"]]]
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newargs[["Dimnames"]] <- lapply(.Dim, mkDN)[.i]
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newargs[["x"]] <- lapply(.Dim, mkX)[.i]
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if (is.sy) {
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iD <- Matrix:::indDiag
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if (extends(Class, "corMatrix"))
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newargs[["x"]] <-
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lapply(newargs[["x"]], replace, iD(n), 1)
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else if (extends(Class, "copMatrix"))
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newargs[["x"]] <-
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Map(function(x, upper) replace(x, iD(n, upper, TRUE), 1),
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newargs[["x"]], newargs[["uplo"]] == "U")
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}
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## Test the matrices generated by each set of arguments to 'new'
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all(unlist(.mapply(testDenseMatrix, newargs, list(Class = Class))))
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}
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testDenseMatrix <- function(Class, ...) {
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is.p <- extends(Class, packedMatrix)
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is.ge <- extends(Class, generalMatrix)
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is.sy <- !is.ge && extends(Class, symmetricMatrix)
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is.tr <- !is.ge && !is.sy
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is.d <- extends(Class, dMatrix)
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is.l <- !is.d && extends(Class, lMatrix)
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is.n <- !is.d && !is.l
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## This class needs special care because it has an additional 'sd' slot
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is.cr <- is.sy &&
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(extends(Class, "corMatrix") || extends(Class, "copMatrix"))
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newargs <- list(Class = Class, ...)
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if (is.cr)
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newargs[["sd"]] <- rep.int(1, newargs[["Dim"]][2L])
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.M <- M <- do.call(new, newargs)
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m <- M@Dim[1L]
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n <- M@Dim[2L]
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r <- min(m, n)
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p0 <- (n * (n - 1L)) %/% 2L
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p1 <- (n * (n + 1L)) %/% 2L
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.ZERO <- as.vector(0, typeof(M@x))
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.ONE <- as.vector(1, typeof(M@x))
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.NA <- as.vector(NA, typeof(M@x))
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loup <- if (is.ge) NA_character_ else if (M@uplo == "U") "L" else "U"
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## For conveniently getting and setting (non)trivial triangles
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## of _traditional_ symmetric or triangular matrices
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if (!is.ge) {
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if (M@uplo == "U") {
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tri1 <- U; `tri1<-` <- `U<-`
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tri0 <- L; `tri0<-` <- `L<-`
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} else {
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tri1 <- L; `tri1<-` <- `L<-`
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tri0 <- U; `tri0<-` <- `U<-`
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}
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}
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.m <- m1 <- m2 <-
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if (is.p)
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`tri1<-`(array(.ZERO, dim = M@Dim, dimnames = M@Dimnames),
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diag = TRUE, M@x)
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else
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array(M@x, dim = M@Dim, dimnames = M@Dimnames)
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diag(.M) <- diag(.m) <-
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if (is.d)
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rlnorm(r)
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else
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sample(c(.NA, .ZERO, .ONE), r, TRUE)
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if (is.sy) {
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tri0(m2, diag = TRUE) <- tri0(t(m2), diag = TRUE)
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dimnames(m2) <- Matrix:::symDN(M@Dimnames)
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}
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if (is.tr && M@diag == "U") {
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diag(m2) <- .ONE
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}
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pM <-
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if (is.p)
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M
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else if (!is.ge)
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do.call(new, replace(newargs, c("Class", "x"),
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list(packedClass(Class),
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tri1(m1, diag = TRUE))))
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upM <-
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if (!is.p)
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M
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else
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do.call(new, replace(newargs, c("Class", "x"),
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list(unpackedClass(Class), as.vector(m1))))
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tM <- do.call(new, replace(newargs,
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c("Dim", "Dimnames", "x",
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if (!is.ge) "uplo"),
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c(list(M@Dim[2:1],
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M@Dimnames[if (is.sy) 1:2 else 2:1],
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if (is.p)
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tri0(t(m1), diag = TRUE)
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else
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as.vector(t(m1))),
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if (!is.ge) list(loup))))
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dM <- do.call(new, replace(newargs[names(newargs) != "sd"],
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c("Class", "x", if (is.tr) "diag"),
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c(list(...Class(Class),
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if (is.p)
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tri1(.m, diag = TRUE)
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else
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as.vector(.m)),
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if (is.tr) list("N"))))
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stopifnot(is.ge || identical(pack(M), pM),
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identical(unpack(M), upM),
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identical(t(M), tM),
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identical(diag(M, names = FALSE), diag(m2, names = FALSE)),
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identical(diag(M, names = TRUE), diag(m2, names = TRUE)),
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identical(.M, dM))
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if (is.ge) {
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if (m == n) {
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## Not symmetric and not triangular
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U(m2) <- if (is.d) rlnorm(p0) else rep_len(c(.NA, .ZERO, .ONE), p0)
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L(m2) <- if (is.d) -rlnorm(p0) else rep_len(c(.ZERO, .ONE, .NA), p0)
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M@x <- as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE) == (n <= 1L),
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isTriangular(M, upper = NA) == (n <= 1L),
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isDiagonal(M) == (n <= 1L))
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## Symmetric but not triangular
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L(m2) <- L(t(m2))
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M@x <- as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE),
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isTriangular(M, upper = NA) == (n <= 1L),
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isDiagonal(M) == (n <= 1L))
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## Not symmetric but triangular
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L(m2) <- .ZERO
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M@x <- as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE) == (n <= 1L),
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identical(isTriangular(M, upper = TRUE), TRUE),
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identical(isTriangular(M, upper = FALSE), FALSE),
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identical(isTriangular(M, upper = NA),
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`attr<-`(TRUE, "kind", "U")),
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isDiagonal(M) == (n <= 1L))
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## Symmetric and triangular
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U(m2) <- .ZERO
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M@x <- as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE),
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identical(isTriangular(M, upper = TRUE), TRUE),
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identical(isTriangular(M, upper = FALSE), TRUE),
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identical(isTriangular(M, upper = NA),
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`attr<-`(TRUE, "kind", "U")),
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isDiagonal(M))
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} else {
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## Non-square ... _never_ symmetric, triangular, or diagonal
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stopifnot(!isSymmetric(M, tol = 0, checkDN = FALSE),
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!isTriangular(M, upper = NA),
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!isDiagonal(M))
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}
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} else if (is.sy) {
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## Not triangular
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tri1(m2) <- if (is.d) rlnorm(p0) else rep_len(c(.NA, .ZERO, .ONE), p0)
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M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE),
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isTriangular(M, upper = NA) == (n <= 1L),
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isDiagonal(M) == (n <= 1L))
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## Triangular
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tri1(m2) <- .ZERO
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M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE),
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identical(isTriangular(M, upper = TRUE), TRUE),
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identical(isTriangular(M, upper = FALSE), TRUE),
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identical(isTriangular(M, upper = NA),
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`attr<-`(TRUE, "kind", M@uplo)),
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isDiagonal(M))
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} else {
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## Not symmetric
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tri1(m2) <- if (is.d) rlnorm(p0) else rep_len(c(.NA, .ZERO, .ONE), p0)
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M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE) == (n <= 1L),
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identical(isTriangular(M, upper = M@uplo == "U"), TRUE),
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identical(isTriangular(M, upper = M@uplo != "U"), n <= 1L),
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identical(isTriangular(M, upper = NA),
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`attr<-`(TRUE, "kind", M@uplo)),
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isDiagonal(M) == (n <= 1L))
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## Symmetric
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tri1(m2) <- .ZERO
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M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2)
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stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE),
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identical(isTriangular(M, upper = M@uplo == "U"), TRUE),
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identical(isTriangular(M, upper = M@uplo != "U"), TRUE),
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identical(isTriangular(M, upper = NA),
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`attr<-`(TRUE, "kind", M@uplo)),
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isDiagonal(M))
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}
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TRUE
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}
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.dense.subclasses <- c(names(getClassDef("packedMatrix")@subclasses),
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names(getClassDef("unpackedMatrix")@subclasses))
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stopifnot(all(vapply(.dense.subclasses, testDenseClass, NA, n = 4L)))
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## diag(<non-square .geMatrix>, names = TRUE) preserves names
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## if head of longer character vector matches shorter character vector
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n <- 4L
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m <- array(rnorm(n * (n + 1L)), dim = c(n, n + 1L))
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M <- new("dgeMatrix", x = as.vector(m), Dim = dim(m))
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rn <- letters[seq_len(n)]
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cn <- letters[seq_len(n + 1L)]
|
||
|
|
ldn <- list(list(rn, cn), list(rn, replace(cn, 1L, "")))
|
||
|
|
for (dn in ldn) {
|
||
|
|
stopifnot(identical(diag(`slot<-`(M, "Dimnames", TRUE, dn), names = TRUE),
|
||
|
|
diag(`dimnames<-`(m, dn), names = TRUE)))
|
||
|
|
}
|
||
|
|
|
||
|
|
cat("Time elapsed:", proc.time(), "\n") # "stats"
|