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Type 'q()' to quit R. > ## These are tests related to the replacement of many methods for the > ## proper subclasses of 'denseMatrix' with methods for the (new, more > ## general) virtual subclasses '(un)?packedMatrix'. > > ## for R_DEFAULT_PACKAGES=NULL : > library(stats) > > library(Matrix) > set.seed(145206) > > if (interactive()) { + options(Matrix.verbose = TRUE, warn = 1, error = recover) + } else { + options(Matrix.verbose = TRUE, warn = 1) + } > > U <- function(x, diag = FALSE) x[upper.tri(x, diag)] > L <- function(x, diag = FALSE) x[lower.tri(x, diag)] > `U<-` <- function(x, diag = FALSE, value) { x[upper.tri(x, diag)] <- value; x } > `L<-` <- function(x, diag = FALSE, value) { x[lower.tri(x, diag)] <- value; x } > > mkDN <- function(Dim) list(A = paste0("a", seq_len(Dim[1L])), + B = paste0("b", seq_len(Dim[2L]))) > > denseMatrix <- getClassDef("denseMatrix") > packedMatrix <- getClassDef("packedMatrix") > unpackedMatrix <- getClassDef("unpackedMatrix") > generalMatrix <- getClassDef("generalMatrix") > symmetricMatrix <- getClassDef("symmetricMatrix") > triangularMatrix <- getClassDef("triangularMatrix") > dMatrix <- getClassDef("dMatrix") > lMatrix <- getClassDef("lMatrix") > nMatrix <- getClassDef("nMatrix") > > ## FIXME: Implement in C?? > unpackedClass <- function(packedClass) { + getClassDef(c(dspMatrix = "dsyMatrix", + lspMatrix = "lsyMatrix", + nspMatrix = "nsyMatrix", + dtpMatrix = "dtrMatrix", + ltpMatrix = "ltrMatrix", + ntpMatrix = "ntrMatrix", + dppMatrix = "dpoMatrix", + pcorMatrix = "corMatrix", + pCholesky = "Cholesky")[[packedClass@className]]) + } > packedClass <- function(unpackedClass) { + getClassDef(c(dgeMatrix = NA, + lgeMatrix = NA, + ngeMatrix = NA, + dsyMatrix = "dspMatrix", + lsyMatrix = "lspMatrix", + nsyMatrix = "nspMatrix", + dtrMatrix = "dtpMatrix", + ltrMatrix = "ltpMatrix", + ntrMatrix = "ntpMatrix", + dpoMatrix = "dppMatrix", + corMatrix = "pcorMatrix", + Cholesky = "pCholesky")[[unpackedClass@className]]) + } > ...Class <- function(denseClass) { + cl <- "...Matrix" + substr(cl, 1L, 1L) <- + if (d <- extends(denseClass, dMatrix)) + "d" + else if (extends(denseClass, lMatrix)) + "l" + else + "n" + substr(cl, 2L, 3L) <- + if (g <- extends(denseClass, generalMatrix)) + "ge" + else if (extends(denseClass, symmetricMatrix)) + "sy" + else + "tr" + if (!g && extends(denseClass, packedMatrix)) { + substr(cl, 3L, 3L) <- "p" + } + getClassDef(cl) + } > > ## Tests methods for packed (unpacked) class 'Class' > ## using randomly generated matrices of size 'n' > testDenseClass <- function(Class, n) { + if (!is(Class, "classRepresentation")) { + Class <- getClassDef(Class) + } + stopifnot(extends(Class, denseMatrix), !isVirtualClass(Class)) + + is.p <- extends(Class, packedMatrix) + is.ge <- extends(Class, generalMatrix) + is.sy <- !is.ge && extends(Class, symmetricMatrix) + is.tr <- !is.ge && !is.sy + is.d <- extends(Class, dMatrix) + is.l <- !is.d && extends(Class, lMatrix) + is.n <- !is.d && !is.l + + ## For randomly generating matrix data + .mkX <- if (is.d) + function(n) rlnorm(n) # not rnorm(n), for validObject() + else + function(n) sample(c(NA, FALSE, TRUE), n, TRUE) + mkX <- if (is.p) + function(Dim) .mkX((Dim[1L] * (Dim[1L] + 1L)) %/% 2L) + else + function(Dim) .mkX(prod(Dim)) + + ## "Full factorial" design with varying 'Dim', 'uplo', 'diag' slots + .Dim <- c(list(c(n, n)), if (is.ge) list(c(n+1L, n), c(n, n+1L))) + .a <- c(list(Dim = seq_along(.Dim)), + if (!is.ge) list(uplo = c("U", "L")), + if ( is.tr) list(diag = c("N", "U")), + list(stringsAsFactors = FALSE)) + newargs <- do.call(expand.grid, .a) + newargs[["Dim"]] <- .Dim[.i <- newargs[["Dim"]]] + newargs[["Dimnames"]] <- lapply(.Dim, mkDN)[.i] + newargs[["x"]] <- lapply(.Dim, mkX)[.i] + + if (is.sy) { + iD <- Matrix:::indDiag + if (extends(Class, "corMatrix")) + newargs[["x"]] <- + lapply(newargs[["x"]], replace, iD(n), 1) + else if (extends(Class, "pcorMatrix")) + newargs[["x"]] <- + Map(function(x, upper) replace(x, iD(n, upper, TRUE), 1), + newargs[["x"]], newargs[["uplo"]] == "U") + } + + ## Test the matrices generated by each set of arguments to 'new' + all(unlist(.mapply(testDenseMatrix, newargs, list(Class = Class)))) + } > > testDenseMatrix <- function(Class, ...) { + is.p <- extends(Class, packedMatrix) + is.ge <- extends(Class, generalMatrix) + is.sy <- !is.ge && extends(Class, symmetricMatrix) + is.tr <- !is.ge && !is.sy + is.d <- extends(Class, dMatrix) + is.l <- !is.d && extends(Class, lMatrix) + is.n <- !is.d && !is.l + + ## This class needs special care because it has an additional 'sd' slot + is.cr <- is.sy && + (extends(Class, "corMatrix") || extends(Class, "pcorMatrix")) + + newargs <- list(Class = Class, ...) + if (is.cr) + newargs[["sd"]] <- rep.int(1, newargs[["Dim"]][2L]) + .M <- M <- do.call(new, newargs) + + m <- M@Dim[1L] + n <- M@Dim[2L] + r <- min(m, n) + p0 <- (n * (n - 1L)) %/% 2L + p1 <- (n * (n + 1L)) %/% 2L + .ZERO <- as.vector(0, typeof(M@x)) + .ONE <- as.vector(1, typeof(M@x)) + .NA <- as.vector(NA, typeof(M@x)) + loup <- if (is.ge) NA_character_ else if (M@uplo == "U") "L" else "U" + + ## For conveniently getting and setting (non)trivial triangles + ## of _traditional_ symmetric or triangular matrices + if (!is.ge) { + if (M@uplo == "U") { + tri1 <- U; `tri1<-` <- `U<-` + tri0 <- L; `tri0<-` <- `L<-` + } else { + tri1 <- L; `tri1<-` <- `L<-` + tri0 <- U; `tri0<-` <- `U<-` + } + } + + .m <- m1 <- m2 <- + if (is.p) + `tri1<-`(array(.ZERO, dim = M@Dim, dimnames = M@Dimnames), + diag = TRUE, M@x) + else + array(M@x, dim = M@Dim, dimnames = M@Dimnames) + + diag(.M) <- diag(.m) <- + if (is.d) + rlnorm(r) + else + sample(c(.NA, .ZERO, .ONE), r, TRUE) + + if (is.sy) { + tri0(m2, diag = TRUE) <- tri0(t(m2), diag = TRUE) + dimnames(m2) <- Matrix:::symDN(M@Dimnames) + } + if (is.tr && M@diag == "U") { + diag(m2) <- .ONE + } + + pM <- + if (is.p) + M + else if (!is.ge) + do.call(new, replace(newargs, c("Class", "x"), + list(packedClass(Class), + tri1(m1, diag = TRUE)))) + + upM <- + if (!is.p) + M + else + do.call(new, replace(newargs, c("Class", "x"), + list(unpackedClass(Class), as.vector(m1)))) + + tM <- do.call(new, replace(newargs, + c("Dim", "Dimnames", "x", + if (!is.ge) "uplo"), + c(list(M@Dim[2:1], + M@Dimnames[if (is.sy) 1:2 else 2:1], + if (is.p) + tri0(t(m1), diag = TRUE) + else + as.vector(t(m1))), + if (!is.ge) list(loup)))) + + dM <- do.call(new, replace(newargs[names(newargs) != "sd"], + c("Class", "x", if (is.tr) "diag"), + c(list(...Class(Class), + if (is.p) + tri1(.m, diag = TRUE) + else + as.vector(.m)), + if (is.tr) list("N")))) + + stopifnot(is.ge || identical(pack(M), pM), + identical(unpack(M), upM), + identical(t(M), tM), + identical(diag(M, names = FALSE), diag(m2, names = FALSE)), + identical(diag(M, names = TRUE), diag(m2, names = TRUE)), + identical(.M, dM)) + + if (is.ge) { + if (m == n) { + ## Not symmetric and not triangular + U(m2) <- if (is.d) rlnorm(p0) else rep_len(c(.NA, .ZERO, .ONE), p0) + L(m2) <- if (is.d) -rlnorm(p0) else rep_len(c(.ZERO, .ONE, .NA), p0) + M@x <- as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE) == (n <= 1L), + isTriangular(M, upper = NA) == (n <= 1L), + isDiagonal(M) == (n <= 1L)) + + ## Symmetric but not triangular + L(m2) <- L(t(m2)) + M@x <- as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE), + isTriangular(M, upper = NA) == (n <= 1L), + isDiagonal(M) == (n <= 1L)) + + ## Not symmetric but triangular + L(m2) <- .ZERO + M@x <- as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE) == (n <= 1L), + identical(isTriangular(M, upper = TRUE), TRUE), + identical(isTriangular(M, upper = FALSE), FALSE), + identical(isTriangular(M, upper = NA), + `attr<-`(TRUE, "kind", "U")), + isDiagonal(M) == (n <= 1L)) + + ## Symmetric and triangular + U(m2) <- .ZERO + M@x <- as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE), + identical(isTriangular(M, upper = TRUE), TRUE), + identical(isTriangular(M, upper = FALSE), TRUE), + identical(isTriangular(M, upper = NA), + `attr<-`(TRUE, "kind", "U")), + isDiagonal(M)) + } else { + ## Non-square ... _never_ symmetric, triangular, or diagonal + stopifnot(!isSymmetric(M, tol = 0, checkDN = FALSE), + !isTriangular(M, upper = NA), + !isDiagonal(M)) + } + + } else if (is.sy) { + ## Not triangular + tri1(m2) <- if (is.d) rlnorm(p0) else rep_len(c(.NA, .ZERO, .ONE), p0) + M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE), + isTriangular(M, upper = NA) == (n <= 1L), + isDiagonal(M) == (n <= 1L)) + + ## Triangular + tri1(m2) <- .ZERO + M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE), + identical(isTriangular(M, upper = TRUE), TRUE), + identical(isTriangular(M, upper = FALSE), TRUE), + identical(isTriangular(M, upper = NA), + `attr<-`(TRUE, "kind", M@uplo)), + isDiagonal(M)) + } else { + ## Not symmetric + tri1(m2) <- if (is.d) rlnorm(p0) else rep_len(c(.NA, .ZERO, .ONE), p0) + M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE) == (n <= 1L), + identical(isTriangular(M, upper = M@uplo == "U"), TRUE), + identical(isTriangular(M, upper = M@uplo != "U"), n <= 1L), + identical(isTriangular(M, upper = NA), + `attr<-`(TRUE, "kind", M@uplo)), + isDiagonal(M) == (n <= 1L)) + + ## Symmetric + tri1(m2) <- .ZERO + M@x <- if (is.p) tri1(m2, diag = TRUE) else as.vector(m2) + stopifnot(isSymmetric(M, tol = 0, checkDN = FALSE), + identical(isTriangular(M, upper = M@uplo == "U"), TRUE), + identical(isTriangular(M, upper = M@uplo != "U"), TRUE), + identical(isTriangular(M, upper = NA), + `attr<-`(TRUE, "kind", M@uplo)), + isDiagonal(M)) + } + + TRUE + } > > .dense.subclasses <- c(names(getClassDef("packedMatrix")@subclasses), + names(getClassDef("unpackedMatrix")@subclasses)) > stopifnot(all(vapply(.dense.subclasses, testDenseClass, NA, n = 4L))) > > > ## diag(, names = TRUE) preserves names > ## if head of longer character vector matches shorter character vector > n <- 4L > m <- array(rnorm(n * (n + 1L)), dim = c(n, n + 1L)) > M <- new("dgeMatrix", x = as.vector(m), Dim = dim(m)) > rn <- letters[seq_len(n)] > 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" Time elapsed: 1.43 0.12 1.53 NA NA > > proc.time() user system elapsed 1.43 0.12 1.53