library(Matrix) source(system.file("test-tools.R", package = "Matrix"))# identical3() etc if(interactive()) options(error = recover) #### Automatically display the class inheritance structure #### possibly augmented with methods allCl <- getClasses("package:Matrix") cat("actual and virtual classes:\n") tt <- table( isVirt <- sapply(allCl, isVirtualClass) ) names(tt) <- c('"actual"', "virtual") tt ## The "actual" Matrix classes: aCl <- allCl[!isVirt] (aMcl <- aCl[grep("Matrix$", aCl)]) # length 48 aMc2 <- aCl[sapply(aCl, extends, class2 = "Matrix")] stopifnot(all( aMcl %in% aMc2 )) aMc2[!(aMc2 %in% aMcl)] ## only 4 : p?Cholesky & p?BunchKaufman ## Really nice would be to construct an inheritance graph and display ## it. Following things are computational variations on the theme.. ## We use a version of canCoerce() that works with two *classes* instead of ## canCoerce <- function (object, Class) classCanCoerce <- function (class1, class2) { extends(class1, class2) || !is.null(selectMethod("coerce", optional = TRUE, signature = c(from = class1, to = class2), useInherited = c(from = TRUE, to = FALSE))) } .dq <- function(ch) paste0('"', ch, '"') for(n in allCl) { if(isVirtualClass(n)) cat("Virtual class", .dq(n),"\n") else { cat("\"Actual\" class", .dq(n),":\n") x <- new(n) for(m in allCl) if(classCanCoerce(n,m)) { ext <- extends(n, m) if(ext) { cat(sprintf(" extends %20s %20s \n", "", .dq(m))) } else { cat(sprintf(" can coerce: %20s -> %20s: ", .dq(n), .dq(m))) tt <- try(as(x, m), silent = TRUE) if(inherits(tt, "try-error")) { cat("\t *ERROR* !!\n") } else { cat("as() ok; validObject: ") vo <- validObject(tt, test = TRUE) cat(if(isTRUE(vo)) "ok" else paste("OOOOOOPS:", vo), "\n") } } } cat("---\n") } } cat('Time elapsed: ', proc.time(),'\n') # for the above "part I" if(!interactive()) { # don't want to see on source() cat("All classes in the 'Matrix' package:\n") for(cln in allCl) { cat("\n-----\n\nClass", dQuote(cln),":\n ", paste(rep("~",nchar(cln)),collapse=''),"\n") ## A smarter version would use getClass() instead of showClass(), ## build the "graph" and only then display. ## showClass(cln) } cat("\n \n") ## One could extend the `display' by using (something smarter than) ## are the "coerce" methods showing more than the 'Extends' output above? cat("All (S4) methods in the 'Matrix' package:\n") showMethods(where="package:Matrix") } # end{non-interactive} ## 1-indexing instead of 0-indexing for direct "dgT" should give error: ii <- as.integer(c(1,2,2)) jj <- as.integer(c(1,1,3)) assertError(new("dgTMatrix", i=ii, j=jj, x= 10*(1:3), Dim=2:3)) assertError(new("dgTMatrix", i=ii, j=jj - 1:1, x= 10*(1:3), Dim=2:3)) assertError(new("dgTMatrix", i=ii - 1:1, j=jj, x= 10*(1:3), Dim=2:3)) (mm <- new("dgTMatrix", i=ii - 1:1, j=jj - 1:1, x= 10*(1:3), Dim=2:3)) validObject(mm) ### Sparse Logical: m <- Matrix(c(0,0,2:0), 3,5) mT <- as(mC <- as(m, "CsparseMatrix"), "TsparseMatrix") stopifnot(identical(as(mT,"CsparseMatrix"), mC)) (mC. <- as(mT[1:2, 2:3], "CsparseMatrix")) (mlC <- as(mC. , "lMatrix")) as(mlC,"ltCMatrix") ### Test all classes: validObject(new( * )) should be fulfilled ----------- ## need stoplist for now: Rcl.struc <- c("gR", "sR", "tR") (dR.classes <- paste0(paste0("d", Rcl.struc[Rcl.struc != "gR"]), "Matrix")) (.R.classes <- paste0(sort(outer(c("l", "n"), Rcl.struc, paste0)), "Matrix")) # have only stub implementation ## not.ok..: are left out almost completely not.ok.classes <- NULL ## was .R.classes ## From the rest, those that don't show {have no coerce to "dge":} no.show.classes <- NULL ## was dR.classes ## Mat.MatFact <- c("Cholesky", "pCholesky", "BunchKaufman", "pBunchKaufman")##, "LDL" no.t.etc <- c(no.show.classes, .R.classes, dR.classes, Mat.MatFact) no.t.classes <- c(no.t.etc) # no t() available no.norm.classes <- no.t.classes not.Ops <- no.show.classes # "Ops", e.g. "+" fails not.coerce0 <- no.show.classes # not coercable to "matrix" & "dgeMatrix" not.coerce1 <- no.t.etc # not coercable from "dgeMatrix" not.coerce2 <- no.t.etc # not coercable from "matrix" tstMatrixClass <- function(cl, mM = Matrix(c(2,1,1,2) + 0, 2,2, dimnames=rep( list(c("A","B")), 2)), # dimnames: *symmetric* mm = as(mM, "matrix"), recursive = TRUE, offset = 0) { ## Purpose: Test 'Matrix' class {and do this for all of them} ## ---------------------------------------------------------------------- ## Arguments: cl: class object of a class that extends "Matrix" ## mM: a "Matrix"-matrix which will be coerced to class 'cl' ## mm: a S3-matrix which will be coerced to class 'cl' ## ---------------------------------------------------------------------- ## Author: Martin Maechler ## This is sfsmisc::bl.string(): bl.string <- function (no) paste(rep(" ", no), collapse = "") ## Compute a few things only once : mM <- as(mM, "dgeMatrix") trm <- mm; trm[lower.tri(mm)] <- 0 summList <- lapply(getGroupMembers("Summary"), get, envir = asNamespace("Matrix")) if(recursive) cList <- character(0) extraValid <- function(m, cl = class(m)) { sN <- slotNames(cl) sN <- sN[sN != "factors"] for(nm in sN) if(!is.null(a <- attributes(slot(m, nm)))) stop(sprintf("slot '%s' with %d attributes, named: ", nm, length(a)), paste(names(a), collapse=", ")) invisible(TRUE) } ## This is the recursive function dotestMat <- function(cl, offset) { cat. <- function(...) cat(bl.string(offset), ...) clNam <- cl@subClass cat("\n") cat.(clNam) ##--------- if(isVirtualClass(clNam)) { cat(" - is virtual\n") if(recursive) { cat.("----- begin{class :", clNam, "}----new subclasses----\n") for(ccl in getClass(clNam)@subclasses) { cclN <- ccl@subClass if(cclN %in% cList) cat.(cclN,": see above\n") else { cList <<- c(cList, cclN) dotestMat(ccl, offset = offset + 3) } } cat.("----- end{class :", clNam, "}---------------------\n") } } else { ## --- actual class --- genC <- extends(clNam, "generalMatrix") symC <- extends(clNam, "symmetricMatrix") triC <- extends(clNam, "triangularMatrix") diaC <- extends(clNam, "diagonalMatrix") if(!(genC || symC || triC || diaC)) stop("does not extend one of 'general', 'symmetric', 'triangular', or 'diagonal'") sparseC <- extends(clNam, "sparseMatrix") denseC <- extends(clNam, "denseMatrix") if(!(sparseC || denseC)) stop("does not extend either 'sparse' or 'dense'") cat("; new(..): ") m <- new(clNam) ; cat("ok; ") is_p <- extends(clNam, "pMatrix") is_cor <- (clNam == "corMatrix") # has diagonal divided out if(canCoerce(mm, clNam)) { ## replace 'm' by `non-empty' version cat("canCoerce() ") m0 <- { if(triC) trm else if(is_p) mm == 1 # logical *and* "true" permutation else mm } if(extends(clNam, "lMatrix") || extends(clNam, "nMatrix")) storage.mode(m0) <- "logical" else if(extends(clNam, "zMatrix")) storage.mode(m0) <- "complex" validObject(m) ## validity of trivial 'm' before replacing m <- as(m0, clNam) if(is_cor) m0 <- cov2cor(m0) } else { m0 <- vector(Matrix:::.type.kind[Matrix:::.M.kindC(clNam)]) dim(m0) <- c(0L,0L) } ## m0 is the 'matrix' version of our 'Matrix' m m. <- if(is_p) as.integer(m0) else m0 EQ <- if(is_cor) all.equal else identical stopifnot(EQ(m0[FALSE], m[FALSE]) , EQ(m.[TRUE], m[TRUE]) , if(length(m) >= 2) EQ(m.[2:1], m[2:1]) else TRUE) if(all(dim(m) > 0)) { ## matrix(0,0,0)[FALSE,] is invalid too m00 <- m[FALSE,FALSE] m.. <- m[TRUE , TRUE] stopifnot(dim(m00) == c(0L,0L), dim(m..) == dim(m)) ## not yet , class(m00) == clNam , identical(m.. , m) } if(any(clNam == not.ok.classes)) { cat("in 'stop list' - no validity\n") } else { cat("valid: ", validObject(m), extraValid(m, clNam)) ## This can only work as long as 'm' has no NAs : ## not yet -- have version in not.Ops below ## once we have is.na(): ## stopifnot(all(m == m | is.na(m))) ## check all() and "==" [Compare] ## if(any(m != m && !is.na(m))) stopifnot(all(m == m)) ## check all() and "==" [Compare] if(any(m != m)) stop(" any (m != m) should not be true") if(clNam %in% no.t.classes) { cat(" in t()-'stop list'\n") } else { cat("; t(t(m)) ==?== m :") stopifnot(Qidentical(m, t(t(m)))) cat(" ok\n") } if(all(clNam != no.show.classes)) show(m) ## improve: cat.( captureOutput(show(m) ) ) else cat.(" -- no show() yet \n") if(clNam %in% no.norm.classes) { cat.(" in norm()-'stop list'\n") } else { cat.(sprintf(" norm(m [%d x %d]) :", nrow(m), ncol(m))) for(typ in c("1","I","F","M")) { cat('', typ, '') stopifnot(all.equal(norm(m,typ), norm(m0,typ))) } cat(" ok\n") } cat.(" Summary: ") for(f in summList) { #cat(f@generic, "() ", sep='') stopifnot(if(clNam == "corMatrix") all.equal(f(m), f(m0)) else f(m) == f(m0)) } cat(" ok\n") if(all(clNam != not.coerce0)) {## coerce to 'matrix' m.m <- as(m, "matrix") ## and test 'dim()' as well: stopifnot(identical(dim(m.m), dim(m)), if(clNam %in% no.t.classes) TRUE else identical(diag(m), diag(t(m))), ## TODO: also === diag(band(m,0,0)) diag(m) == diag(m.m), nnzero(m) == sum(m.m != 0)) } else stopifnot(length(dim(m)) == 2) ### FIXME: organize differently : ### 1) produce 'mM' and 'mm' for the other cases, ### 2) use identical code for all cases ## use non-square matrix when "allowed": ## "!" should work (via as(*, "l...")) : m11 <- as(as(!!m,"CsparseMatrix"), "lMatrix") m12 <- as(as( m, "lMatrix"),"CsparseMatrix") if(!identical(m11, m12)) stopifnot(identical(as(m11, "generalMatrix"), as(m12, "generalMatrix"))) if(is(m, "dMatrix") && all(clNam != not.Ops)) { ## makes sense with non-trivial m (!) cat("2*m =?= m+m: ") if(identical(2*m, m+m)) cat("identical\n") else { stopifnot(as(2*m,"matrix") == as(m+m, "matrix")) cat("ok\n") } ## m == m etc, now for all, see above cat("m >= m for all: ") stopifnot(all(m >= m)); cat("ok\n") cat("m < m for none: ") stopifnot(all(! m < m)); cat("ok\n") } if(is(m, "dMatrix") && is(m, "compMatrix")) { if(any(clNam == not.coerce1)) cat.("not coercable_1\n") else { cat.("as(dge*, <(super)class>): ") if(canCoerce(mM, clNam)) m2 <- as(mM, clNam) else { ## find superclass to which to coerce if(extends(clNam, "sparseMatrix")) { if(is.na(newcl <- Matrix:::.sp.class(clNam))) stop("internal failure from .sp.class()") m2 <- as(mM, newcl) } else { ## ddense & (general or symmetric) stop("don't know what to coerce to - error test-logic") } } cat("valid:", validObject(m2), "\n") if(!is_cor) ## as.vector() stopifnot(as.vector(m2) == as.vector(mM)) cat.("[cr]bind2():"); mm2 <- cbind2(m2,m2) stopifnot(dim(rbind2(m2,m2)) == 2:1 * dim(mM)); cat(" ok") if(genC && class(mm2) == clNam)## non-square matrix when "allowed" m2 <- mm2 dd <- diag(m2) cat("; `diag<-` ") diag(m2) <- 10*dd stopifnot(is_cor || identical(dd, diag(mM)), identical(10*dd, diag(m2))); cat("ok ") } if(all(clNam != not.coerce2)) { cat.("as(matrix, ): ") m3 <- as(mm, clNam) cat("valid:", validObject(m3), "\n") } } else { ## not numeric composite: logical / triangular/diagonal .. if(any(clNam == not.coerce1)) cat.("not coercable_1\n") else { ## FIXME: also add tests for these if(is(m, "lMatrix")) { ## should fulfill even with NA: stopifnot(identical(m, m & TRUE), identical(m, FALSE | m), all(m | !m), !any(!m & m)) } else if(is(m, "triangularMatrix")) { mm. <- mm i0 <- if(m@uplo == "L") upper.tri(mm.) else lower.tri(mm.) mm.[i0] <- 0 cat.("as(triang.matrix, ): ") m3 <- as(mm., clNam) cat("valid:", validObject(m3), "\n") } else { ## diagonal (only one)? ## TODO } } } ## if(is(m, "denseMatrix")) { ## ## ......... ## cat.("as dsparse* ") ## msp <- as(m, "dsparseMatrix") ## cat.("; valid coercion: ", validObject(msp), "\n") ## } else if(is(m, "sparseMatrix")) { ## } else cat.("-- not dense nor sparse -- should not happen(!?)\n") if(is(m, "dsparseMatrix")) { if(any(clNam == not.coerce1)) cat.("not coercable_1\n") else { ## make sure we can coerce to dgT* -- needed, e.g. for "image" ## change: use Tsparse instead of dgT, unless it *is* Tsparse: isT <- is(m, "TsparseMatrix") prefix <- if(isT) "dgT" else "Tsparse" Tcl <- paste(prefix, "Matrix", sep='') cat.(sprintf("as %s* ", prefix)) mgT <- as(m, Tcl) cat(sprintf("; valid %s* coercion: %s\n", prefix, validObject(mgT))) } } } } } # end{dotestMat} for(scl in getClass(cl)@subclasses) dotestMat(scl, offset + 1) } tstMatrixClass("Matrix") if(FALSE)## or just a sub class tstMatrixClass("triangularMatrix") cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons'' if(!interactive()) warnings()