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library(Matrix)
source(system.file("test-tools.R", package = "Matrix"))# identical3(),
# further checkMatrix(), etc
if(interactive()) options(error = recover)
options(warn=1)# show as they happen
cat("doExtras:",doExtras,"\n")
setClass("myDGC", contains = "dgCMatrix")
(M <- new("myDGC", as(Matrix(c(-2:4, rep(0,9)), 4), "CsparseMatrix")))
stopifnot(exprs = {
M[-4L, 2L] == 2:4
MatrixClass( "myDGC") == "dgCMatrix"
MatrixClass( "dpoMatrix") == "dsyMatrix"
MatrixClass( "dppMatrix") == "dspMatrix"
MatrixClass( "corMatrix") == "dsyMatrix"
MatrixClass( "copMatrix") == "dspMatrix"
identical(MatrixClass("indMatrix"), character(0L))
identical(MatrixClass( "pMatrix"), character(0L))
})
## [matrix-Bugs][6182] Coercion method doesn't work on child class
## Bugs item #6182, at 2015-09-01 17:49 by Vitalie Spinu
setClass("A", contains = "ngCMatrix")
ngc <- as(as(as(diag(3), "CsparseMatrix"), "generalMatrix"), "nMatrix")
validObject(dd <- as(ngc, "dMatrix")) # fine
A. <- as(ngc, "A")
stopifnot(identical(as(A., "dMatrix"), dd))
## as(.) coercion failed in Matrix <= 1.2.3
stopifnot(all( abs(A.)# failed too
== diag(3)))
d <- Diagonal(3)
(dC <- as(d, "CsparseMatrix")) # "dtCMatrix" (unitriangular)
(dgC <- as(dC, "generalMatrix"))
stopifnot(exprs = {
is(dgC, "dgCMatrix") # was wrong in Matrix 1.3.2
## identical(dgC, as(dC, "dgCMatrix")) # deprecated
identical(dC , new("dtCMatrix", p = rep(0L, 4), Dim = c(3L, 3L), diag = "U"))
identical(dC , diagN2U(as(dgC, "triangularMatrix")))
})
setClass("posDef", contains = "dspMatrix")
N <- as(crossprod(M) + Diagonal(4), "packedMatrix")
(N <- new("posDef", N))
stopifnot(is(N[1:2, 1:2], "symmetricMatrix"))
#### 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, '"')
.subclasses <- function(cnam) {
cd <- getClass(cnam)
unique(c(cd@className, unlist(lapply(names(cd@subclasses), .subclasses))))
}
for(n in allCl) {
if(isVirtualClass(n))
cat("Virtual class", .dq(n),"\n")
else {
cat("\"Actual\" class", .dq(n),":\n")
x <- new(n)
if(doExtras) 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(doExtras && !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, "triangularMatrix")
if(!doExtras && !interactive()) q("no") ## (saving testing time)
### 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
Mat.MatFact <- c("Cholesky", "pCholesky",
"BunchKaufman", "pBunchKaufman")##, "LDL"
##FIXME maybe move to ../../MatrixModels/tests/ :
## (modmat.classes <- .subclasses("modelMatrix"))
no.t.etc <- c(.R.classes, dR.classes, Mat.MatFact)#, modmat.classes)
no.t.classes <- c(no.t.etc) # no t() available
no.norm.classes <- no.t.classes
not.Ops <- NULL # "Ops", e.g. "+" fails
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
## from pkg sfsmisc :
bl.string <- function(no) sprintf("%*s", no, "")
## Compute a few things only once :
mM <- as(as(as(mM, "unpackedMatrix"), "generalMatrix"), "dMatrix") # dge
trm <- mm; trm[lower.tri(mm)] <- 0
## not yet used:
## 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
deprecated <- grepl("^[dln](ge|tr|sy|tp|sp|[gts][CRT])Matrix$", clNam)
cat("\n==>")
cat.(clNam)
##---------
clD <- getClassDef(clNam)
if(isVirtualClass(clD)) {
cat(" - is virtual\n")
if(recursive) {
cat.("----- begin{class :", clNam, "}----new subclasses----\n")
for(ccl in clD@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(clD, "generalMatrix")
symC <- extends(clD, "symmetricMatrix")
triC <- extends(clD, "triangularMatrix")
diaC <- extends(clD, "diagonalMatrix")
indC <- extends(clD, "indMatrix")
if(!(genC || symC || triC || diaC || indC))
stop("does not extend one of 'general', 'symmetric', 'triangular', 'diagonal', 'ind'")
sparseC <- extends(clD, "sparseMatrix")
denseC <- extends(clD, "denseMatrix")
if(!(sparseC || denseC))
stop("does not extend either 'sparse' or 'dense'")
cat("; new(*): ")
m <- new(clNam) ; cat("ok; ")
m0 <- matrix(,0,0)
if(canCoerce(m0, clNam)) {
cat("; canCoerce(matrix(,0,0), *) => as(m0, <.>): ")
m0. <-
if(deprecated)
eval(Matrix:::.as.via.virtual(
"matrix", clNam, quote(m0)))
else as(m0, clNam)
if(.hasSlot(m, "diag") && .hasSlot(m0., "diag") &&
identical(m@diag, "N") && identical(m0.@diag, "U"))
## tolerate as(0-by-0, .) formally having unit diagonal
m0.@diag <- "N"
stopifnot(Qidentical(m, m0.)); cat("ok; ")
}
is_p <- extends(clD, "indMatrix")
is_cor <- extends(clD, "corMatrix") || extends(clD, "copMatrix")
## ^^^ has diagonal divided out
if(canCoerce(mm, clNam)) { ## replace 'm' by `non-empty' version
cat("canCoerce(mm, *) ")
m0 <- {
if(triC) trm
else if(is_p)
mm == 1 # logical *and* "true" permutation
else mm
}
if(extends(clD, "lMatrix") ||
extends(clD, "nMatrix"))
storage.mode(m0) <- "logical"
else if(extends(clD, "zMatrix"))
storage.mode(m0) <- "complex"
validObject(m) ## validity of trivial 'm' before replacing
m <-
if(deprecated)
eval(Matrix:::.as.via.virtual(
"matrix", clNam, quote(m0)))
else as(m0, clNam)
if(is_cor)
m0 <- cov2cor(m0)
} else {
m0 <- vector(Matrix:::.type.kind[Matrix:::.M.kind(m)])
dim(m0) <- c(0L,0L)
}
## m0 is the 'matrix' version of our 'Matrix' m
m. <- m0 ##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)
}
cat("valid: ", validObject(m), extraValid(m, clNam),"\n")
## 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)))
show(m)
## coerce to 'matrix'
m.m <- as(m, "matrix")
##=========##
checkMatrix(m, m.m,
##=========##
do.t= !(clNam %in% no.t.classes),
doNorm= !(clNam %in% no.norm.classes),
doOps = all(clNam != not.Ops),
doCoerce = all(clNam != not.coerce1),
catFUN = cat.)
### FIXME: organize differently :
### 1) produce 'mM' and 'mm' for the other cases,
### 2) use identical code for all cases
if(is(m, "dMatrix") &&
(is(m, "generalMatrix") || is(m, "symmetricMatrix"))) {
if(any(clNam == not.coerce1))
cat.("not coercable_1\n")
else if(canCoerce(mM, clNam)) {
m2 <-
if(deprecated)
eval(Matrix:::.as.via.virtual(
class(mM), clNam, quote(mM)))
else as(mM, clNam)
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)) {
if(canCoerce("matrix", clNam)) {
cat.("as(matrix, <class>): ")
m3 <-
if(deprecated)
eval(Matrix:::.as.via.virtual(
"matrix", clNam, quote(mm)))
else as(mm, clNam)
cat("valid:", validObject(m3), "\n")
} else cat.(" not coerceable from \"matrix\"\n")
## }
}
## else { ... no happens in tstMatrix() above .. }
## 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"
cat.("as dgT* ")
mgT <- eval(Matrix:::.as.via.virtual(
class(m), "dgTMatrix", quote(m)))
cat(sprintf("; valid dgT* coercion: %s\n",
validObject(mgT)))
}
}
}
} # end{dotestMat}
for(scl in getClass(cl)@subclasses)
dotestMat(scl, offset + 1)
}
## in case we want to make progress:
## codetools::checkUsage(tstMatrixClass, all=TRUE)
tstMatrixClass("Matrix")
if(FALSE)## or just a sub class
tstMatrixClass("triangularMatrix")
cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''
if(!interactive()) warnings()
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