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#setAutoRealizationBackend("RleArray")
#setAutoRealizationBackend("HDF5Array")
### Toy integer 3D SparseArraySeed.
.make_toy_sas1 <- function()
{
dim1 <- 5:3
nzindex1 <- Lindex2Mindex(1:prod(dim1), dim1)
set.seed(123)
nzindex1 <- nzindex1[sample(nrow(nzindex1), 30), , drop=FALSE]
nzdata1 <- 24:-5
nzdata1[2:3] <- NA
nzdata1[4:5] <- 0L
SparseArraySeed(dim1, nzindex1, nzdata1)
}
### Toy integer 2D SparseArraySeed with no zeros or NAs.
.make_toy_sas1b <- function()
{
dim1b <- 5:4
nzindex1b <- Lindex2Mindex(1:prod(dim1b), dim1b)
set.seed(123)
nzindex1b <- nzindex1b[sample(nrow(nzindex1b)), , drop=FALSE]
nzdata1b <- sample(10L, nrow(nzindex1b), replace=TRUE)
SparseArraySeed(dim1b, nzindex1b, nzdata1b)
}
### Toy numeric 3D SparseArraySeed.
.make_toy_sas2 <- function()
{
sas1 <- .make_toy_sas1()
nzdata2 <- sas1@nzdata + 0.01
nzdata2[2:3] <- NA
nzdata2[4:5] <- 0
nzdata2[6:8] <- c(NaN, Inf, -Inf)
SparseArraySeed(dim(sas1), sas1@nzindex, nzdata2)
}
### Toy character 3D SparseArraySeed.
.make_toy_sas3 <- function()
{
sas1 <- .make_toy_sas1()
nzdata3 <- paste0(sas1@nzdata, "aXb")
nzdata3[2:3] <- NA
nzdata3[4:5] <- ""
SparseArraySeed(dim(sas1), sas1@nzindex, nzdata3)
}
### Toy logical 3D SparseArraySeed.
.make_toy_sas4 <- function()
{
sas1 <- .make_toy_sas1()
set.seed(123)
nzdata4 <- sample(c(TRUE, FALSE, NA), length(sas1@nzdata), replace=TRUE)
SparseArraySeed(dim(sas1), sas1@nzindex, nzdata4)
}
test_abind_SparseArraySeed_objects <- function()
{
abind_SparseArraySeed_objects <-
DelayedArray:::abind_SparseArraySeed_objects
simple_abind <- DelayedArray:::simple_abind
test_on <- function(..., along) {
objects <- list(...)
current <- abind_SparseArraySeed_objects(objects, along)
checkTrue(is(current, "SparseArraySeed"))
arrays <- lapply(unname(objects), as.array)
target <- do.call(simple_abind, c(arrays, list(along=along)))
checkIdentical(target, as.array(current))
}
do_tests <- function(x1, x2, x3, x4, along) {
test_on(x1, along=along)
test_on(x2, along=along)
test_on(x3, along=along)
test_on(x4, along=along)
test_on(x1, x2, along=along)
test_on(x2, x1, along=along)
test_on(x1, x3, along=along)
test_on(x3, x1, along=along)
test_on(x1, x4, along=along)
test_on(x4, x1, along=along)
test_on(x2, x3, along=along)
test_on(x3, x2, along=along)
test_on(x2, x4, along=along)
test_on(x4, x2, along=along)
test_on(x3, x4, along=along)
test_on(x4, x3, along=along)
test_on(x1, x2, x3, along=along)
test_on(x1, x3, x2, along=along)
test_on(x2, x1, x3, along=along)
test_on(x2, x3, x1, along=along)
test_on(x3, x1, x2, along=along)
test_on(x3, x2, x1, along=along)
test_on(x1, x2, x3, x4, along=along)
}
sas1 <- .make_toy_sas1() # integer 3D SparseArraySeed
sas2 <- .make_toy_sas2() # numeric 3D SparseArraySeed
dimnames(sas2) <- list(NULL, letters[1:4], letters[24:26])
sas3 <- .make_toy_sas3() # character 3D SparseArraySeed
dimnames(sas3) <- list(NULL, LETTERS[1:4], NULL)
sas4 <- .make_toy_sas4() # logical 3D SparseArraySeed
x1 <- extract_sparse_array(sas1, list(1L, NULL, NULL))
x2 <- extract_sparse_array(sas1, list(1:3, NULL, NULL))
x3 <- extract_sparse_array(sas1, list(integer(0), NULL, NULL))
x4 <- extract_sparse_array(sas1, list(1:2, NULL, NULL))
do_tests(x1, x2, x3, x4, along=1L)
x1 <- extract_sparse_array(sas1, list(NULL, 1L, NULL))
x2 <- extract_sparse_array(sas1, list(NULL, 1:3, NULL))
x3 <- extract_sparse_array(sas1, list(NULL, integer(0), NULL))
x4 <- extract_sparse_array(sas1, list(NULL, 1:2, NULL))
do_tests(x1, x2, x3, x4, along=2L)
x1 <- extract_sparse_array(sas1, list(NULL, NULL, 1L))
x2 <- extract_sparse_array(sas1, list(NULL, NULL, 1:3))
x3 <- extract_sparse_array(sas1, list(NULL, NULL, integer(0)))
x4 <- extract_sparse_array(sas1, list(NULL, NULL, 1:2))
do_tests(x1, x2, x3, x4, along=3L)
}
test_SparseArraySeed_unary_iso_ops <- function()
{
do_tests <- function(.Generic, sas) {
GENERIC <- match.fun(.Generic)
current <- GENERIC(sas)
checkTrue(is(current, "SparseArraySeed"))
checkIdentical(dim(sas), dim(current))
checkIdentical(GENERIC(as.array(sas)), as.array(current))
}
sas1 <- .make_toy_sas1() # integer 3D SparseArraySeed
sas2 <- .make_toy_sas2() # numeric 3D SparseArraySeed
sas4 <- .make_toy_sas4() # logical 3D SparseArraySeed
for (.Generic in c("is.na", "is.infinite", "is.nan")) {
do_tests(.Generic, sas1)
do_tests(.Generic, sas2)
do_tests(.Generic, sas4)
}
sas3 <- .make_toy_sas3() # character 3D SparseArraySeed
for (.Generic in c("nchar", "tolower", "toupper")) {
do_tests(.Generic, sas3)
}
}
test_SparseArraySeed_anyNA <- function()
{
do_test <- function(sas)
checkIdentical(anyNA(as.array(sas)), anyNA(sas))
sas1 <- .make_toy_sas1() # integer 3D SparseArraySeed
sas1b <- .make_toy_sas1b() # integer 2D SparseArraySeed (no zeros or NAs)
sas2 <- .make_toy_sas2() # numeric 3D SparseArraySeed
sas3 <- .make_toy_sas3() # character 3D SparseArraySeed
sas4 <- .make_toy_sas4() # logical 3D SparseArraySeed
do_test(sas1)
do_test(sas1b)
do_test(sas2)
do_test(sas3)
do_test(sas4)
}
test_SparseArraySeed_which <- function()
{
sas4 <- .make_toy_sas4() # logical 3D SparseArraySeed
checkIdentical(which(as.array(sas4)), which(sas4))
checkIdentical(which(as.array(sas4), arr.ind=TRUE, useNames=FALSE),
which(sas4, arr.ind=TRUE))
sas0 <- SparseArraySeed(5:4, nzindex=cbind(3:5, 4L), nzdata=FALSE)
target1 <- integer(0)
target2 <- matrix(integer(0), ncol=2)
checkIdentical(target1, which(sas0))
checkIdentical(target2, which(sas0, arr.ind=TRUE))
}
test_SparseArraySeed_Summary <- function()
{
do_tests <- function(.Generic, sas) {
GENERIC <- match.fun(.Generic)
checkIdentical(GENERIC(as.array(sas)),
GENERIC(sas))
checkIdentical(GENERIC(as.array(sas), na.rm=TRUE),
GENERIC(sas, na.rm=TRUE))
}
sas1 <- .make_toy_sas1() # integer 3D SparseArraySeed
sas1b <- .make_toy_sas1b() # integer 2D SparseArraySeed (no zeros or NAs)
sas2 <- .make_toy_sas2() # numeric 3D SparseArraySeed
sas4 <- .make_toy_sas4() # logical 3D SparseArraySeed
for (.Generic in c("max", "min", "range", "sum", "prod")) {
do_tests(.Generic, sas1)
do_tests(.Generic, sas1b)
do_tests(.Generic, sas2)
do_tests(.Generic, sas4)
}
for (.Generic in c("any", "all")) {
do_tests(.Generic, sas1)
do_tests(.Generic, sas1b)
suppressWarnings(do_tests(.Generic, sas2))
do_tests(.Generic, sas4)
}
}
test_SparseArraySeed_mean <- function()
{
do_tests <- function(sas) {
checkIdentical(mean(as.array(sas)), mean(sas))
checkIdentical(mean(as.array(sas), na.rm=TRUE), mean(sas, na.rm=TRUE))
}
sas1 <- .make_toy_sas1() # integer 3D SparseArraySeed
sas1b <- .make_toy_sas1b() # integer 2D SparseArraySeed (no zeros or NAs)
sas2 <- .make_toy_sas2() # numeric 3D SparseArraySeed
sas4 <- .make_toy_sas4() # logical 3D SparseArraySeed
do_tests(sas1)
do_tests(sas1b)
do_tests(sas2)
do_tests(sas4)
}
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