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library("matrixStats")
## Create isFALSE() if running on an old version of R
if (!exists("isFALSE", mode="function")) {
isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
}
rowQuantiles_R <- function(x, probs = c(0, 0.25, 0.50, 0.75, 1), na.rm = FALSE, drop = TRUE, type = 7L, ..., useNames = TRUE) {
q <- apply(x, MARGIN = 1L, FUN = function(x, probs, na.rm) {
if (!na.rm && any(is.na(x))) {
na_value <- NA_real_
if (type != 7L) storage.mode(na_value) <- storage.mode(x)
rep(na_value, times = length(probs))
} else {
as.vector(quantile(x, probs = probs, na.rm = na.rm, type = type, names = FALSE, ...))
}
}, probs = probs, na.rm = na.rm)
if (!is.null(dim(q))) q <- t(q)
else dim(q) <- c(nrow(x), length(probs))
colnames(q) <- matrixStats:::quantile_probs_names(probs)
rownames(q) <- rownames(x)
if (isFALSE(useNames)) dimnames(q) <- NULL
if (drop) q <- drop(q)
q
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Test with multiple quantiles
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for (mode in c("logical", "integer", "double")) {
cat("mode: ", mode, "\n", sep = "")
x <- matrix(1:40 + 0.1, nrow = 8, ncol = 5)
storage.mode(x) <- mode
dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
str(x)
probs <- c(0, 0.5, 1)
# Test with and without dimnames on x
for (setDimnames in c(TRUE, FALSE)) {
if (setDimnames) dimnames(x) <- dimnames
else dimnames(x) <- NULL
# Check names attribute
for (useNames in c(TRUE, FALSE)) {
q0 <- rowQuantiles_R(x, probs = probs, useNames = useNames)
print(q0)
q1 <- rowQuantiles(x, probs = probs, useNames = useNames)
print(q1)
stopifnot(all.equal(q1, q0))
q2 <- colQuantiles(t(x), probs = probs, useNames = useNames)
stopifnot(all.equal(q2, q0))
}
}
} # for (mode ...)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Test with a single quantile
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
for (mode in c("logical", "integer", "double")) {
cat("mode: ", mode, "\n", sep = "")
x <- matrix(1:40, nrow = 8, ncol = 5)
storage.mode(x) <- mode
dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
str(x)
probs <- c(0.5)
# Test with and without dimnames on x
for (setDimnames in c(TRUE, FALSE)) {
if (setDimnames) dimnames(x) <- dimnames
else dimnames(x) <- NULL
# Check names attribute
for (useNames in c(TRUE, FALSE)) {
q0 <- rowQuantiles_R(x, probs = probs, useNames = useNames)
print(q0)
q1 <- rowQuantiles(x, probs = probs, useNames = useNames)
print(q1)
stopifnot(all.equal(q1, q0))
q2 <- colQuantiles(t(x), probs = probs, useNames = useNames)
stopifnot(all.equal(q2, q0))
}
}
} # for (mode ...)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Consistency checks
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
set.seed(1)
probs <- seq(from = 0, to = 1, by = 0.25)
cat("Consistency checks:\n")
n_sims <- if (Sys.getenv("_R_CHECK_USE_VALGRIND_") != "") 6L else 24L
for (kk in seq_len(n_sims)) {
cat("Random test #", kk, "\n", sep = "")
# Simulate data in a matrix of any shape
dim <- sample(20:60, size = 2L)
n <- prod(dim)
x <- rnorm(n, sd = 100)
dim(x) <- dim
dimnames <- lapply(dim(x), FUN = function(n) rep(letters, length.out = n))
# Add NAs?
has_na <- ((kk %% 2) == 0L)
if (has_na) {
cat("Adding NAs\n")
nna <- sample(n, size = 1)
na_values <- c(NA_real_, NaN)
t <- sample(na_values, size = nna, replace = TRUE)
x[sample(length(x), size = nna)] <- t
}
# Logical, integer, or double?
mode <- "numeric"
if ((kk %% 6) %in% 1:2) {
cat("Coercing to logical\n")
mode <- "logical"
} else if ((kk %% 6) %in% 3:4) {
cat("Coercing to integers\n")
mode <- "integer"
}
storage.mode(x) <- mode
str(x)
# rowQuantiles():
for (type in 1:9) {
cat(sprintf("type=%d, has_na=%s:\n", type, has_na))
# Test with and without dimnames on x
for (setDimnames in c(TRUE, FALSE)) {
if (setDimnames) dimnames(x) <- dimnames
else dimnames(x) <- NULL
# Check names attribute
for (useNames in c(TRUE, FALSE)) {
q0 <- rowQuantiles_R(x, probs = probs, na.rm = has_na, type = type, useNames = useNames)
q1 <- rowQuantiles(x, probs = probs, na.rm = has_na, type = type, useNames = useNames)
stopifnot(all.equal(q1, q0))
q2 <- colQuantiles(t(x), probs = probs, na.rm = has_na, type = type, useNames = useNames)
stopifnot(all.equal(q2, q0))
}
}
}
} # for (kk ...)
for (mode in c("logical", "integer", "double")) {
naValue <- NA_real_
storage.mode(naValue) <- mode
someValue <- 1
storage.mode(someValue) <- mode
for (type in 1:9) {
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# All NA
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
x <- matrix(naValue, nrow = 3L, ncol = 4L)
dimnames <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
# Test with and without dimnames on x
for (setDimnames in c(TRUE, FALSE)) {
if (setDimnames) dimnames(x) <- dimnames
else dimnames(x) <- NULL
# Check names attribute
for (useNames in c(TRUE, FALSE)) {
qr0 <- rowQuantiles_R(x, type = type, useNames = useNames)
qr <- rowQuantiles(x, type = type, useNames = useNames)
stopifnot(identical(qr, qr0))
# x <- matrix(naValue, nrow = 4L, ncol = 3L)
qc <- colQuantiles(t(x), type = type, useNames = useNames)
stopifnot(identical(qc, qr))
}
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Empty matrices
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
probs <- c(0, 0.25, 0.75, 1)
x <- matrix(naValue, nrow = 0L, ncol = 0L)
dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
q <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
stopifnot(identical(dim(q), c(nrow(x), length(probs))))
q <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
stopifnot(identical(dim(q), c(ncol(x), length(probs))))
x <- matrix(naValue, nrow = 2L, ncol = 0L)
dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
q <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
stopifnot(identical(dim(q), c(nrow(x), length(probs))))
x <- matrix(naValue, nrow = 0L, ncol = 2L)
dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
q <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
stopifnot(identical(dim(q), c(ncol(x), length(probs))))
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Single column matrices
# - - - - - - - - - - - - - - - - - - - - - - - - - - - -
probs <- c(0, 0.25, 0.75, 1)
x <- matrix(someValue, nrow = 2L, ncol = 1L)
dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
qr <- rowQuantiles(x, probs = probs, type = type, useNames = TRUE)
print(qr)
x <- matrix(someValue, nrow = 1L, ncol = 2L)
dimnames(x) <- lapply(dim(x), FUN = function(n) letters[seq_len(n)])
qc <- colQuantiles(x, probs = probs, type = type, useNames = TRUE)
print(qc)
stopifnot(identical(qc, qr))
}
}
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