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Solves #338 - assertions for safe_t_test #352

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munoztd0 merged 2 commits into from
May 28, 2026
+89 −100
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Solves #338 - assertions for safe_t_test #352

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614f2e6
assertions for safe_t_test()
wwojciech May 27, 2026
4dafbf4
refine assertions for safe_t_test() + update and add unit tests.
wwojciech May 27, 2026
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25 changes: 23 additions & 2 deletions R/safe_t_test.r
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,10 @@
#' observations) would otherwise stop execution.
#'
#' @details
#' Inputs `x` and `y` must be numeric vectors containing only finite,
#' non-missing values. In particular, `NA`, `NaN`, `Inf`, and `-Inf` values are
#' not allowed and will trigger an error before [stats::t.test()] is evaluated.
#'
#' When [stats::t.test()] succeeds, the resulting `"htest"` object is returned
#' unchanged except that `data.name` is reconstructed from the original
#' expressions supplied to `x` and `y`.
Expand All @@ -32,6 +36,10 @@
#' }
#'
#' @inheritParams stats::t.test
#' @param x (`numeric`)\cr A numeric vector containing only finite, non-missing
#' values.
#' @param y (`numeric`)\cr An optional numeric vector containing only finite,
#' non-missing values.
#'
#' @return
#' An object of class `"htest"`.
Expand Down Expand Up @@ -71,6 +79,19 @@ safe_t_test <- function(
x_expr <- substitute(x)
y_expr <- substitute(y)
alternative <- match.arg(alternative)

checkmate::assert_numeric(x, any.missing = FALSE, finite = TRUE)
if (paired) {
checkmate::assert_numeric(y, finite = TRUE, any.missing = FALSE, len = length(x))
} else {
checkmate::assert_numeric(y, finite = TRUE, any.missing = FALSE, null.ok = TRUE)
}
checkmate::assert_choice(alternative, choices = c("two.sided", "less", "greater"))
checkmate::assert_number(mu, finite = TRUE)
checkmate::assert_flag(paired)
checkmate::assert_flag(var.equal)
checkmate::assert_number(conf.level, lower = 0, upper = 1, finite = TRUE)

tryCatch(
{
res <- stats::t.test(
Expand Down Expand Up @@ -99,12 +120,12 @@ safe_t_test <- function(
}

if (is.null(y)) {
estimate <- c(mean(x, na.rm = TRUE))
estimate <- mean(x)
dname <- deparse1(x_expr)
method <- ifelse(paired, "Paired t-test", "One Sample t-test")
names(estimate) <- ifelse(paired, "mean difference", "mean of x")
} else {
estimate <- c(mean(x, na.rm = TRUE), mean(y, na.rm = TRUE))
estimate <- c(mean(x), mean(y))
dname <- paste(deparse1(x_expr), "and", deparse1(y_expr))
method <- paste(if (!var.equal) "Welch", "Two Sample t-test")
names(estimate) <- c("mean of x", "mean of y")
Expand Down
164 changes: 66 additions & 98 deletions tests/testthat/test-safe_t_test.r
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Original file line number Diff line number Diff line change
@@ -1,3 +1,14 @@
test_that("safe_t_test() preserves the argument order of t.test()", {
x <- c(41, 40, 13, 71, 3, 96)
y <- c(1, 50, 43, 76, 94, 77)

result <- expect_silent(
safe_t_test(x, y, "greater", 4, TRUE, TRUE, 0.5)
)
expected <- t.test(x, y, "greater", 4, TRUE, TRUE, 0.5)
expect_identical(result, expected)
})

test_that("safe_t_test() is identical to t.test() for regular data (x only)", {
# Intentionally named xx (not x) because we want to check whether
# safe_t_test() preserves the variable name
Expand Down Expand Up @@ -54,15 +65,9 @@ test_that("safe_t_test() is identical to t.test() for regular data", {
expect_identical(result_cl, expected_cl)
})

test_that("safe_t_test() preserves the argument order of t.test()", {
x <- c(41, 40, 13, 71, 3, 96)
y <- c(1, 50, 43, 76, 94, 77)

result <- expect_silent(
safe_t_test(x, y, "greater", 4, TRUE, TRUE, 0.5)
)
expected <- t.test(x, y, "greater", 4, TRUE, TRUE, 0.5)
expect_identical(result, expected)
test_that("safe_t_test() does not fail for nearly constant data", {
x <- c(1.709999999999999964473, rep(1.710000000000000186517, 4))
expect_silent(safe_t_test(x, x))
})

test_that("safe_t_test() returns NaN for constant data (paired)", {
Expand All @@ -83,19 +88,15 @@ test_that("safe_t_test() returns NaN for constant data (paired, var.equal)", {
expect_identical(result, expected)
})

test_that("safe_t_test() warns for constant paired samples of different lengths", {
x <- c(2, NA, NA, 2, 2, NA, 2)
y <- c(NA, 2, 2, 2, 2, NA)
expect_warning(
safe_t_test(x, y, paired = TRUE, conf.level = 0.5)
test_that("safe_t_test() fails for constant paired samples of different lengths", {
x <- rep(2, 6)
y <- c(x, 2)
expect_error(
safe_t_test(x, y, paired = TRUE, conf.level = 0.5),
"length"
)
})

test_that("safe_t_test() does not fail for nearly constant data", {
x <- c(1.709999999999999964473, rep(1.710000000000000186517, 4))
expect_silent(safe_t_test(x, x))
})

test_that("safe_t_test() returns NA for constant data (x only)", {
x <- rep(2, 5)
result <- expect_silent(
Expand Down Expand Up @@ -144,66 +145,6 @@ test_that("safe_t_test() returns NA for constant data", {
expect_identical(result, expected)
})

test_that("safe_t_test() returns NA for constant data (x only, many NAs)", {
x <- c(2, NA, NA, 2, 2, NA, 2)
result <- expect_silent(
safe_t_test(x, conf.level = 0.5)
)

expected <- list(
statistic = setNames(NA_real_, "t"),
parameter = setNames(NA_real_, "df"),
p.value = NA_real_,
conf.int = c(NA_real_, NA_real_),
estimate = setNames(2, "mean of x"),
null.value = setNames(0, "mean"),
stderr = NA_real_,
alternative = "two.sided",
method = "One Sample t-test (failed: data are essentially constant)",
data.name = "x"
)
attr(expected$conf.int, "conf.level") <- 0.5
class(expected) <- "htest"

expect_identical(result, expected)
})

test_that("safe_t_test() returns NA for constant data (many NAs)", {
x <- c(2, NA, NA, 2, 2, NA, 2)
y <- c(NA, 2, 2, 2, 2, NA)
result <- expect_silent(
safe_t_test(x, x, conf.level = 0.5)
)

expected <- list(
statistic = setNames(NA_real_, "t"),
parameter = setNames(NA_real_, "df"),
p.value = NA_real_,
conf.int = c(NA_real_, NA_real_),
estimate = setNames(c(2, 2), c("mean of x", "mean of y")),
null.value = setNames(0, "difference in means"),
stderr = NA_real_,
alternative = "two.sided",
method = "Welch Two Sample t-test (failed: data are essentially constant)",
data.name = "x and x"
)
attr(expected$conf.int, "conf.level") <- 0.5
class(expected) <- "htest"

expect_identical(result, expected)
})

test_that("safe_t_test() returns NaN for constant data (many NAs, paired)", {
x <- c(2, NA, NA, 2, 2, 2)
y <- c(NA, 2, 2, 2, 2, NA)
result <- expect_silent(
safe_t_test(x, y, paired = TRUE, conf.level = 0.5)
)

expected <- t.test(x, y, paired = TRUE, conf.level = 0.5)
expect_identical(result, expected)
})

test_that("safe_t_test() returns NA for constant data (var.equal)", {
x <- rep(2, 5)
result <- expect_silent(
Expand Down Expand Up @@ -303,27 +244,54 @@ test_that("safe_t_test() returns NA for not enough observations", {
expect_identical(result, expected)
})

test_that("safe_t_test() returns NA for not enough observations (NA)", {
test_that("safe_t_test() fails for NA", {
x <- c(1, 3, 5, 20, 31, NA, 23)
y <- c(11, 16, 19, 28, 7, 20, 21, 1)

expect_error(safe_t_test(x), "missing")
expect_error(safe_t_test(x, y), "missing")
expect_error(safe_t_test(x, y, paired = TRUE), "missing")
})

test_that("safe_t_test() fails for NA (1 non-NA obs.)", {
x <- c(1, NA, NA)
y <- c(2, NA, NA)
result <- expect_silent(
safe_t_test(x, y, var.equal = TRUE, conf.level = 0.5)
)

expected <- list(
statistic = setNames(NA_real_, "t"),
parameter = setNames(NA_real_, "df"),
p.value = NA_real_,
conf.int = c(NA_real_, NA_real_),
estimate = setNames(c(1, 2), c("mean of x", "mean of y")),
null.value = setNames(0, "difference in means"),
stderr = NA_real_,
alternative = "two.sided",
method = " Two Sample t-test (failed: not enough observations)",
data.name = "x and y"
)
attr(expected$conf.int, "conf.level") <- 0.5
class(expected) <- "htest"
expect_error(safe_t_test(x), "missing")
expect_error(safe_t_test(x, y), "missing")
expect_error(safe_t_test(x, y, paired = TRUE), "missing")
})

expect_identical(result, expected)
test_that("safe_t_test() fails for NA (constant data)", {
x <- c(2, NA, NA, 2, 2, NA, 2)
y <- c(NA, 2, 2, 2, 2, NA)

expect_error(safe_t_test(x), "missing")
expect_error(safe_t_test(x, y), "missing")
expect_error(safe_t_test(x, y, paired = TRUE), "missing")
})

test_that("safe_t_test() fails for NaN", {
x <- c(1, 3, 5, NaN, 31, 34, 23)
y <- c(11, 16, 32, 28, 7, 20, 21, 1)

expect_error(safe_t_test(x), "missing")
expect_error(safe_t_test(x, y), "missing")
expect_error(safe_t_test(x, y, paired = TRUE), "missing")
})

test_that("safe_t_test() fails for Inf", {
x <- c(1, 3, 5, 20, 31, Inf, 23)
y <- c(11, 16, 19, 28, 7, 20, 21, 1)

expect_error(safe_t_test(x), "finite")
expect_error(safe_t_test(x, y), "finite")
expect_error(safe_t_test(x, y, paired = TRUE), "finite")
})

test_that("safe_t_test() fails for paired data of different lengths", {
x <- c(1, 3, 5, 20, 31, 23)
y <- c(11, 16, 19, 28, 7, 20, 21, 1)

expect_error(safe_t_test(x, y, paired = TRUE), "length")
})