Adding ard_chisqtest()

NAMESPACE

@@ -3,6 +3,7 @@
 export("%>%")
 export(all_of)
 export(any_of)
+export(ard_chisqtest)
 export(ard_paired_ttest)
 export(ard_paired_wilcoxtest)
 export(ard_ttest)

R/ard_chisqtest.R

@@ -0,0 +1,57 @@
+#' ARD Chi-squared Test
+#'
+#' @description
+#' Analysis results data for Pearson's Chi-squared Test.
+#' Calculated with `chisq.test(x = data[[variable]], y = data[[by]], ...)`
+#'
+#'
+#' @param data (`data.frame`)\cr
+#'   a data frame.
+#' @param by,variable ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column names to compare
+#' @param ... additional arguments passed to `fisher.test(...)`
+#'
+#' @return ARD data frame
+#' @export
+#'
+#' @examples
+#' cards::ADSL |>
+#'   ard_chisqtest(by = "ARM", variable = "AGEGR1")
+ard_chisqtest <- function(data, by, variable, ...) {
+  # check installed packages ---------------------------------------------------
+  cards::check_pkg_installed("broom.helpers", reference_pkg = "cards")
+
+  # check/process inputs -------------------------------------------------------
+  check_not_missing(data)
+  check_not_missing(variable)
+  check_not_missing(by)
+  check_class_data_frame(x = data)
+  cards::process_selectors(data, by = {{ by }}, variable = {{ variable }})
+  check_scalar(by)
+  check_scalar(variable)
+
+  # build ARD ------------------------------------------------------------------
+  cards::tidy_as_ard(
+    lst_tidy =
+      cards::eval_capture_conditions(
+        stats::chisq.test(x = data[[variable]], y = data[[by]], ...) |>
+          broom::tidy()
+      ),
+    tidy_result_names = c("statistic", "p.value", "parameter", "method"),
+    fun_args_to_record =
+      c("correct", "p", "rescale.p", "simulate.p.value", "B"),
+    formals = formals(stats::chisq.test),
+    passed_args = dots_list(...),
+    lst_ard_columns = list(group1 = by, variable = variable, context = "chisqtest")
+  ) |>
+    dplyr::mutate(
+      .after = "stat_name",
+      stat_label =
+        dplyr::case_when(
+          .data$stat_name %in% "statistic" ~ "X-squared Statistic",
+          .data$stat_name %in% "p.value" ~ "p-value",
+          .data$stat_name %in% "parameter" ~ "Degrees of Freedom",
+          TRUE ~ .data$stat_name,
+        )
+    )
+}

_pkgdown.yml

@@ -25,4 +25,5 @@ reference:
   - subtitle: "Inference"
   - contents:
       - ard_ttest
+      - ard_chisqtest
       - ard_wilcoxtest

tests/testthat/_snaps/ard_chisqtest.md

@@ -0,0 +1,17 @@
+# shuffle_ard fills missing group levels if the group is meaningful
+
+    Code
+      as.data.frame(cards::shuffle_ard(cards::bind_ard(ard_chisqtest(data = adsl_sub,
+        by = "ARM", variable = "AGEGR1"), ard_chisqtest(data = adsl_sub, by = "SEX",
+        variable = "AGEGR1"))))
+    Output
+                ARM         SEX variable   context stat_name    statistic
+      1 Overall ARM        <NA>   AGEGR1 chisqtest statistic 5.079442e+00
+      2 Overall ARM        <NA>   AGEGR1 chisqtest   p.value 7.888842e-02
+      3 Overall ARM        <NA>   AGEGR1 chisqtest parameter 2.000000e+00
+      4 Overall ARM        <NA>   AGEGR1 chisqtest         B 2.000000e+03
+      5        <NA> Overall SEX   AGEGR1 chisqtest statistic 1.039442e+00
+      6        <NA> Overall SEX   AGEGR1 chisqtest   p.value 5.946864e-01
+      7        <NA> Overall SEX   AGEGR1 chisqtest parameter 2.000000e+00
+      8        <NA> Overall SEX   AGEGR1 chisqtest         B 2.000000e+03
+

tests/testthat/test-ard_chisqtest.R

@@ -0,0 +1,39 @@
+test_that("ard_chisqtest() works", {
+  expect_error(
+    ard_chisqtest <-
+      cards::ADSL |>
+      ard_chisqtest(by = ARM, variable = AGEGR1),
+    NA
+  )
+
+  expect_equal(
+    ard_chisqtest |>
+      cards::get_ard_statistics(stat_name %in% c("statistic", "p.value")),
+    with(cards::ADSL, chisq.test(AGEGR1, ARM)) |>
+      broom::tidy() |>
+      dplyr::select(statistic, p.value) |>
+      unclass(),
+    ignore_attr = TRUE
+  )
+})
+
+test_that("shuffle_ard fills missing group levels if the group is meaningful", {
+  adsl_sub <- cards::ADSL |> dplyr::filter(ARM %in% unique(ARM)[1:2])
+
+  expect_snapshot(
+    cards::bind_ard(
+      ard_chisqtest(
+        data = adsl_sub,
+        by = "ARM",
+        variable = "AGEGR1"
+      ),
+      ard_chisqtest(
+        data = adsl_sub,
+        by = "SEX",
+        variable = "AGEGR1"
+      )
+    ) |>
+      cards::shuffle_ard() |>
+      as.data.frame()
+  )
+})