Adding Wilcoxon Rank-Sum Tests

NAMESPACE

@@ -4,7 +4,9 @@ export("%>%")
 export(all_of)
 export(any_of)
 export(ard_paired_ttest)
+export(ard_paired_wilcoxtest)
 export(ard_ttest)
+export(ard_wilcoxtest)
 export(contains)
 export(ends_with)
 export(everything)

R/ard_wilcoxtest.R

@@ -0,0 +1,201 @@
+#' ARD Wilcoxon Rank-Sum Test
+#'
+#' @description
+#' Analysis results data for paired and non-paired Wilcoxon Rank-Sum tests.
+#'
+#' @param data (`data.frame`)\cr
+#'   a data frame. See below for details.
+#' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column name to compare by
+#' @param variable ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column name to be compared
+#' @param id ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column name of the subject or participant ID
+#' @param ... arguments passed to `wilcox.test(...)`
+#'
+#' @return ARD data frame
+#' @name ard_wilcoxtest
+#'
+#' @details
+#' For the `ard_wilcoxtest()` function, the data is expected to be one row per subject.
+#' The data is passed as `wilcox.test(data[[variable]] ~ data[[by]], paired = FALSE, ...)`.
+#'
+#' For the `ard_paired_wilcoxtest()` function, the data is expected to be one row
+#' per subject per by level. Before the t-test is calculated, the data are
+#' reshaped to a wide format to be one row per subject.
+#' The data are then passed as
+#' `wilcox.test(x = data_wide[[<by level 1>]], y = data_wide[[<by level 2>]], paired = TRUE, ...)`.
+#'
+#' @examples
+#' cards::ADSL |>
+#'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
+#'   ard_wilcoxtest(by = "ARM", variable = "AGE")
+#'
+#' # constructing a paired data set,
+#' # where patients receive both treatments
+#' cards::ADSL[c("ARM", "AGE")] |>
+#'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
+#'   dplyr::mutate(.by = ARM, USUBJID = dplyr::row_number()) |>
+#'   dplyr::arrange(USUBJID, ARM) |>
+#'   ard_paired_wilcoxtest(by = ARM, variable = AGE, id = USUBJID)
+NULL
+
+#' @rdname ard_wilcoxtest
+#' @export
+ard_wilcoxtest <- function(data, by, variable, ...) {
+  # check installed packages ---------------------------------------------------
+  cards::check_pkg_installed("broom", reference_pkg = "cardx")
+
+  # check/process inputs -------------------------------------------------------
+  check_not_missing(data)
+  check_not_missing(variable)
+  check_not_missing(by)
+  check_class_data_frame(x = data)
+  data <- dplyr::ungroup(data)
+  cards::process_selectors(data, by = {{ by }}, variable = {{ variable }})
+  check_scalar(by)
+  check_scalar(variable)
+
+  # build ARD ------------------------------------------------------------------
+  .format_wilcoxtest_results(
+    by = by,
+    variable = variable,
+    lst_tidy =
+      cards::eval_capture_conditions(
+        stats::wilcox.test(data[[variable]] ~ data[[by]], paired = FALSE, ...) |>
+          broom::tidy()
+      ),
+    paired = FALSE,
+    ...
+  )
+}
+
+#' @rdname ard_wilcoxtest
+#' @export
+ard_paired_wilcoxtest <- function(data, by, variable, id, ...) {
+  # check installed packages ---------------------------------------------------
+  cards::check_pkg_installed("broom", reference_pkg = "cardx")
+
+  # check/process inputs -------------------------------------------------------
+  check_not_missing(data)
+  check_not_missing(variable)
+  check_not_missing(by)
+  check_not_missing(id)
+  check_class_data_frame(x = data)
+  data <- dplyr::ungroup(data)
+  cards::process_selectors(data, by = {{ by }}, variable = {{ variable }}, id = {{ id }})
+  check_scalar(by)
+  check_scalar(variable)
+  check_scalar(id)
+
+  # build ARD ------------------------------------------------------------------
+  .format_wilcoxtest_results(
+    by = by,
+    variable = variable,
+    lst_tidy =
+      cards::eval_capture_conditions({
+        # adding this reshape inside the eval, so if there is an error it's captured in the ARD object
+        data_wide <- .paired_data_pivot_wider(data, by = by, variable = variable, id = id)
+        # perform paried t-test
+        stats::wilcox.test(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ...) |>
+          broom::tidy()
+      }),
+    paired = TRUE,
+    ...
+  )
+}
+
+#' Convert t-test to ARD
+#'
+#' @inheritParams cards::tidy_as_ard
+#' @inheritParams stats::wilcox.test
+#' @param by (`string`)\cr by column name
+#' @param variable (`string`)\cr variable column name
+#' @param ... passed to `wilcox.test(...)`
+#'
+#' @return ARD data frame
+#' @keywords internal
+#' @examples
+#' cardx:::.format_wilcoxtest_results(
+#'   by = "ARM",
+#'   variable = "AGE",
+#'   paired = FALSE,
+#'   lst_tidy =
+#'     cards::eval_capture_conditions(
+#'       stats::wilcox.test(ADSL[["AGE"]] ~ ADSL[["ARM"]], paired = FALSE) |>
+#'         broom::tidy()
+#'     )
+#' )
+.format_wilcoxtest_results <- function(by, variable, lst_tidy, paired, ...) {
+  # build ARD ------------------------------------------------------------------
+  ret <-
+    cards::tidy_as_ard(
+      lst_tidy = lst_tidy,
+      tidy_result_names = c("statistic", "p.value", "method", "alternative"),
+      fun_args_to_record = c(
+        "mu", "paired", "exact", "correct", "conf.int",
+        "conf.level", "tol.root", "digits.rank"
+      ),
+      formals = formals(asNamespace("stats")[["wilcox.test.default"]]),
+      passed_args = c(list(paired = paired), dots_list(...)),
+      lst_ard_columns = list(group1 = by, variable = variable, context = "ttest")
+    )
+
+  # add the stat label ---------------------------------------------------------
+  ret |>
+    dplyr::left_join(
+      .df_wilcoxtest_stat_labels(),
+      by = "stat_name"
+    ) |>
+    dplyr::mutate(stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name)) |>
+    cards::tidy_ard_column_order()
+}
+
+
+#' Convert long paired data to wide
+#'
+#'
+#' @param data (`data.frame`)\cr a data frame that is one line per subject per group
+#' @param by (`string`)\cr by column name
+#' @param variable (`string`)\cr variable column name
+#' @param id (`string`)\cr subject id column name
+#' @param env (`environment`) used for error messaging. Default is `rlang::caller_env()`
+#'
+#' @return a wide data frame
+#' @keywords internal
+#' @examples
+#' cards::ADSL[c("ARM", "AGE")] |>
+#'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
+#'   dplyr::mutate(.by = ARM, USUBJID = dplyr::row_number()) |>
+#'   dplyr::arrange(USUBJID, ARM) |>
+#'   cardx:::.paired_data_pivot_wider(by = "ARM", variable = "AGE", id = "USUBJID")
+.paired_data_pivot_wider <- function(data, by, variable, id, env = rlang::caller_env()) {
+  # check the number of levels before pivoting data to wider format
+  if (dplyr::n_distinct(data[[by]], na.rm = TRUE) != 2L) {
+    cli::cli_abort("The {.arg by} argument must have two and only two levels.", call = env)
+  }
+
+  data |>
+    # arrange data so the first group always appears first
+    dplyr::arrange(.data[[by]]) |>
+    tidyr::pivot_wider(
+      id_cols = all_of(id),
+      names_from = all_of(by),
+      values_from = all_of(variable)
+    ) |>
+    stats::setNames(c(id, "by1", "by2"))
+}
+
+.df_wilcoxtest_stat_labels <- function() {
+  dplyr::tribble(
+    ~stat_name, ~stat_label,
+    "statistic", "X-squared Statistic",
+    "parameter", "Degrees of Freedom",
+    "estimate", "Median of the Difference",
+    "p.value", "p-value",
+    "conf.low", "CI Lower Bound",
+    "conf.high", "CI Upper Bound",
+    "paired", "Paired test",
+    "conf.level", "CI Confidence Level",
+  )
+}

_pkgdown.yml

@@ -25,3 +25,4 @@ reference:
   - subtitle: "Inference"
   - contents:
       - ard_ttest
+      - ard_wilcoxtest