add ard_aov and ard_onewaytest

NAMESPACE

@@ -3,6 +3,8 @@
 export("%>%")
 export(all_of)
 export(any_of)
+export(ard_aov)
+export(ard_onewaytest)
 export(ard_paired_ttest)
 export(ard_ttest)
 export(contains)

R/ard_aov.R

@@ -0,0 +1,60 @@
+#' ARD ANOVA
+#'
+#' @description
+#' Analysis results data for Analysis of Variance.
+#' Calculated with `aov(data[[variable]] ~ as.factor(data[[by]]), data = data, ...)`
+#'
+#' @param data (`data.frame`)\cr
+#'   a data frame.
+#' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column name to compare by. Should be a factor variable.
+#' @param variable ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column name to be compared. Should be a continuous variable.
+#'
+#' @return ARD data frame
+#' @export
+#'
+#' @examples
+#' cards::ADSL |>
+#'   ard_aov(by = "ARM", variable = "AGE")
+ard_aov <- 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)
+  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::aov(stats::reformulate(by, response = variable), data = data) |>
+          broom::tidy() |>
+          dplyr::slice_head()
+      ),
+    tidy_result_names = c("term", "df", "sumsq", "meansq", "statistic", "p.value"),
+    fun_args_to_record =
+      c("formula"),
+    formals = formals(stats::aov),
+    lst_ard_columns = list(group1 = by, variable = variable, context = "aov")
+  ) |>
+    dplyr::mutate(
+      .after = "stat_name",
+      stat_label =
+        dplyr::case_when(
+          .data$stat_name %in% "term" ~ "Term",
+          .data$stat_name %in% "sumsq" ~ "Sum of Squares",
+          .data$stat_name %in% "meansq" ~ "Mean of Sum of Squares",
+          .data$stat_name %in% "statistic" ~ "F Statistic",
+          .data$stat_name %in% "p.value" ~ "p-value",
+          .data$stat_name %in% "df" ~ "Degrees of Freedom",
+          TRUE ~ .data$stat_name,
+        )
+    )
+}

R/ard_onewaytest.R

@@ -0,0 +1,60 @@
+#' ARD One-way Test
+#'
+#' @description
+#' Analysis results data for Testing Equal Means in a One-Way Layout.
+#' Calculated with `oneway.test(data[[variable]] ~ as.factor(data[[by]]), data = data, ...)`
+#'
+#' @param data (`data.frame`)\cr
+#'   a data frame
+#' @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 ... additional arguments passed to `oneway.test(...)`
+#'
+#' @return ARD data frame
+#' @export
+#'
+#' @examples
+#' cards::ADSL |>
+#'   ard_onewaytest(by = "ARM", variable = "AGE")
+ard_onewaytest <- 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)
+  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::oneway.test(stats::reformulate(by, response = variable), data = data) |>
+          broom::tidy()
+      ),
+    tidy_result_names = c("num.df", "den.df", "statistic", "p.value", "method"),
+    fun_args_to_record =
+      c("var.equal"),
+    formals = formals(stats::oneway.test),
+    passed_args = dots_list(...),
+    lst_ard_columns = list(group1 = by, variable = variable, context = "Oneway.test")
+  ) |>
+    dplyr::mutate(
+      .after = "stat_name",
+      stat_label =
+        dplyr::case_when(
+          .data$stat_name %in% "num.df" ~ "Degrees of Freedom",
+          .data$stat_name %in% "den.df" ~ "Denominator Degrees of Freedom",
+          .data$stat_name %in% "statistic" ~ "F Statistic",
+          .data$stat_name %in% "p.value" ~ "p-value",
+          .data$stat_name %in% "method" ~ "Method",
+          TRUE ~ .data$stat_name,
+        )
+    )
+}

_pkgdown.yml

@@ -24,4 +24,7 @@ reference:
   - title: "ARD Creation"
   - subtitle: "Inference"
   - contents:
+      - ard_aov
+      - ard_onewaytest
       - ard_ttest
+

tests/testthat/_snaps/ard_aov.md

@@ -0,0 +1,15 @@
+# ard_aov() works
+
+    Code
+      as.data.frame(dplyr::select(ard_aov(cards::ADSL, by = ARM, variable = AGEGR1),
+      c("group1", "variable", "stat_name", "error")))
+    Output
+        group1 variable stat_name             error
+      1    ARM   AGEGR1      term NA/NaN/Inf in 'y'
+      2    ARM   AGEGR1        df NA/NaN/Inf in 'y'
+      3    ARM   AGEGR1     sumsq NA/NaN/Inf in 'y'
+      4    ARM   AGEGR1    meansq NA/NaN/Inf in 'y'
+      5    ARM   AGEGR1 statistic NA/NaN/Inf in 'y'
+      6    ARM   AGEGR1   p.value NA/NaN/Inf in 'y'
+      7    ARM   AGEGR1   formula NA/NaN/Inf in 'y'
+

tests/testthat/_snaps/ard_onewaytest.md

@@ -0,0 +1,14 @@
+# ard_onewaytest() works
+
+    Code
+      as.data.frame(dplyr::select(ard_onewaytest(cards::ADSL, by = ARM, variable = AGEGR1),
+      c("group1", "variable", "stat_name", "error")))
+    Output
+        group1 variable stat_name error
+      1    ARM   AGEGR1    num.df  NULL
+      2    ARM   AGEGR1    den.df  NULL
+      3    ARM   AGEGR1 statistic  NULL
+      4    ARM   AGEGR1   p.value  NULL
+      5    ARM   AGEGR1    method  NULL
+      6    ARM   AGEGR1 var.equal  NULL
+

tests/testthat/test-ard_aov.R

@@ -0,0 +1,30 @@
+test_that("ard_aov() works", {
+  expect_error(
+    ard_aov <-
+      cards::ADSL |>
+      ard_aov(by = ARM, variable = AGE),
+    NA
+  )
+
+  expect_equal(
+    ard_aov |>
+      cards::get_ard_statistics(stat_name %in% c("term", "sumsq", "statistic")),
+    aov(
+      AGE ~ ARM,
+      data = cards::ADSL
+    ) |>
+      broom::tidy() |>
+      dplyr::slice_head() |>
+      dplyr::select(term, sumsq, statistic) |>
+      unclass(),
+    ignore_attr = TRUE
+  )
+
+  # errors are properly handled - "variable" should be continuous, not factor
+  expect_snapshot(
+    cards::ADSL |>
+      ard_aov(by = ARM, variable = AGEGR1) |>
+      dplyr::select(c("group1", "variable", "stat_name", "error")) |>
+      as.data.frame()
+  )
+})

tests/testthat/test-ard_onewaytest.R

@@ -0,0 +1,29 @@
+test_that("ard_onewaytest() works", {
+  expect_error(
+    ard_onewaytest <-
+      cards::ADSL |>
+      ard_onewaytest(by = ARM, variable = AGE),
+    NA
+  )
+
+  expect_equal(
+    ard_onewaytest |>
+      cards::get_ard_statistics(stat_name %in% c("num.df", "statistic", "method")),
+    oneway.test(
+      AGE ~ ARM,
+      data = cards::ADSL
+    ) |>
+      broom::tidy() |>
+      dplyr::select(num.df, statistic, method) |>
+      unclass(),
+    ignore_attr = TRUE
+  )
+
+  # errors are properly handled - "variable" should be continuous, not factor
+  expect_snapshot(
+    cards::ADSL |>
+      ard_onewaytest(by = ARM, variable = AGEGR1) |>
+      dplyr::select(c("group1", "variable", "stat_name", "error")) |>
+      as.data.frame()
+  )
+})