Adding one-sample CI functions (#156)

**What changes are proposed in this pull request?**
- `ard_stats_wilcox_test_onesample()` for calculating one-sample
results.
  - `ard_stats_t_test_onesample()` for calculating one-sample results.
 


--------------------------------------------------------------------------------

Pre-review Checklist (if item does not apply, mark is as complete)
- [x] **All** GitHub Action workflows pass with a ✅
- [x] PR branch has pulled the most recent updates from master branch:
`usethis::pr_merge_main()`
- [x] If a bug was fixed, a unit test was added.
- [x] If a new `ard_*()` function was added, it passes the ARD
structural checks from `cards::check_ard_structure()`.
- [x] If a new `ard_*()` function was added, `set_cli_abort_call()` has
been set.
- [x] If a new `ard_*()` function was added and it depends on another
package (such as, `broom`), `is_pkg_installed("broom", reference_pkg =
"cardx")` has been set in the function call and the following added to
the roxygen comments: `@examplesIf
do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom"",
reference_pkg = "cardx"))`
- [x] Code coverage is suitable for any new functions/features
(generally, 100% coverage for new code): `devtools::test_coverage()`

Reviewer Checklist (if item does not apply, mark is as complete)

- [x] If a bug was fixed, a unit test was added.
- [x] Code coverage is suitable for any new functions/features:
`devtools::test_coverage()`

When the branch is ready to be merged:
- [x] Update `NEWS.md` with the changes from this pull request under the
heading "`# cardx (development version)`". If there is an issue
associated with the pull request, reference it in parentheses at the end
update (see `NEWS.md` for examples).
- [x] **All** GitHub Action workflows pass with a ✅
- [x] Approve Pull Request
- [x] Merge the PR. Please use "Squash and merge" or "Rebase and merge".

NAMESPACE

@@ -40,7 +40,9 @@ export(ard_stats_paired_t_test)
 export(ard_stats_paired_wilcox_test)
 export(ard_stats_prop_test)
 export(ard_stats_t_test)
+export(ard_stats_t_test_onesample)
 export(ard_stats_wilcox_test)
+export(ard_stats_wilcox_test_onesample)
 export(ard_survey_svychisq)
 export(ard_survey_svyranktest)
 export(ard_survey_svyttest)

NEWS.md

@@ -37,6 +37,8 @@ ard_moodtest()          -> ard_stats_mood_test()
   - `ard_survey_svyranktest()` for weighted/survey rank tests using `survey::svyranktest()`. (#71)
   - `ard_car_vif()` for calculating the variance inflation factor using `car::vif()`. (#10)
   - `ard_emmeans_mean_difference()` for calculating the least-squares mean differences using the {emmeans} package. (#34)
+  - `ard_stats_wilcox_test_onesample()` for calculating one-sample results.
+  - `ard_stats_t_test_onesample()` for calculating one-sample results.
 
 * Updated functions `ard_stats_t_test()`, `ard_stats_paired_t_test()`, `ard_stats_wilcox_test()`, `ard_stats_paired_wilcox_test()`, `ard_stats_chisq_test()`, `ard_stats_fisher_test()`, `ard_stats_kruskal_test()`, `ard_stats_mcnemar_test()`, and `ard_stats_mood_test()` to accept multiple variables at once. Independent tests are calculated for each variable. The `variable` argument is renamed to `variables`. (#77)
 

R/ard_stats_t_test_onesample.R

@@ -0,0 +1,71 @@
+#' ARD one-sample t-test
+#'
+#' @description
+#' Analysis results data for one-sample t-tests.
+#' Result may be stratified by including the `by` argument.
+#'
+#' @param data (`data.frame`)\cr
+#'   a data frame. See below for details.
+#' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column names to be analyzed. Independent t-tests will be computed for
+#'   each variable.
+#' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   optional column name to stratify results by.
+#' @inheritParams ard_stats_t_test
+#'
+#' @return ARD data frame
+#' @export
+#'
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
+#' cards::ADSL |>
+#'   ard_stats_t_test_onesample(by = ARM, variables = AGE)
+ard_stats_t_test_onesample <- function(data, variables, by = dplyr::group_vars(data), conf.level = 0.95, ...) {
+  set_cli_abort_call()
+
+  # check installed packages ---------------------------------------------------
+  check_pkg_installed("broom", reference_pkg = "cardx")
+
+  # check/process inputs -------------------------------------------------------
+  check_not_missing(data)
+  check_not_missing(variables)
+  check_data_frame(data)
+  data <- dplyr::ungroup(data)
+  cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
+  check_scalar_range(conf.level, range = c(0, 1))
+
+  # if no variables selected, return empty tibble ------------------------------
+  if (is_empty(variables)) {
+    return(dplyr::tibble())
+  }
+
+  cards::ard_continuous(
+    data = data,
+    variables = all_of(variables),
+    by = all_of(by),
+    statistic = all_of(variables) ~ list(t_test_onesample = \(x) stats::t.test(x = x, conf.level = conf.level, ...) |> broom::tidy())
+  ) |>
+    cards::bind_ard(
+      cards::ard_continuous(
+        data = data,
+        variables = all_of(variables),
+        by = all_of(by),
+        statistic =
+          all_of(variables) ~
+            list(conf.level = \(x) {
+              formals(asNamespace("stats")[["t.test.default"]])["mu"] |>
+                utils::modifyList(list(conf.level = conf.level, ...))
+            })
+      )
+    ) |>
+    dplyr::select(-"stat_label") |>
+    dplyr::left_join(
+      .df_ttest_stat_labels(by = NULL),
+      by = "stat_name"
+    ) |>
+    dplyr::mutate(
+      stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name),
+      context = "ard_stats_t_test_onesample",
+    ) |>
+    cards::tidy_ard_row_order() |>
+    cards::tidy_ard_column_order()
+}

R/ard_stats_wilcox_test_onesample.R

@@ -0,0 +1,72 @@
+#' ARD one-sample Wilcox Rank-sum
+#'
+#' @description
+#' Analysis results data for one-sample Wilcox Rank-sum.
+#' Result may be stratified by including the `by` argument.
+#'
+#' @param data (`data.frame`)\cr
+#'   a data frame. See below for details.
+#' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   column names to be analyzed. Independent Wilcox Rank-sum tests will be computed for
+#'   each variable.
+#' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
+#'   optional column name to stratify results by.
+#' @inheritParams ard_stats_wilcox_test
+#'
+#' @return ARD data frame
+#' @export
+#'
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
+#' cards::ADSL |>
+#'   ard_stats_wilcox_test_onesample(by = ARM, variables = AGE)
+ard_stats_wilcox_test_onesample <- function(data, variables, by = dplyr::group_vars(data), conf.level = 0.95, ...) {
+  set_cli_abort_call()
+
+  # check installed packages ---------------------------------------------------
+  check_pkg_installed("broom", reference_pkg = "cardx")
+
+  # check/process inputs -------------------------------------------------------
+  check_not_missing(data)
+  check_not_missing(variables)
+  check_data_frame(data)
+  data <- dplyr::ungroup(data)
+  cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
+  check_scalar_range(conf.level, range = c(0, 1))
+
+  # if no variables selected, return empty tibble ------------------------------
+  if (is_empty(variables)) {
+    return(dplyr::tibble())
+  }
+
+  cards::ard_continuous(
+    data = data,
+    variables = all_of(variables),
+    by = all_of(by),
+    statistic = all_of(variables) ~ list(t_test_onesample = \(x) stats::wilcox.test(x = x, conf.level = conf.level, ...) |> broom::tidy())
+  ) |>
+    cards::bind_ard(
+      cards::ard_continuous(
+        data = data,
+        variables = all_of(variables),
+        by = all_of(by),
+        statistic =
+          all_of(variables) ~
+            list(conf.level = \(x) {
+              formals(asNamespace("stats")[["wilcox.test.default"]])[c("mu", "exact", "conf.int", "tol.root", "digits.rank")] |>
+                utils::modifyList(list(conf.level = conf.level, ...)) |>
+                compact()
+            })
+      )
+    ) |>
+    dplyr::select(-"stat_label") |>
+    dplyr::left_join(
+      .df_ttest_stat_labels(by = NULL),
+      by = "stat_name"
+    ) |>
+    dplyr::mutate(
+      stat_label = dplyr::coalesce(.data$stat_label, .data$stat_name),
+      context = "ard_stats_wilcox_test_onesample",
+    ) |>
+    cards::tidy_ard_row_order() |>
+    cards::tidy_ard_column_order()
+}

README.Rmd

@@ -5,7 +5,7 @@ editor_options:
     wrap: 72
 ---
 
-# cardx <a href="https://insightsengineering.github.io/cardx"><img src="man/figures/logo.png" alt="cardx website" align="right" height="138"/></a>
+# cardx <a href="https://insightsengineering.github.io/cardx/"><img src="man/figures/logo.png" alt="cardx website" align="right" height="138"/></a>
 
 [![R-CMD-check](https://github.com/insightsengineering/cardx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/insightsengineering/cardx/actions/workflows/R-CMD-check.yaml)
 [![Codecov test

README.md

@@ -1,5 +1,5 @@
 
-# cardx <a href="https://insightsengineering.github.io/cardx"><img src="man/figures/logo.png" alt="cardx website" align="right" height="138"/></a>
+# cardx <a href="https://insightsengineering.github.io/cardx/"><img src="man/figures/logo.png" alt="cardx website" align="right" height="138"/></a>
 
 [![R-CMD-check](https://github.com/insightsengineering/cardx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/insightsengineering/cardx/actions/workflows/R-CMD-check.yaml)
 [![Codecov test

_pkgdown.yml

@@ -34,7 +34,9 @@ reference:
       - ard_stats_oneway_test
       - ard_stats_prop_test
       - ard_stats_t_test
+      - ard_stats_t_test_onesample
       - ard_stats_wilcox_test
+      - ard_stats_wilcox_test_onesample
 
   - subtitle: "{aod} package"
   - contents:

tests/testthat/test-ard_stats_t_test_onesample.R

@@ -0,0 +1,50 @@
+skip_if_not(is_pkg_installed("broom", reference_pkg = "cardx"))
+
+test_that("ard_stats_t_test_onesample() works", {
+  # first calculate an object to test against
+  expect_silent(
+    ard1 <- ard_stats_t_test_onesample(
+      cards::ADSL,
+      variables = AGE,
+      by = ARM,
+      conf.level = 0.9,
+      mu = 1
+    )
+  )
+
+  # first check arguments passed and returned correctly
+  expect_equal(
+    cards::get_ard_statistics(
+      ard1,
+      group1_level %in% "Placebo"
+    )[c("mu", "conf.level")],
+    list(mu = 1, conf.level = 0.9)
+  )
+  # check results are correct
+  expect_equal(
+    cards::get_ard_statistics(
+      ard1,
+      group1_level %in% "Placebo"
+    )[c("estimate", "conf.low", "conf.high", "p.value")],
+    t.test(
+      cards::ADSL$AGE[cards::ADSL$ARM == "Placebo"],
+      conf.level = 0.9,
+      mu = 1
+    ) |>
+      broom::tidy() |>
+      dplyr::select(c("estimate", "conf.low", "conf.high", "p.value")) |>
+      as.list()
+  )
+
+  # test the structure is good
+  expect_silent(cards::check_ard_structure(ard1))
+
+  # empty tibble returned with no variables
+  expect_equal(
+    ard_stats_t_test_onesample(
+      cards::ADSL,
+      variables = character(0)
+    ),
+    dplyr::tibble()
+  )
+})

tests/testthat/test-ard_stats_wilcox_test_onesample.R

@@ -0,0 +1,52 @@
+skip_if_not(is_pkg_installed("broom", reference_pkg = "cardx"))
+
+test_that("ard_stats_wilcox_test_onesample() works", {
+  # first calculate an object to test against
+  expect_silent(
+    ard1 <- ard_stats_wilcox_test_onesample(
+      cards::ADSL,
+      variables = AGE,
+      by = ARM,
+      conf.level = 0.9,
+      conf.int = TRUE,
+      mu = 1
+    )
+  )
+
+  # first check arguments passed and returned correctly
+  expect_equal(
+    cards::get_ard_statistics(
+      ard1,
+      group1_level %in% "Placebo"
+    )[c("mu", "conf.level")],
+    list(mu = 1, conf.level = 0.9)
+  )
+  # check results are correct
+  expect_equal(
+    cards::get_ard_statistics(
+      ard1,
+      group1_level %in% "Placebo"
+    )[c("estimate", "conf.low", "conf.high", "p.value")],
+    wilcox.test(
+      cards::ADSL$AGE[cards::ADSL$ARM == "Placebo"],
+      conf.level = 0.9,
+      mu = 1,
+      conf.int = TRUE
+    ) |>
+      broom::tidy() |>
+      dplyr::select(c("estimate", "conf.low", "conf.high", "p.value")) |>
+      as.list()
+  )
+
+  # test the structure is good
+  expect_silent(cards::check_ard_structure(ard1))
+
+  # empty tibble returned with no variables
+  expect_equal(
+    ard_stats_wilcox_test_onesample(
+      cards::ADSL,
+      variables = character(0)
+    ),
+    dplyr::tibble()
+  )
+})