From 90f2c230d70e15d129f0adc82ee024f2ac9eb41b Mon Sep 17 00:00:00 2001
From: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Date: Mon, 15 Apr 2024 18:28:04 -0400
Subject: [PATCH] Add `@examplesIf` to internal examples where applicable
 (#120)

**What changes are proposed in this pull request?**
* Added `@examplesIf` to applicable internal function examples. (#118,
@edelarua)

Closes #118


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

Pre-review Checklist (if item does not apply, mark is as complete)
- [x] **All** GitHub Action workflows pass with a :white_check_mark:
- [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] 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)

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

When the branch is ready to be merged:
- [ ] 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).
- [ ] **All** GitHub Action workflows pass with a :white_check_mark:
- [ ] Approve Pull Request
- [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".
---
 R/ard_aod_wald_test.R                 | 2 --
 R/ard_effectsize_cohens_d.R           | 2 +-
 R/ard_effectsize_hedges_g.R           | 2 +-
 R/ard_stats_mcnemar_test.R            | 2 +-
 R/ard_stats_mood_test.R               | 2 +-
 R/ard_stats_t_test.R                  | 2 +-
 R/ard_stats_wilcox_test.R             | 2 +-
 R/ard_survival_survfit.R              | 6 +++---
 R/proportion_ci.R                     | 1 +
 man/dot-format_cohens_d_results.Rd    | 2 ++
 man/dot-format_hedges_g_results.Rd    | 2 ++
 man/dot-format_mcnemartest_results.Rd | 3 ++-
 man/dot-format_moodtest_results.Rd    | 2 ++
 man/dot-format_survfit_results.Rd     | 3 ++-
 man/dot-format_ttest_results.Rd       | 2 ++
 man/dot-format_wilcoxtest_results.Rd  | 3 ++-
 man/dot-process_survfit_probs.Rd      | 3 ++-
 man/dot-process_survfit_time.Rd       | 3 ++-
 18 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/R/ard_aod_wald_test.R b/R/ard_aod_wald_test.R
index 6e068c82c..ec87532ab 100644
--- a/R/ard_aod_wald_test.R
+++ b/R/ard_aod_wald_test.R
@@ -104,12 +104,10 @@ ard_aod_wald_test <- function(x, ...) {
 
 #' Extract data from wald.test object
 #'
-#'
 #' @param wald_test (`data.frame`)\cr wald test object object from `aod::wald.test()`
 #'
 #' @return a data frame containing the wald test results.
 #' @keywords internal
-
 .extract_wald_results <- function(wald_test) {
   df <- wald_test$result$chi2[("df")]
   statistic <- wald_test$result$chi2[("chi2")]
diff --git a/R/ard_effectsize_cohens_d.R b/R/ard_effectsize_cohens_d.R
index 32c9f2f48..a0c298d93 100644
--- a/R/ard_effectsize_cohens_d.R
+++ b/R/ard_effectsize_cohens_d.R
@@ -159,7 +159,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
 #' cardx:::.format_cohens_d_results(
 #'   by = "ARM",
 #'   variable = "AGE",
diff --git a/R/ard_effectsize_hedges_g.R b/R/ard_effectsize_hedges_g.R
index aa849de88..8b5b9da6f 100644
--- a/R/ard_effectsize_hedges_g.R
+++ b/R/ard_effectsize_hedges_g.R
@@ -151,7 +151,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
 #' cardx:::.format_hedges_g_results(
 #'   by = "ARM",
 #'   variable = "AGE",
diff --git a/R/ard_stats_mcnemar_test.R b/R/ard_stats_mcnemar_test.R
index 07de733c0..4a928d561 100644
--- a/R/ard_stats_mcnemar_test.R
+++ b/R/ard_stats_mcnemar_test.R
@@ -71,7 +71,7 @@ ard_stats_mcnemar_test <- function(data, by, variables, ...) {
 #'
 #' @return ARD data frame
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cardx:::.format_mcnemartest_results(
 #'   by = "ARM",
 #'   variable = "AGE",
diff --git a/R/ard_stats_mood_test.R b/R/ard_stats_mood_test.R
index 9473fac4e..8882cb067 100644
--- a/R/ard_stats_mood_test.R
+++ b/R/ard_stats_mood_test.R
@@ -73,7 +73,7 @@ ard_stats_mood_test <- function(data, by, variables, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cardx:::.format_moodtest_results(
 #'   by = "SEX",
 #'   variable = "AGE",
diff --git a/R/ard_stats_t_test.R b/R/ard_stats_t_test.R
index 6758fc5e6..d00e05fa9 100644
--- a/R/ard_stats_t_test.R
+++ b/R/ard_stats_t_test.R
@@ -141,7 +141,7 @@ ard_stats_paired_t_test <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cardx:::.format_ttest_results(
 #'   by = "ARM",
 #'   variable = "AGE",
diff --git a/R/ard_stats_wilcox_test.R b/R/ard_stats_wilcox_test.R
index e4a1048e4..adff590f9 100644
--- a/R/ard_stats_wilcox_test.R
+++ b/R/ard_stats_wilcox_test.R
@@ -148,7 +148,7 @@ ard_stats_paired_wilcox_test <- function(data, by, variables, id, ...) {
 #'
 #' @return ARD data frame
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' # Pre-processing ADSL to have grouping factor (ARM here) with 2 levels
 #' ADSL <- cards::ADSL |>
 #'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
diff --git a/R/ard_survival_survfit.R b/R/ard_survival_survfit.R
index 1022119a7..eee2764a8 100644
--- a/R/ard_survival_survfit.R
+++ b/R/ard_survival_survfit.R
@@ -113,7 +113,7 @@ ard_survival_survfit <- function(x, times = NULL, probs = NULL, type = NULL) {
 #'
 #' @return a `tibble`
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("survival", "broom"), reference_pkg = "cardx"))
 #' survival::survfit(survival::Surv(AVAL, CNSR) ~ TRTA, cards::ADTTE) |>
 #'   cardx:::.process_survfit_time(times = c(60, 180), type = "risk")
 #'
@@ -221,7 +221,7 @@ ard_survival_survfit <- function(x, times = NULL, probs = NULL, type = NULL) {
 #'
 #' @return a `tibble`
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survival", reference_pkg = "cardx"))
 #' survival::survfit(survival::Surv(AVAL, CNSR) ~ TRTA, cards::ADTTE) |>
 #'   cardx:::.process_survfit_probs(probs = c(0.25, 0.75))
 #'
@@ -281,7 +281,7 @@ extract_multi_strata <- function(x, df_stat) {
 #'
 #' @return an ARD data frame of class 'card'
 #'
-#' @examples
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("survival", "broom"), reference_pkg = "cardx"))
 #' cardx:::.format_survfit_results(
 #'   broom::tidy(survival::survfit(survival::Surv(AVAL, CNSR) ~ TRTA, cards::ADTTE))
 #' )
diff --git a/R/proportion_ci.R b/R/proportion_ci.R
index 7c4dc069a..34aef53d2 100644
--- a/R/proportion_ci.R
+++ b/R/proportion_ci.R
@@ -375,6 +375,7 @@ proportion_ci_strat_wilson <- function(x,
 #' @seealso [proportion_ci_strat_wilson()]
 #'
 #' @keywords internal
+#'
 #' @examples
 #' strata_data <- table(data.frame(
 #'   "f1" = sample(c(TRUE, FALSE), 100, TRUE),
diff --git a/man/dot-format_cohens_d_results.Rd b/man/dot-format_cohens_d_results.Rd
index 87de50e57..20edfa95e 100644
--- a/man/dot-format_cohens_d_results.Rd
+++ b/man/dot-format_cohens_d_results.Rd
@@ -28,6 +28,7 @@ ARD data frame
 Convert Cohen's D Test to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 cardx:::.format_cohens_d_results(
   by = "ARM",
   variable = "AGE",
@@ -38,5 +39,6 @@ cardx:::.format_cohens_d_results(
         parameters::standardize_names(style = "broom")
     )
 )
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-format_hedges_g_results.Rd b/man/dot-format_hedges_g_results.Rd
index 3d119c5ca..d22e5b762 100644
--- a/man/dot-format_hedges_g_results.Rd
+++ b/man/dot-format_hedges_g_results.Rd
@@ -28,6 +28,7 @@ ARD data frame
 Convert Hedge's G Test to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 cardx:::.format_hedges_g_results(
   by = "ARM",
   variable = "AGE",
@@ -38,5 +39,6 @@ cardx:::.format_hedges_g_results(
         parameters::standardize_names(style = "broom")
     )
 )
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-format_mcnemartest_results.Rd b/man/dot-format_mcnemartest_results.Rd
index 5d6725c69..a373a3f6b 100644
--- a/man/dot-format_mcnemartest_results.Rd
+++ b/man/dot-format_mcnemartest_results.Rd
@@ -24,6 +24,7 @@ ARD data frame
 Convert McNemar's test to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 cardx:::.format_mcnemartest_results(
   by = "ARM",
   variable = "AGE",
@@ -33,6 +34,6 @@ cardx:::.format_mcnemartest_results(
         broom::tidy()
     )
 )
-
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-format_moodtest_results.Rd b/man/dot-format_moodtest_results.Rd
index dbc9a11b8..a3be12b12 100644
--- a/man/dot-format_moodtest_results.Rd
+++ b/man/dot-format_moodtest_results.Rd
@@ -24,6 +24,7 @@ ARD data frame
 Convert mood test results to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 cardx:::.format_moodtest_results(
   by = "SEX",
   variable = "AGE",
@@ -33,5 +34,6 @@ cardx:::.format_moodtest_results(
         broom::tidy()
     )
 )
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-format_survfit_results.Rd b/man/dot-format_survfit_results.Rd
index 824e876ac..0e52d8fe4 100644
--- a/man/dot-format_survfit_results.Rd
+++ b/man/dot-format_survfit_results.Rd
@@ -13,9 +13,10 @@ an ARD data frame of class 'card'
 Convert Tidied Survival Fit to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("survival", "broom"), reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 cardx:::.format_survfit_results(
   broom::tidy(survival::survfit(survival::Surv(AVAL, CNSR) ~ TRTA, cards::ADTTE))
 )
-
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-format_ttest_results.Rd b/man/dot-format_ttest_results.Rd
index b00306f68..5896cc6d5 100644
--- a/man/dot-format_ttest_results.Rd
+++ b/man/dot-format_ttest_results.Rd
@@ -27,6 +27,7 @@ ARD data frame
 Convert t-test to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 cardx:::.format_ttest_results(
   by = "ARM",
   variable = "AGE",
@@ -37,5 +38,6 @@ cardx:::.format_ttest_results(
         broom::tidy()
     )
 )
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-format_wilcoxtest_results.Rd b/man/dot-format_wilcoxtest_results.Rd
index 083893241..ad4cbd2fe 100644
--- a/man/dot-format_wilcoxtest_results.Rd
+++ b/man/dot-format_wilcoxtest_results.Rd
@@ -26,6 +26,7 @@ ARD data frame
 Convert Wilcoxon test to ARD
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 # Pre-processing ADSL to have grouping factor (ARM here) with 2 levels
 ADSL <- cards::ADSL |>
   dplyr::filter(ARM \%in\% c("Placebo", "Xanomeline High Dose")) |>
@@ -41,6 +42,6 @@ cardx:::.format_wilcoxtest_results(
         broom::tidy()
     )
 )
-
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-process_survfit_probs.Rd b/man/dot-process_survfit_probs.Rd
index dc1f588e4..036f9039f 100644
--- a/man/dot-process_survfit_probs.Rd
+++ b/man/dot-process_survfit_probs.Rd
@@ -20,8 +20,9 @@ a \code{tibble}
 Process Survival Fit For Quantile Estimates
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survival", reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 survival::survfit(survival::Surv(AVAL, CNSR) ~ TRTA, cards::ADTTE) |>
   cardx:::.process_survfit_probs(probs = c(0.25, 0.75))
-
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}
diff --git a/man/dot-process_survfit_time.Rd b/man/dot-process_survfit_time.Rd
index 7f1c673a8..c6f9bee25 100644
--- a/man/dot-process_survfit_time.Rd
+++ b/man/dot-process_survfit_time.Rd
@@ -30,8 +30,9 @@ a \code{tibble}
 Process Survival Fit For Time Estimates
 }
 \examples{
+\dontshow{if (do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("survival", "broom"), reference_pkg = "cardx"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 survival::survfit(survival::Surv(AVAL, CNSR) ~ TRTA, cards::ADTTE) |>
   cardx:::.process_survfit_time(times = c(60, 180), type = "risk")
-
+\dontshow{\}) # examplesIf}
 }
 \keyword{internal}