213 update standalone@main (#225)

remove "reference_pkg = cardx" argument for package install checks.
update standalone scripts to pull from insightsengineering repo

closes #213 



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

Pre-review Checklist (if item does not apply, mark is as complete)
- [ ] **All** GitHub Action workflows pass with a ✅
- [ ] PR branch has pulled the most recent updates from master branch:
`usethis::pr_merge_main()`
- [ ] If a bug was fixed, a unit test was added.
- [ ] If a new `ard_*()` function was added, it passes the ARD
structural checks from `cards::check_ard_structure()`.
- [ ] If a new `ard_*()` function was added, `set_cli_abort_call()` has
been set.
- [ ] 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"))`
- [ ] 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 ✅
- [ ] Approve Pull Request
- [ ] Merge the PR. Please use "Squash and merge" or "Rebase and merge".

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,7 +14,7 @@ Pre-review Checklist (if item does not apply, mark is as complete)
 - [ ] If a bug was fixed, a unit test was added.
 - [ ] If a new `ard_*()` function was added, it passes the ARD structural checks from `cards::check_ard_structure()`.
 - [ ] If a new `ard_*()` function was added, `set_cli_abort_call()` has been set.
-- [ ] 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")$is_pkg_installed, list(pkg = "broom"", reference_pkg = "cardx"))`
+- [ ] If a new `ard_*()` function was added and it depends on another package (such as, `broom`), `is_pkg_installed("broom")` has been set in the function call and the following added to the roxygen comments: `@examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom""))`
 - [ ] 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)

R/add_total_n.survey.design.R

@@ -9,7 +9,7 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examplesIf cardx:::is_pkg_installed("survey", reference_pkg = "cardx")
+#' @examplesIf cardx:::is_pkg_installed("survey")
 #' svy_titanic <- survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)
 #'
 #' ard_total_n(svy_titanic)

R/ard_aod_wald_test.R

@@ -11,14 +11,14 @@
 #' @return data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("aod", "broom.helpers"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("aod", "broom.helpers")))
 #' lm(AGE ~ ARM, data = cards::ADSL) |>
 #'   ard_aod_wald_test()
 ard_aod_wald_test <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or_parameters, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(c("aod", "broom.helpers"), reference_pkg = "cardx")
+  check_pkg_installed(c("aod", "broom.helpers"))
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)

R/ard_attributes.survey.design.R

@@ -21,7 +21,7 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey"))
 #' data(api, package = "survey")
 #' dclus1 <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
 #'

R/ard_car_anova.R

@@ -8,7 +8,7 @@
 #' @return data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("broom.helpers", "car", "parameters"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("broom.helpers", "car", "parameters")))
 #' lm(AGE ~ ARM, data = cards::ADSL) |>
 #'   ard_car_anova()
 #'
@@ -18,7 +18,7 @@ ard_car_anova <- function(x, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(pkg = c("broom.helpers", "car", "parameters"), reference_pkg = "cardx")
+  check_pkg_installed(pkg = c("broom.helpers", "car", "parameters"))
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)

R/ard_car_vif.R

@@ -14,14 +14,14 @@
 #' @rdname ard_car_vif
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "car", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "car"))
 #' lm(AGE ~ ARM + SEX, data = cards::ADSL) |>
 #'   ard_car_vif()
 ard_car_vif <- function(x, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed("car", reference_pkg = "cardx")
+  check_pkg_installed("car")
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)

R/ard_categorical.survey.design.R

@@ -38,7 +38,7 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examplesIf cardx:::is_pkg_installed("survey", reference_pkg = "cardx")
+#' @examplesIf cardx:::is_pkg_installed("survey")
 #' svy_titanic <- survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)
 #'
 #' ard_categorical(svy_titanic, variables = c(Class, Age), by = Survived)
@@ -58,7 +58,7 @@ ard_categorical.survey.design <- function(data,
                                           ),
                                           ...) {
   set_cli_abort_call()
-  check_pkg_installed(pkg = "survey", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "survey")
   check_dots_empty()
   deff <- TRUE # we may update in the future to make this an argument for users
 

R/ard_categorical_ci.R

@@ -27,7 +27,7 @@
 #' @return an ARD data frame
 #' @name ard_categorical_ci
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom"))
 #' # compute CI for binary variables
 #' ard_categorical_ci(mtcars, variables = c(vs, am), method = "wilson")
 #'
@@ -63,7 +63,7 @@ ard_categorical_ci.data.frame <- function(data,
   check_dots_empty()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(pkg = "broom", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "broom")
 
   # process inputs -------------------------------------------------------------
   cards::process_selectors(data, variables = {{ variables }}, by = {{ by }})

R/ard_categorical_ci.survey.design.R

@@ -15,7 +15,7 @@
 #' @return ARD data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey"))
 #' data(api, package = "survey")
 #' dclus1 <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
 #'

R/ard_continuous.survey.design.R

@@ -35,7 +35,7 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey"))
 #' data(api, package = "survey")
 #' dclus1 <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
 #'
@@ -53,7 +53,7 @@ ard_continuous.survey.design <- function(data, variables, by = NULL,
   check_dots_empty()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(pkg = "survey", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "survey")
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(variables)

R/ard_continuous_ci.R

@@ -11,7 +11,7 @@
 #' @return ARD data frame
 #' @name ard_continuous_ci
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom"))
 #' ard_continuous_ci(mtcars, variables = c(mpg, hp), method = "wilcox.test")
 #' ard_continuous_ci(mtcars, variables = mpg, by = am, method = "t.test")
 NULL

R/ard_continuous_ci.survey.design.R

@@ -19,7 +19,7 @@
 #' @return ARD data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "survey"))
 #' data(api, package = "survey")
 #' dclus1 <- survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc)
 #'

R/ard_dichotomous.survey.design.R

@@ -11,7 +11,7 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examplesIf cardx:::is_pkg_installed("survey", reference_pkg = "cardx")
+#' @examplesIf cardx:::is_pkg_installed("survey")
 #' survey::svydesign(ids = ~1, data = mtcars, weights = ~1) |>
 #'   ard_dichotomous(by = vs, variables = c(cyl, am), value = list(cyl = 4))
 ard_dichotomous.survey.design <- function(data,
@@ -32,7 +32,7 @@ ard_dichotomous.survey.design <- function(data,
                                           ...) {
   set_cli_abort_call()
   check_dots_empty()
-  check_pkg_installed(pkg = "survey", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "survey")
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(variables)

R/ard_effectsize_cohens_d.R

@@ -30,7 +30,7 @@
 #' The data are then passed as
 #' `effectsize::cohens_d(x = data_wide[[<by level 1>]], y = data_wide[[<by level 2>]], paired = TRUE, ...)`.
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters")))
 #' cards::ADSL |>
 #'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
 #'   ard_effectsize_cohens_d(by = ARM, variables = AGE)
@@ -52,7 +52,7 @@ ard_effectsize_cohens_d <- function(data, by, variables, conf.level = 0.95, ...)
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(c("effectsize", "parameters"), reference_pkg = "cardx")
+  check_pkg_installed(c("effectsize", "parameters"))
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(data)
@@ -103,7 +103,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, conf.level =
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(c("effectsize", "parameters"), reference_pkg = "cardx")
+  check_pkg_installed(c("effectsize", "parameters"))
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(data)
@@ -175,7 +175,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, conf.level =
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters")))
 #' cardx:::.format_cohens_d_results(
 #'   by = "ARM",
 #'   variable = "AGE",

R/ard_effectsize_hedges_g.R

@@ -30,7 +30,7 @@
 #' The data are then passed as
 #' `effectsize::hedges_g(x = data_wide[[<by level 1>]], y = data_wide[[<by level 2>]], paired = TRUE, ...)`.
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters")))
 #' cards::ADSL |>
 #'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
 #'   ard_effectsize_hedges_g(by = ARM, variables = AGE)
@@ -52,7 +52,7 @@ ard_effectsize_hedges_g <- function(data, by, variables, conf.level = 0.95, ...)
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(c("effectsize", "parameters"), reference_pkg = "cardx")
+  check_pkg_installed(c("effectsize", "parameters"))
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(data)
@@ -101,7 +101,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, conf.level =
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(c("effectsize", "parameters"), reference_pkg = "cardx")
+  check_pkg_installed(c("effectsize", "parameters"))
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(data)
@@ -158,7 +158,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, conf.level =
 #'
 #' @return ARD data frame
 #' @keywords internal
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("effectsize", "parameters")))
 #' cardx:::.format_hedges_g_results(
 #'   by = "ARM",
 #'   variable = "AGE",

R/ard_emmeans_mean_difference.R

@@ -29,7 +29,7 @@
 #' @return ARD data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "emmeans", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "emmeans"))
 #' ard_emmeans_mean_difference(
 #'   data = mtcars,
 #'   formula = mpg ~ am + cyl,
@@ -55,7 +55,7 @@ ard_emmeans_mean_difference <- function(data, formula, method,
   set_cli_abort_call()
 
   # check package installation -------------------------------------------------
-  check_pkg_installed(c("emmeans", package), reference_pkg = "cardx")
+  check_pkg_installed(c("emmeans", package))
   check_not_missing(data)
   check_not_missing(formula)
   check_not_missing(method)

R/ard_missing.survey.design.R

@@ -7,7 +7,7 @@
 #' @return an ARD data frame of class 'card'
 #' @export
 #'
-#' @examplesIf cardx:::is_pkg_installed("survey", reference_pkg = "cardx")
+#' @examplesIf cardx:::is_pkg_installed("survey")
 #' svy_titanic <- survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)
 #'
 #' ard_missing(svy_titanic, variables = c(Class, Age), by = Survived)
@@ -37,7 +37,7 @@ ard_missing.survey.design <- function(data,
                                       ...) {
   set_cli_abort_call()
   check_dots_empty()
-  check_pkg_installed(pkg = "survey", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "survey")
 
   # process inputs -------------------------------------------------------------
   check_not_missing(variables)

R/ard_regression.R

@@ -11,7 +11,7 @@
 #' @return data frame
 #' @name ard_regression
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom.helpers", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom.helpers"))
 #' lm(AGE ~ ARM, data = cards::ADSL) |>
 #'   ard_regression(add_estimate_to_reference_rows = TRUE)
 NULL
@@ -28,7 +28,7 @@ ard_regression.default <- function(x, tidy_fun = broom.helpers::tidy_with_broom_
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(pkg = "broom.helpers", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "broom.helpers")
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)

R/ard_regression_basic.R

@@ -26,7 +26,7 @@
 #' @name ard_regression_basic
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom.helpers", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom.helpers"))
 #' lm(AGE ~ ARM, data = cards::ADSL) |>
 #'   ard_regression_basic()
 ard_regression_basic <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or_parameters,
@@ -38,7 +38,7 @@ ard_regression_basic <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(pkg = "broom.helpers", reference_pkg = "cardx")
+  check_pkg_installed(pkg = "broom.helpers")
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)

R/ard_smd_smd.R

@@ -23,14 +23,14 @@
 #' @return ARD data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "smd", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "smd"))
 #' ard_smd_smd(cards::ADSL, by = SEX, variables = AGE)
 #' ard_smd_smd(cards::ADSL, by = SEX, variables = AGEGR1)
 ard_smd_smd <- function(data, by, variables, std.error = TRUE, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed("smd", reference_pkg = "cardx")
+  check_pkg_installed("smd")
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(data)

R/ard_stats_anova.R

@@ -37,7 +37,7 @@
 #' @return ARD data frame
 #' @name ard_stats_anova
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("broom", "withr", "lme4"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("broom", "withr", "lme4")))
 #' anova(
 #'   lm(mpg ~ am, mtcars),
 #'   lm(mpg ~ am + hp, mtcars)
@@ -73,7 +73,7 @@ ard_stats_anova.anova <- function(x, method_text = "ANOVA results from `stats::a
 
   # check inputs ---------------------------------------------------------------
   check_dots_empty()
-  check_pkg_installed("broom", reference_pkg = "cardx")
+  check_pkg_installed("broom")
   check_string(method_text)
 
   # return df in cards formats -------------------------------------------------
@@ -100,7 +100,7 @@ ard_stats_anova.data.frame <- function(x,
 
   # check inputs ---------------------------------------------------------------
   check_dots_empty()
-  check_pkg_installed(c("broom", "withr", package), reference_pkg = "cardx")
+  check_pkg_installed(c("broom", "withr", package))
   check_not_missing(formulas)
   check_class(formulas, cls = "list")
   walk(

R/ard_stats_aov.R

@@ -10,13 +10,13 @@
 #' @return ARD data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("broom.helpers", "parameters"), reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = c("broom.helpers", "parameters")))
 #' ard_stats_aov(AGE ~ ARM, data = cards::ADSL)
 ard_stats_aov <- function(formula, data, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed(c("broom.helpers", "parameters"), reference_pkg = "cardx")
+  check_pkg_installed(c("broom.helpers", "parameters"))
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(formula)

R/ard_stats_chisq_test.R

@@ -17,14 +17,14 @@
 #' @return ARD data frame
 #' @export
 #'
-#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
+#' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom"))
 #' cards::ADSL |>
 #'   ard_stats_chisq_test(by = "ARM", variables = "AGEGR1")
 ard_stats_chisq_test <- function(data, by, variables, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
-  check_pkg_installed("broom", reference_pkg = "cardx")
+  check_pkg_installed("broom")
 
   # check/process inputs -------------------------------------------------------
   check_not_missing(data)