1994 update standalone@main (#2046)

* redirect standalone scripts to pull from insightsengineering repo * remove "reference_pkg" argument for package install checks. * add "ref = cardx" argument * missed file
ddsjoberg · Oct 23, 2024 · 901cc30 · 901cc30
1 parent 2a05ed9
commit 901cc30
Show file tree

Hide file tree

Showing 129 changed files with 320 additions and 258 deletions.
diff --git a/R/add_ci.R b/R/add_ci.R
@@ -40,7 +40,7 @@
 #' @return gtsummary table
 #' @name add_ci
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed("cardx") && gtsummary:::is_pkg_installed("broom", ref = "cardx")
 #' # Example 1 ----------------------------------
 #' trial |>
 #'   tbl_summary(

diff --git a/R/add_ci.tbl_svysummary.R b/R/add_ci.tbl_svysummary.R
@@ -31,7 +31,7 @@
 #' @export
 #' @name add_ci.tbl_svysummary
 #'
-#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "survey"), reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "survey")) && gtsummary:::is_pkg_installed("broom",  ref = "cardx")
 #' data(api, package = "survey")
 #' survey::svydesign(id = ~dnum, weights = ~pw, data = apiclus1, fpc = ~fpc) |>
 #'   tbl_svysummary(

diff --git a/R/add_difference.R b/R/add_difference.R
@@ -41,7 +41,7 @@ add_difference <- function(x, ...) {
 #' @export
 #' @return a gtsummary table of class `"tbl_summary"`
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed("cardx") && gtsummary:::is_pkg_installed("broom", ref = "cardx")
 #' # Example 1 ----------------------------------
 #' trial |>
 #'   select(trt, age, marker, response, death) %>%

diff --git a/R/add_difference.tbl_svysummary.R b/R/add_difference.tbl_svysummary.R
@@ -24,7 +24,7 @@
 #' @export
 #' @return a gtsummary table of class `"tbl_summary"`
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed("cardx") && gtsummary:::is_pkg_installed("broom", ref = "cardx")
 add_difference.tbl_svysummary <- function(x,
                                           test = NULL,
                                           group = NULL,

diff --git a/R/add_glance.R b/R/add_glance.R
@@ -79,7 +79,7 @@ add_glance_table <- function(x,
   # check inputs ---------------------------------------------------------------
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(add_glance_table = match.call()))
-  check_pkg_installed("broom", reference_pkg = "gtsummary")
+  check_pkg_installed("broom")
   check_not_missing(x)
   check_class(x, "tbl_regression")
 
@@ -134,7 +134,7 @@ add_glance_source_note <- function(x,
   # check inputs ---------------------------------------------------------------
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(add_glance_source_note = match.call()))
-  check_pkg_installed("broom", reference_pkg = "gtsummary")
+  check_pkg_installed("broom")
   check_not_missing(x)
   check_class(x, "tbl_regression")
   text_interpret <- arg_match(text_interpret)

diff --git a/R/add_global_p.R b/R/add_global_p.R
@@ -29,7 +29,7 @@
 #' @author Daniel D. Sjoberg
 #' @name add_global_p
 #'
-#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "broom", "car"), reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "broom", "car"))
 #' # Example 1 ----------------------------------
 #' lm(marker ~ age + grade, trial) |>
 #'   tbl_regression() |>

diff --git a/R/add_n.tbl_survfit.R b/R/add_n.tbl_survfit.R
@@ -7,7 +7,7 @@
 #' @param ... Not used
 #' @export
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("survival", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("survival")
 #' library(survival)
 #' fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
 #' fit2 <- survfit(Surv(ttdeath, death) ~ trt, trial)

diff --git a/R/add_nevent.R b/R/add_nevent.R
@@ -3,7 +3,7 @@
 #' @inheritParams add_n_regression
 #' @name add_nevent_regression
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("broom.helpers", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("broom.helpers")
 #' # Example 1 ----------------------------------
 #' trial |>
 #'   select(response, trt, grade) |>

diff --git a/R/add_nevent.tbl_survfit.R b/R/add_nevent.tbl_survfit.R
@@ -7,7 +7,7 @@
 #' @param ... Not used
 #' @export
 #' @family tbl_survfit tools
-#' @examplesIf gtsummary:::is_pkg_installed(c("survival", "broom"), reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed(c("survival", "broom"))
 #' library(survival)
 #' fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
 #' fit2 <- survfit(Surv(ttdeath, death) ~ trt, trial)
@@ -21,7 +21,7 @@ add_nevent.tbl_survfit <- function(x, ...) {
   set_cli_abort_call()
   check_dots_empty()
   updated_call_list <- c(x$call_list, list(add_nevent = match.call()))
-  check_pkg_installed("broom", reference_pkg = "gtsummary")
+  check_pkg_installed("broom")
 
   # checking survfit is a standard (not multi-state)
   if (some(x$inputs$x, ~ !rlang::is_empty(setdiff(class(.x), c("survfit", "survfit2"))))) {

diff --git a/R/add_p.R b/R/add_p.R
@@ -83,7 +83,7 @@ add_p <- function(x, ...) {
 #'
 #'  - `"ancova"` when variable is continuous and `by` variable has two levels.
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed("cardx") && gtsummary:::is_pkg_installed("broom", ref = "cardx")
 #' # Example 1 ----------------------------------
 #' trial |>
 #'   tbl_summary(by = trt, include = c(age, grade)) |>

diff --git a/R/add_p.tbl_continuous.R b/R/add_p.tbl_continuous.R
@@ -11,7 +11,7 @@
 #' @export
 #' @return 'tbl_continuous' object
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("cardx")
 #' trial |>
 #'   tbl_continuous(variable = age, by = trt, include = grade) |>
 #'   add_p()

diff --git a/R/add_p.tbl_survfit.R b/R/add_p.tbl_survfit.R
@@ -41,7 +41,7 @@
 #' If you utilize the `tbl_survfit.data.frame()` S3 method, this is handled for you.
 #'
 #' @export
-#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "survival", "broom"), reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "survival", "broom"))
 #' library(survival)
 #'
 #' gts_survfit <-

diff --git a/R/add_p.tbl_svysummary.R b/R/add_p.tbl_svysummary.R
@@ -16,7 +16,7 @@
 #' @return a gtsummary table of class `"tbl_svysummary"`
 #' @export
 #'
-#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "survey"), reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "survey")) && gtsummary:::is_pkg_installed("broom", ref = "cardx")
 #' # Example 1 ----------------------------------
 #' # A simple weighted dataset
 #' survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq) |>
@@ -48,7 +48,7 @@ add_p.tbl_svysummary <- function(x,
                               test.args = NULL,
                               ...) {
   set_cli_abort_call()
-  check_pkg_installed("survey", reference_pkg = "gtsummary")
+  check_pkg_installed("survey")
 
   # check/process inputs -------------------------------------------------------
   check_dots_empty()

diff --git a/R/add_q.R b/R/add_q.R
@@ -15,7 +15,7 @@
 #'
 #' @author Daniel D. Sjoberg, Esther Drill
 #' @export
-#' @examplesIf gtsummary:::is_pkg_installed("cardx", reference_pkg = "gtsummary") && gtsummary:::is_pkg_installed("broom", reference_pkg = "cardx")
+#' @examplesIf gtsummary:::is_pkg_installed("cardx") && gtsummary:::is_pkg_installed("broom", ref = "cardx")
 #' # Example 1 ----------------------------------
 #' add_q_ex1 <-
 #'   trial |>

diff --git a/R/add_significance_stars.R b/R/add_significance_stars.R
@@ -23,7 +23,7 @@
 #' @export
 #' @return a 'gtsummary' table
 #'
-#' @examplesIf gtsummary:::is_pkg_installed("car", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("car")
 #' tbl <-
 #'   lm(time ~ ph.ecog + sex, survival::lung) |>
 #'   tbl_regression(label = list(ph.ecog = "ECOG Score", sex = "Sex"))

diff --git a/R/add_vif.R b/R/add_vif.R
@@ -11,7 +11,7 @@
 #' @seealso Review [list, formula, and selector syntax][syntax] used throughout gtsummary
 #' @export
 #'
-#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "car"), reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "car"))
 #' # Example 1 ----------------------------------
 #' lm(age ~ grade + marker, trial) |>
 #'   tbl_regression() |>
@@ -23,7 +23,7 @@
 #'   add_vif(c("aGVIF", "df"))
 add_vif <- function(x, statistic = NULL, estimate_fun = label_style_sigfig(digits = 2)) {
   set_cli_abort_call()
-  check_pkg_installed(c("car", "cardx"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("car", "cardx"))
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)

diff --git a/R/as_flex_table.R b/R/as_flex_table.R
@@ -22,15 +22,15 @@
 #' @return A 'flextable' object
 #'
 #' @author Daniel D. Sjoberg
-#' @examplesIf gtsummary:::is_pkg_installed("flextable", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("flextable")
 #' trial |>
 #'   select(trt, age, grade) |>
 #'   tbl_summary(by = trt) |>
 #'   add_p() |>
 #'   as_flex_table()
 as_flex_table <- function(x, include = everything(), return_calls = FALSE, ...) {
   set_cli_abort_call()
-  check_pkg_installed("flextable", reference_pkg = "gtsummary")
+  check_pkg_installed("flextable")
 
   # deprecated arguments -------------------------------------------------------
   dots <- rlang::dots_list(...)

diff --git a/R/as_hux_table.R b/R/as_hux_table.R
@@ -20,7 +20,7 @@
 #' @return A \{huxtable\} object
 #'
 #' @author David Hugh-Jones, Daniel D. Sjoberg
-#' @examplesIf gtsummary:::is_pkg_installed("huxtable", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("huxtable")
 #' trial |>
 #'   tbl_summary(by = trt, include = c(age, grade)) |>
 #'   add_p() |>
@@ -33,7 +33,7 @@ as_hux_table <- function(x, include = everything(), return_calls = FALSE,
                          strip_md_bold = FALSE) {
   set_cli_abort_call()
   check_class(x, "gtsummary")
-  check_pkg_installed("huxtable", reference_pkg = "gtsummary")
+  check_pkg_installed("huxtable")
   check_scalar_logical(return_calls)
 
   if (!isFALSE(strip_md_bold)) {
@@ -86,7 +86,7 @@ as_hux_table <- function(x, include = everything(), return_calls = FALSE,
 as_hux_xlsx <- function(x, file, include = everything(), bold_header_rows = TRUE) {
   set_cli_abort_call()
   check_class(x, "gtsummary")
-  check_pkg_installed(c("huxtable", "openxlsx"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("huxtable", "openxlsx"))
   check_scalar_logical(bold_header_rows)
 
   # save list of expressions to run --------------------------------------------

diff --git a/R/as_kable_extra.R b/R/as_kable_extra.R
@@ -52,7 +52,7 @@
 #' @return A \{kableExtra\} table
 #'
 #' @author Daniel D. Sjoberg
-#' @examplesIf gtsummary:::is_pkg_installed("kableExtra", reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed("kableExtra")
 #' # basic gtsummary tbl to build upon
 #' as_kable_extra_base <-
 #'   trial |>
@@ -89,7 +89,7 @@ as_kable_extra <- function(x,
                            addtl_fmt = TRUE,
                            return_calls = FALSE) {
   set_cli_abort_call()
-  check_pkg_installed(c("kableExtra", "knitr"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("kableExtra", "knitr"))
 
   # process inputs -------------------------------------------------------------
   check_class(x, "gtsummary")

diff --git a/R/combine_terms.R b/R/combine_terms.R
@@ -37,7 +37,7 @@
 combine_terms <- function(x, formula_update, label = NULL, quiet, ...) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(combine_terms = match.call()))
-  check_pkg_installed("cardx", reference_pkg = "gtsummary")
+  check_pkg_installed("cardx")
 
   # deprecation ----------------------------------------------------------------
   if (!missing(quiet)) {

diff --git a/R/custom_tidiers.R b/R/custom_tidiers.R
@@ -61,7 +61,7 @@
 #' @name custom_tidiers
 #' @rdname custom_tidiers
 #' @export
-#' @examplesIf gtsummary:::is_pkg_installed(c("effectsize", "mice", "parameters"), reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed(c("effectsize", "mice", "parameters"))
 #' # Example 1 ----------------------------------
 #' mod <- lm(age ~ marker + grade, trial)
 #'
@@ -92,7 +92,7 @@ tidy_standardize <- function(x,
                              ...,
                              quiet = FALSE) {
   set_cli_abort_call()
-  check_pkg_installed(c("parameters", "effectsize"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("parameters", "effectsize"))
   check_scalar_logical(exponentiate)
   check_scalar_logical(conf.int)
   check_scalar_range(conf.level, range = c(0, 1))
@@ -136,7 +136,7 @@ tidy_bootstrap <- function(x,
                            ...,
                            quiet = FALSE) {
   set_cli_abort_call()
-  check_pkg_installed("parameters", reference_pkg = "gtsummary")
+  check_pkg_installed("parameters")
   check_scalar_logical(exponentiate)
   check_scalar_logical(conf.int)
   check_scalar_range(conf.level, range = c(0, 1))
@@ -182,7 +182,7 @@ tidy_robust <- function(x,
                         ...,
                         quiet = FALSE) {
   set_cli_abort_call()
-  check_pkg_installed(c("parameters", "insight"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("parameters", "insight"))
   check_scalar_logical(exponentiate)
   check_scalar_logical(conf.int)
   check_scalar_range(conf.level, range = c(0, 1))
@@ -238,7 +238,7 @@ tidy_robust <- function(x,
 #' @export
 pool_and_tidy_mice <- function(x, pool.args = NULL, ..., quiet = FALSE) {
   set_cli_abort_call()
-  check_pkg_installed("mice", reference_pkg = "gtsummary")
+  check_pkg_installed("mice")
 
   if (!missing(quiet)) {
     lifecycle::deprecate_stop(
@@ -285,7 +285,7 @@ tidy_gam <- function(x, conf.int = FALSE, exponentiate = FALSE, conf.level = 0.9
 #' @export
 tidy_wald_test <- function(x, tidy_fun = NULL, ...) {
   set_cli_abort_call()
-  check_pkg_installed(c("aod", "broom.helpers"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("aod", "broom.helpers"))
 
   tidy_fun <- tidy_fun %||% broom.helpers::tidy_with_broom_or_parameters
 

diff --git a/R/gather_ard.R b/R/gather_ard.R
@@ -8,7 +8,7 @@
 #' @return list
 #' @export
 #'
-#' @examplesIf gtsummary:::is_pkg_installed('cardx', reference_pkg = 'gtsummary')
+#' @examplesIf gtsummary:::is_pkg_installed('cardx')
 #' tbl_summary(trial, by = trt, include = age) |>
 #'   add_overall() |>
 #'   add_p() |>
@@ -28,7 +28,7 @@ gather_ard <- function(x) {
 
   # the ARD for regression models is an additional calculation, so we don't do it by default
   if (inherits(x, "tbl_regression")) {
-    check_pkg_installed("cardx", reference_pkg = "gtsummary")
+    check_pkg_installed("cardx")
     return(cardx::ard_regression(x$inputs$x))
   }
 

diff --git a/R/glance_fun.R b/R/glance_fun.R
@@ -27,15 +27,15 @@ glance_fun_s3 <- function(x, ...) {
 #' @name glance_fun_s3
 #' @export
 glance_fun_s3.default <- function(x, ...) {
-  check_pkg_installed("broom", reference_pkg = "gtsummary")
+  check_pkg_installed("broom")
   check_dots_empty()
   broom::glance
 }
 
 #' @name glance_fun_s3
 #' @export
 glance_fun_s3.mira <- function(x, ...) {
-  check_pkg_installed(c("broom",  "mice"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("broom",  "mice"))
   check_dots_empty()
   \(x) broom::glance(mice::pool(x))
 }
diff --git a/R/global_pvalue_fun.R b/R/global_pvalue_fun.R
@@ -14,7 +14,7 @@
 #' @return data frame
 #' @keywords internal
 #'
-#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "broom", "car"), reference_pkg = "gtsummary")
+#' @examplesIf gtsummary:::is_pkg_installed(c("cardx", "broom", "car"))
 #' lm(age ~ stage + grade, trial) |>
 #'   global_pvalue_fun(type = "III")
 NULL
@@ -28,15 +28,15 @@ global_pvalue_fun <- function(x, type, ...) {
 #' @rdname global_pvalue_fun
 #' @export
 global_pvalue_fun.default <- function(x, type, ...) {
-  check_pkg_installed(c("cardx"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("cardx"))
 
   cardx::ard_car_anova(x, type = type, ...)
 }
 
 #' @rdname global_pvalue_fun
 #' @export
 global_pvalue_fun.geeglm <- function(x, type, ...) {
-  check_pkg_installed(c("cardx"), reference_pkg = "gtsummary")
+  check_pkg_installed(c("cardx"))
 
   cardx::ard_aod_wald_test(x, ...)
 }