From 92ca979ebb7f09a09ec2d087b6c8075455c2b86d Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Mon, 9 Dec 2024 20:18:05 -0800
Subject: [PATCH] abbreviation updates

---
 R/as_kable_extra.R         | 9 ++++++---
 R/modify_source_note.R     | 5 +++++
 man/modify_abbreviation.Rd | 2 ++
 man/modify_source_note.Rd  | 6 ++++++
 man/tbl_continuous.Rd      | 2 ++
 man/tbl_regression.Rd      | 2 +-
 6 files changed, 22 insertions(+), 4 deletions(-)

diff --git a/R/as_kable_extra.R b/R/as_kable_extra.R
index ea43c539b..19dfe55e1 100644
--- a/R/as_kable_extra.R
+++ b/R/as_kable_extra.R
@@ -353,7 +353,11 @@ table_styling_to_kable_extra_calls <- function(x, escape, format, addtl_fmt, ...
       seq_len(nrow(x$table_styling$source_note)),
       \(i) {
         expr(
-          kableExtra::footnote(number = !!x$table_styling$source_note$source_note[i], escape = !!escape)
+          kableExtra::footnote(
+            general = !!x$table_styling$source_note$source_note[i],
+            escape = !!escape,
+            general_title = ""
+          )
         )
       }
     )
@@ -371,8 +375,7 @@ table_styling_to_kable_extra_calls <- function(x, escape, format, addtl_fmt, ...
                              ": ", .
                            )),
             escape = !!escape,
-            general_title = "",
-            footnote_order = c("number", "alphabet", "symbol", "general")
+            general_title = ""
           )
         ),
       .default = list()
diff --git a/R/modify_source_note.R b/R/modify_source_note.R
index 05ed03c26..a48211ffb 100644
--- a/R/modify_source_note.R
+++ b/R/modify_source_note.R
@@ -22,7 +22,12 @@
 #' @name modify_source_note
 #'
 #' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")
+#' # Example 1 ----------------------------------
+#' tbl <- tbl_summary(trial, include = c(marker, grade), missing = "no") |>
+#'   modify_source_note("Results as of June 26, 2015")
 #'
+#' # Example 2 ----------------------------------
+#' remove_source_note(tbl, source_note_id = 1)
 NULL
 
 #' @export
diff --git a/man/modify_abbreviation.Rd b/man/modify_abbreviation.Rd
index 8a857d867..f0959b145 100644
--- a/man/modify_abbreviation.Rd
+++ b/man/modify_abbreviation.Rd
@@ -29,6 +29,7 @@ All abbreviations will be coalesced when printing the final table into
 a single source note.
 }
 \examples{
+\dontshow{if ((identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")) && gtsummary:::is_pkg_installed(c("cardx", "broom", "broom.helpers"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 # Example 1 ----------------------------------
 tbl_summary(
   trial,
@@ -43,4 +44,5 @@ tbl_summary(
 lm(marker ~ trt, trial) |>
   tbl_regression() |>
   remove_abbreviation("CI = Confidence Interval")
+\dontshow{\}) # examplesIf}
 }
diff --git a/man/modify_source_note.Rd b/man/modify_source_note.Rd
index 00757805b..e771a01cf 100644
--- a/man/modify_source_note.Rd
+++ b/man/modify_source_note.Rd
@@ -38,5 +38,11 @@ Source notes are not supported by \code{as_kable_extra()}.
 }
 \examples{
 \dontshow{if (identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+# Example 1 ----------------------------------
+tbl <- tbl_summary(trial, include = c(marker, grade), missing = "no") |>
+  modify_source_note("Results as of June 26, 2015")
+
+# Example 2 ----------------------------------
+remove_source_note(tbl, source_note_id = 1)
 \dontshow{\}) # examplesIf}
 }
diff --git a/man/tbl_continuous.Rd b/man/tbl_continuous.Rd
index 2b8bcca28..c35703ad4 100644
--- a/man/tbl_continuous.Rd
+++ b/man/tbl_continuous.Rd
@@ -54,6 +54,7 @@ a gtsummary table
 Summarize a continuous variable by one or more categorical variables
 }
 \examples{
+\dontshow{if (identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 # Example 1 ----------------------------------
 tbl_continuous(
   data = trial,
@@ -73,4 +74,5 @@ trial |>
     value = all_subjects ~ 1,
     label = list(all_subjects = "All Subjects")
   )
+\dontshow{\}) # examplesIf}
 }
diff --git a/man/tbl_regression.Rd b/man/tbl_regression.Rd
index 2529d4076..6bd43aa62 100644
--- a/man/tbl_regression.Rd
+++ b/man/tbl_regression.Rd
@@ -103,7 +103,7 @@ to print the random components.
 }
 
 \examples{
-\dontshow{if (gtsummary:::is_pkg_installed(c("cardx", "broom", "broom.helpers"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if ((identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("IN_PKGDOWN"), "true")) && gtsummary:::is_pkg_installed(c("cardx", "broom", "broom.helpers"))) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 # Example 1 ----------------------------------
 glm(response ~ age + grade, trial, family = binomial()) |>
   tbl_regression(exponentiate = TRUE)