Merge branch 'main' into 2157_update_standalone@main

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result Tables
-Version: 2.1.0.9000
+Version: 2.1.0.9003
 Authors@R: c(
     person("Daniel D.", "Sjoberg", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0862-2018")),

NEWS.md

@@ -1,5 +1,13 @@
 # gtsummary (development version)
 
+* The `remove_*()` family of functions default argument values have been updated to remove _all_ footnotes, source notes, abbreviations, column merging, bold and italic styling by default, so the users are not longer required to remove, for example, one source note at a time. The one exception is `remove_spanning_headers()`, which will remove the first level spanning headers be default. (#2161)
+
+* The `tbl_strata_nested_stack(quiet)` argument documentation was updated. (#2164)
+
+* Corrected the class of objects returned from `tbl_strata_nested_stack()`.
+
+* Corrected bug in `tbl_strata_nested_stack()` when the strata variable had a single level. Pervasively, the indentation of the single strata level was not correct.
+
 # gtsummary 2.1.0
 
 ### New Features and Functions
@@ -752,7 +760,7 @@ Updates to address regressions in the v2.0.0 release:
 
 * Added a standardized mean difference method for  `tbl_svysummary()` tables.
 
-* Added `tbl_strata(.stack_group_header=)` argument to include/exclude the headers when tables are combined with `tbl_stack()`
+* Added `tbl_strata(.stack_group_header=)` argument to include/exclude the headers when tables are combined with `tbl_stack()`.
 
 * Added `tbl_strata(.quiet=)` argument.
 

R/deprecated.R

@@ -9,6 +9,7 @@
 NULL
 
 # "soft" deprecation for 6 months: (Sys.Date() - lubridate::dmonths(6)) |> as.Date()
+#  v2.1.0 2025-02-19
 #  v2.0.2 2024-09-05
 #  v2.0.1 2024-08-01
 #  v2.0.0 2024-07-23
@@ -23,9 +24,6 @@ NULL
 #   v1.6.2 2022-09-30
 #   v1.6.1 2022-06-22
 #   v1.6.0 2022-04-25
-#   v1.5.2 2022-01-29
-#   v1.5.1 2022-01-20
-#   v1.5.0 2021-10-16
 
 
 # v1.6.1 ----------------------------------------------------------

R/modify.R

@@ -176,7 +176,7 @@ modify_spanning_header <- function(x, ..., text_interpret = c("md", "html"),
 
 #' @name modify
 #' @export
-remove_spanning_header <- function(x, columns, level = 1L) {
+remove_spanning_header <- function(x, columns = everything(), level = 1L) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(remove_spanning_header = match.call()))
 

R/modify_abbreviation.R

@@ -5,7 +5,8 @@
 #'
 #' @inheritParams modify_footnote2
 #' @param abbreviation (`string`)\cr
-#'   a string
+#'   a string. In `remove_abbreviation()`, the default value is `NULL`, which
+#'   will remove all abbreviation source notes.
 #'
 #' @return Updated gtsummary object
 #' @name modify_abbreviation
@@ -49,13 +50,21 @@ modify_abbreviation <- function(x, abbreviation, text_interpret = c("md", "html"
 
 #' @export
 #' @rdname modify_abbreviation
-remove_abbreviation <- function(x, abbreviation) {
+remove_abbreviation <- function(x, abbreviation = NULL) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(modify_footnote_body = match.call()))
 
   # check inputs ---------------------------------------------------------------
   check_class(x, "gtsummary")
-  check_string(abbreviation)
+  check_string(abbreviation, allow_empty = TRUE)
+
+  # remove all abbreviations if abbreviation=NULL ------------------------------
+  if (is_empty(abbreviation)) {
+    x$table_styling$abbreviation <- x$table_styling$abbreviation[0,]
+    return(x)
+  }
+
+  # check passed abbreviations for validity
   if (nrow(x$table_styling$abbreviation) == 0L) {
     cli::cli_abort("There are no abbreviations to remove.", call = get_cli_abort_call())
   }

R/modify_bold_italic.R

@@ -1,6 +1,7 @@
 #' Modify Bold and Italic
 #'
 #' Add or remove bold and italic styling to a cell in a table.
+#' By default, the remove functions will remove all bold/italic styling.
 #'
 #' @inheritParams modify_footnote2
 #'
@@ -45,7 +46,7 @@ modify_bold <- function(x, columns, rows) {
 
 #' @rdname modify_bold_italic
 #' @export
-remove_bold <- function(x, columns, rows) {
+remove_bold <- function(x, columns = everything(), rows = TRUE) {
   set_cli_abort_call()
 
   # check inputs ---------------------------------------------------------------
@@ -89,7 +90,7 @@ modify_italic <- function(x, columns, rows) {
 
 #' @rdname modify_bold_italic
 #' @export
-remove_italic <- function(x, columns, rows) {
+remove_italic <- function(x, columns = everything(), rows = TRUE) {
   set_cli_abort_call()
 
   # check inputs ---------------------------------------------------------------

R/modify_column_merge.R

@@ -106,7 +106,7 @@ modify_column_merge <- function(x, pattern, rows = NULL) {
 
 #' @export
 #' @name modify_column_merge
-remove_column_merge <- function(x, columns) {
+remove_column_merge <- function(x, columns = everything()) {
   set_cli_abort_call()
   # check inputs ---------------------------------------------------------------
   check_class(x, "gtsummary")

R/modify_footnote.R

@@ -169,7 +169,7 @@ modify_footnote_spanning_header <- function(x, footnote, columns,
 
 #' @export
 #' @rdname modify_footnote2
-remove_footnote_header <- function(x, columns) {
+remove_footnote_header <- function(x, columns = everything()) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(remove_footnote_header = match.call()))
 
@@ -197,7 +197,7 @@ remove_footnote_header <- function(x, columns) {
 
 #' @export
 #' @rdname modify_footnote2
-remove_footnote_body <- function(x, columns, rows) {
+remove_footnote_body <- function(x, columns = everything(), rows = TRUE) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(remove_footnote_body = match.call()))
 
@@ -227,13 +227,13 @@ remove_footnote_body <- function(x, columns, rows) {
 
 #' @export
 #' @rdname modify_footnote2
-remove_footnote_spanning_header <- function(x, columns, level) {
+remove_footnote_spanning_header <- function(x, columns = everything(), level = 1L) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(remove_footnote_body = match.call()))
 
   # check inputs ---------------------------------------------------------------
   check_class(x, "gtsummary")
-  check_scalar_integerish(level)
+  check_scalar_integerish(level, allow_empty = NULL)
   if (level < 1) {
     cli::cli_abort(
       "The {.arg level} argument must be a positive integer.",

R/modify_source_note.R

@@ -12,6 +12,7 @@
 #' @param source_note_id (`integers`)\cr
 #'   Integers specifying the ID of the source note to remove.
 #'   Source notes are indexed sequentially at the time of creation.
+#'   Default is `NULL`, which removes all source notes.
 #' @inheritParams modify
 #'
 #' @details
@@ -62,13 +63,12 @@ modify_source_note <- function(x, source_note, text_interpret = c("md", "html"))
 
 #' @export
 #' @rdname modify_source_note
-remove_source_note <- function(x, source_note_id) {
+remove_source_note <- function(x, source_note_id = NULL) {
   set_cli_abort_call()
   updated_call_list <- c(x$call_list, list(remove_source_note = match.call()))
 
   # check inputs ---------------------------------------------------------------
   check_not_missing(x)
-  check_not_missing(source_note_id)
   check_class(x, "gtsummary")
   check_integerish(source_note_id, allow_empty = TRUE)
 

R/tbl_strata.R

@@ -35,7 +35,6 @@
 #'     - `N` Overall N
 #'
 #'   The evaluated value of `.header` is also available within `tbl_strata2(.tbl_fun)`
-#' @param .stack_group_header `r lifecycle::badge("deprecated")`
 #' @param .quiet `r lifecycle::badge("deprecated")`
 #'
 #' @section Tips:
@@ -101,7 +100,6 @@ tbl_strata <- function(data,
                        .combine_args = NULL,
                        .header =
                          ifelse(.combine_with == "tbl_merge", "**{strata}**", "{strata}"),
-                       .stack_group_header = NULL,
                        .quiet = NULL) {
   set_cli_abort_call()
 
@@ -128,7 +126,6 @@ tbl_strata <- function(data,
     .combine_with = .combine_with,
     .combine_args = .combine_args,
     .header = .header,
-    .stack_group_header = .stack_group_header,
     .parent_fun = "tbl_strata"
   )
 }
@@ -144,7 +141,6 @@ tbl_strata2 <- function(data,
                         .combine_args = NULL,
                         .header =
                           ifelse(.combine_with == "tbl_merge", "**{strata}**", "{strata}"),
-                        .stack_group_header = NULL,
                         .quiet = TRUE) {
   set_cli_abort_call()
 
@@ -171,7 +167,6 @@ tbl_strata2 <- function(data,
     .combine_with = .combine_with,
     .combine_args = .combine_args,
     .header = .header,
-    .stack_group_header = .stack_group_header,
     .parent_fun = "tbl_strata2"
   )
 }
@@ -184,7 +179,6 @@ tbl_strata_internal <- function(data,
                                 .combine_with = c("tbl_merge", "tbl_stack"),
                                 .combine_args = NULL,
                                 .header = NULL,
-                                .stack_group_header = NULL,
                                 .parent_fun) {
   check_string(.header)
 
@@ -245,21 +239,6 @@ tbl_strata_internal <- function(data,
         )
     )
 
-  # deprecated argument --------------------------------------------------------
-  if (!is.null(.stack_group_header) && isTRUE(.combine_with == "tbl_stack")) {
-    lifecycle::deprecate_stop(
-      when = "1.5.1",
-      what = "gtsummary::tbl_strata(.stack_group_header)",
-      details =
-        switch(isFALSE(.stack_group_header),
-               glue(
-                 "Use the following instead:\n",
-                 "gtsummary::tbl_strata(.combine_args = list(group_header = NULL))"
-               )
-        )
-    )
-  }
-
   # combining tbls -------------------------------------------------------------
   .combine_args <-
     # default arguments

R/tbl_strata_nested_stack.R

@@ -1,10 +1,15 @@
 #' Stratified Nested Stacking
 #'
+#' @description
 #' This function stratifies your data frame, builds gtsummary tables, and
 #' stacks the resulting tables in a nested style. The underlying functionality
 #' is similar to `tbl_strata()`, except the resulting tables are nested or indented
 #' within each group.
 #'
+#' **NOTE**: The header from the first table is used for the final table. Oftentimes,
+#'           this header will include incorrect Ns and _must be updated._
+#'
+#' @inheritParams tbl_stack
 #' @inheritParams tbl_strata
 #' @param data (`data.frame`)\cr
 #'   a data frame
@@ -155,7 +160,7 @@ tbl_strata_nested_stack <- function(data, strata, .tbl_fun, ..., row_header = "{
   tbl <- tbl_stack(tbls = tbls, quiet = quiet)
 
   # cycle over the depth and indenting nesting headers
-  for (d in seq_len(nrow(df_headers) - 1L)) {
+  for (d in seq_along(strata)) {
     tbl <- tbl |>
       modify_column_indent(
         columns = all_of(first_non_hidden_col),
@@ -169,7 +174,7 @@ tbl_strata_nested_stack <- function(data, strata, .tbl_fun, ..., row_header = "{
   tbl$inputs = list(tbl_row_split = func_inputs)
   tbl$tbls <- NULL
   tbl |>
-    structure(class = c("tbl_row_split", "gtsummary"))
+    structure(class = c("tbl_strata_nested_stack", "tbl_stack", "gtsummary"))
 }