releases prep

Author: ddsjoberg

DESCRIPTION

@@ -47,7 +47,7 @@ BugReports: https://github.com/ddsjoberg/gtsummary/issues
 Depends: 
     R (>= 4.2)
 Imports: 
-    cards (>= 0.5.1.9012),
+    cards (>= 0.6.0),
     cli (>= 3.6.3),
     dplyr (>= 1.1.3),
     glue (>= 1.8.0),
@@ -62,7 +62,7 @@ Suggests:
     broom.helpers (>= 1.17.0),
     broom.mixed (>= 0.2.9),
     car (>= 3.0-11),
-    cardx (>= 0.2.3.9009),
+    cardx (>= 0.2.4),
     cmprsk,
     effectsize (>= 0.6.0),
     emmeans (>= 1.7.3),
@@ -88,7 +88,6 @@ Suggests:
     testthat (>= 3.2.0),
     withr (>= 2.5.0),
     workflows (>= 0.2.4)
-Remotes: insightsengineering/cards, insightsengineering/cardx
 VignetteBuilder: 
     knitr
 Config/Needs/check: hms

NEWS.md

@@ -1,39 +1,41 @@
 # gtsummary (development version)
 
-* Fixed a bug in `tbl_hierarchical()` where the `group*` variables of the resulting `table_body` were not fully populated. (#2192)
+### New Features and Functions
 
 * Added function `modify_post_fmt_fun()` to perform formatting on cells after the primary formatting function has been applied. The functionality is similar to `gt::text_transform()`. (#2014)
 
 * Data pre-processing has now been re-introduced for calculations in `add_p()` and `add_difference()`. Data pre-processing steps  were removed in the v2.0 release; however, in some cases---particularly `add_difference()` for dichotomous variables---the reduced functionality was affecting the user experience. See `?tests` for details on data pre-processing. (#2165)
 
-* The `add_variable_group_header()` function has been generalized to work with gtsummary tables, where previously only `'tbl_summary'` were accepted. (#2197)
+* The `add_variable_group_header()` function has been generalized to work with any gtsummary table, where previously only `'tbl_summary'` were accepted. (#2197)
 
 * The footnote placed on the p-value column by `add_significance_stars()` no longer replaces any existing footnote. Rather the footnote is added to any existing footnote. (#2184)
 
-* Fixed bug in `tbl_cross()` when a column was named `'missing'`. (#2182)
+* 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)
 
-* Corrected bug causing an error in `tbl_hierarchical()` when more than one `by` variable level had been filtered out of the data. (#2173)
+* Added a new theme element `tbl_svysummary-arg:missing_stat`
 
-* 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)
+* Added functions `sort_hierarchical()` and `filter_hierarchical()` to sort and filter hierarchical tables. (#2096)
+
+### Bug Fixes
 
-* The `tbl_strata_nested_stack(quiet)` argument documentation was updated. (#2164)
+* Fixed a bug in `tbl_hierarchical()` where the `group*` variables of the resulting `table_body` were not fully populated. (#2192)
+
+* Corrected bug causing an error in `tbl_hierarchical()` when more than one `by` variable level had been filtered out of the data. (#2173)
 
 * 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.
+* Corrected bug in `tbl_strata_nested_stack()` when the strata variable had a single level. Previously, the indentation of the single strata level was not correct.
 
-* Fix in theme element `tbl_summary-arg:missing_stat` that was not being applied. (#2176)
+* Fix in `tbl_strata_nested_stack()` when there are unobserved combinations of strata levels. (#2179)
 
-* Added a new theme element `tbl_svysummary-arg:missing_stat`
+* Fixed bug in `tbl_cross()` when a column was named `'missing'`. (#2182)
+
+* Fix in theme element `tbl_summary-arg:missing_stat` that was not being applied. (#2176)
 
 * Corrected bug in `tbl_likert()` where variables in table always appeared in alphabetical order. (#2195) 
 
 * Corrected bug in `add_n.tbl_likert()` where the Ns were not formatted with `style_number()`. (#2195)
 
-* Fix in `tbl_strata_nested_stack()` when there are unobserved combinations of strata levels. (#2179)
-
-* Added functions `sort_hierarchical()` and `filter_hierarchical()` to sort and filter hierarchical tables. (#2096)
-
 # gtsummary 2.1.0
 
 ### New Features and Functions

R/as_flex_table.R

@@ -34,9 +34,6 @@ as_flex_table <- function(x, include = everything(), return_calls = FALSE, ...)
 
   # deprecated arguments -------------------------------------------------------
   dots <- rlang::dots_list(...)
-  if (!is.null(dots$strip_md_bold)) {
-    lifecycle::deprecate_stop("1.6.0", "gtsummary::as_flex_table(strip_md_bold=)")
-  }
 
   # process inputs -------------------------------------------------------------
   check_class(x, "gtsummary")

R/as_hux_table.R

@@ -14,7 +14,6 @@
 #' @inheritParams huxtable::quick_xlsx
 #' @param bold_header_rows (scalar `logical`)\cr
 #'   logical indicating whether to bold header rows. Default is `TRUE`
-#' @param strip_md_bold `r lifecycle::badge("deprecated")`
 #'
 #' @name as_hux_table
 #' @return A \{huxtable\} object
@@ -29,19 +28,12 @@ NULL
 
 #' @export
 #' @rdname as_hux_table
-as_hux_table <- function(x, include = everything(), return_calls = FALSE,
-                         strip_md_bold = FALSE) {
+as_hux_table <- function(x, include = everything(), return_calls = FALSE) {
   set_cli_abort_call()
   check_class(x, "gtsummary")
   check_pkg_installed("huxtable")
   check_scalar_logical(return_calls)
 
-  if (!isFALSE(strip_md_bold)) {
-    lifecycle::deprecate_stop(
-      "1.6.0", "gtsummary::as_hux_table(strip_md_bold=)",
-      details = "Markdown syntax is now recognized by the {huxtable} package."
-    )
-  }
   # running pre-conversion function, if present --------------------------------
   x <- do.call(get_theme_element("pkgwide-fun:pre_conversion", default = identity), list(x))
 

R/as_kable.R

@@ -64,13 +64,6 @@ as_kable <- function(x, ..., include = everything(), return_calls = FALSE) {
 table_styling_to_kable_calls <- function(x, ...) {
   dots <- rlang::enexprs(...)
 
-  if (!is.null(dots[["fmt_missing"]])) {
-    lifecycle::deprecate_stop(
-      when = "1.6.0",
-      what = "gtsummary::as_kable_extra(fmt_missing=)"
-    )
-  }
-
   kable_calls <-
     table_styling_to_tibble_calls(x, col_labels = FALSE, fmt_missing = TRUE)
 

R/as_kable_extra.R

@@ -151,24 +151,9 @@ as_kable_extra <- function(x,
 }
 
 
-
-
 table_styling_to_kable_extra_calls <- function(x, escape, format, addtl_fmt, ...) {
   dots <- rlang::dots_list(...)
 
-  if (!is.null(dots[["strip_md_bold"]])) {
-    lifecycle::deprecate_warn(
-      when = "1.6.0",
-      what = "gtsummary::as_kable_extra(strip_md_bold=)"
-    )
-  }
-  if (!is.null(dots[["fmt_missing"]])) {
-    lifecycle::deprecate_stop(
-      when = "1.6.0",
-      what = "gtsummary::as_kable_extra(fmt_missing=)"
-    )
-  }
-
   # if escape is FALSE and latex output, convert markdown to latex and add linebreaks
   if (!isTRUE(escape) && isTRUE(addtl_fmt) && isTRUE(format == "latex")) {
     x <- .latex_conversion_and_escaping(x)

R/deprecated.R

@@ -9,21 +9,21 @@
 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
+#   v2.2.0 2025-04-11
+#   v2.1.0 2025-02-19
+#   v2.0.2 2024-09-05
+#   v2.0.1 2024-08-01
 
 # "warn" deprecation for 18 months: (Sys.Date() - lubridate::dmonths(24)) |> as.Date()
+#   v2.0.0 2024-07-23
 #   v1.7.2 2023-07-13
-#   v1.7.1 2023-04-27
 
 # "stop" deprecation for 12 months: (Sys.Date() - lubridate::dmonths(36)) |> as.Date()
+#   v1.7.1 2023-04-27
 #   v1.7.0 2023-01-13
 #   v1.6.3 2022-12-06
 #   v1.6.2 2022-09-30
 #   v1.6.1 2022-06-22
-#   v1.6.0 2022-04-25
 
 
 # v1.6.1 ----------------------------------------------------------

R/tbl_strata_nested_stack.R

@@ -104,7 +104,8 @@ tbl_strata_nested_stack <- function(data, strata, .tbl_fun, ..., row_header = "{
           dplyr::mutate(
             strata = .data$variable_level |> unlist(),
             "{strata[i]}_strata" := glue::glue(row_header)
-          ) |>
+          ) %>%
+          structure(., class = c("card", class(.))) |>
           cards::rename_ard_columns() |>
           dplyr::select(any_of(strata), all_of(glue::glue("{strata[i]}_strata")))
       }

cran-comments.md

@@ -9,10 +9,12 @@ We checked 23 reverse dependencies, comparing R CMD check results across CRAN an
  * We saw 0 new problems
  * We failed to check 2 packages
 
+Issues with CRAN packages are summarised below.
+
 ### Failed to check
 
-* brms.mmrm    
-* equatiomatic 
+* brms.mmrm
+* equatiomatic
 
 ## Additional Comments
 

man/as_hux_table.Rd

@@ -252,12 +252,6 @@ test_that("as_hux_table passes missing symbols correctly", {
   )
 })
 
-test_that("as_hux_table(strip_md_bold) causes defunct error", {
-  lifecycle::expect_defunct(
-    my_tbl_summary |> as_hux_table(strip_md_bold = TRUE)
-  )
-})
-
 # as_hux_xlsx ----
 
 test_that("as_hux_xlsx works with standard use", {