Merge branch 'main' into 767_sort_filter_hierarchical

ddsjoberg · Jan 7, 2025 · 5f9f63c · 5f9f63c
2 parents ae03a80 + 14362f7
commit 5f9f63c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result Tables
-Version: 2.0.4.9006
+Version: 2.0.4.9007
 Authors@R: c(
     person("Daniel D.", "Sjoberg", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0862-2018")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -167,6 +167,7 @@ export(modify_fmt_fun)
 export(modify_footnote)
 export(modify_footnote_body)
 export(modify_footnote_header)
+export(modify_footnote_spanning_header)
 export(modify_header)
 export(modify_source_note)
 export(modify_spanning_header)
@@ -188,8 +189,10 @@ export(ratio_summary)
 export(remove_abbreviation)
 export(remove_footnote_body)
 export(remove_footnote_header)
+export(remove_footnote_spanning_header)
 export(remove_row_type)
 export(remove_source_note)
+export(remove_spanning_header)
 export(reset_gtsummary_theme)
 export(scope_header)
 export(scope_table_body)

diff --git a/NEWS.md b/NEWS.md
@@ -8,6 +8,10 @@
 
 * Previously, source notes were an undocumented feature and only a single source note could be included in a table. We now export `modify_source_note()` and `remove_source_note()` to add and remove any number of source notes. Also, when merging and stacking tables, previously due to the one source note limit, only the first source note was retained. Now all source notes will be included below the resulting table. _This is different behavior compared to previous versions of the package and in rare cases may result in a different source note._ Moreover, `kableExtra` output now supports source notes, where previously they were omitted.
 
+* The `modify_spanning_header(level)` argument has been added to allow for multiple levels of spanning headers in the resulting tables. The `remove_spanning_header()` function has also been added to ease the removal of spanning headers. (#2099)
+
+* The `modify_footnote_spanning_header()` function has been added to ease adding footnotes to spanning headers. A companion function, `remove_footnote_spanning_header()`, has been added to remove spanning headers.
+
 * Language translations have been updated with a handful of missing translations. (#2100)
 
 * The `modify_caption(caption)` argument now accepts a vector of captions, instead of just a string. Note, however, that not all print engines support a vector of captions. (#2107)

diff --git a/R/as_flex_table.R b/R/as_flex_table.R
@@ -118,51 +118,60 @@ table_styling_to_flextable_calls <- function(x, ...) {
 
   # add_header_row -------------------------------------------------------------
   # this is the spanning rows
-  any_spanning_header <- any(!is.na(x$table_styling$header$spanning_header))
+  any_spanning_header <- nrow(x$table_styling$spanning_header) > 0L
   if (any_spanning_header == FALSE) {
     flextable_calls[["add_header_row"]] <- list()
   } else {
-    df_header0 <-
-      x$table_styling$header |>
-      dplyr::filter(.data$hide == FALSE) |>
-      dplyr::select("spanning_header") |>
+    flextable_calls[["add_header_row"]] <-
+      tidyr::expand_grid(
+        level = unique(x$table_styling$spanning_header$level),
+        column = x$table_styling$header$column[!x$table_styling$header$hide]
+      ) |>
+      dplyr::left_join(
+        x$table_styling$spanning_header[c("level", "column", "spanning_header")],
+        by = c("level", "column")
+      ) |>
       dplyr::mutate(
-        spanning_header = ifelse(is.na(.data$spanning_header),
-                                 " ", .data$spanning_header
-        ),
+        .by = "level",
+        spanning_header =
+          ifelse(is.na(.data$spanning_header), " ", .data$spanning_header),
         spanning_header_id = dplyr::row_number()
-      )
-    # assigning an ID for each spanning header group
-    for (i in seq(2, nrow(df_header0))) {
-      if (df_header0$spanning_header[i] == df_header0$spanning_header[i - 1]) {
-        df_header0$spanning_header_id[i] <- df_header0$spanning_header_id[i - 1]
-      }
-    }
-
-    df_header <-
-      df_header0 |>
-      dplyr::group_by(.data$spanning_header_id) |>
-      dplyr::mutate(width = dplyr::n()) |>
-      dplyr::distinct() |>
-      dplyr::ungroup() |>
-      dplyr::mutate(
-        column_id = map2(.data$spanning_header_id, .data$width, ~ seq(.x, .x + .y - 1L, by = 1L))
-      )
+      ) |>
+      dplyr::group_by(.data$level) |>
+      dplyr::group_map(
+        \(df_values, df_group) {
+          # assigning an ID for each spanning header group
+          for (i in seq(2, nrow(df_values))) {
+            if (df_values$spanning_header[i] == df_values$spanning_header[i - 1]) {
+              df_values$spanning_header_id[i] <- df_values$spanning_header_id[i - 1]
+            }
+          }
 
-    flextable_calls[["add_header_row"]] <- list(
-      expr(
-        # add the header row with the spanning headers
-        flextable::add_header_row(
-          values = !!df_header$spanning_header,
-          colwidths = !!df_header$width
-        )
-      )
-    )
+          df_header <-
+            dplyr::bind_cols(df_group, df_values) |>
+            dplyr::select(-"column") |>
+            dplyr::group_by(.data$spanning_header_id) |>
+            dplyr::mutate(width = dplyr::n()) |>
+            dplyr::distinct() |>
+            dplyr::ungroup() |>
+            dplyr::mutate(
+              column_id = map2(.data$spanning_header_id, .data$width, ~ seq(.x, .x + .y - 1L, by = 1L))
+            )
 
-    flextable_calls[["compose_header_row"]] <-
-      .chr_with_md_to_ft_compose(
-        x = df_header$spanning_header,
-        j = df_header$column_id
+          c(
+            list(expr(
+              # add the header row with the spanning headers
+              flextable::add_header_row(
+                values = !!df_header$spanning_header,
+                colwidths = !!df_header$width
+              )
+            )),
+            .chr_with_md_to_ft_compose(
+              x = df_header$spanning_header,
+              j = df_header$column_id
+            )
+          )
+        }
       )
   }
 
@@ -207,20 +216,28 @@ table_styling_to_flextable_calls <- function(x, ...) {
   flextable_calls[["autofit"]] <- expr(flextable::autofit())
 
   # footnote_header ------------------------------------------------------------
+  spanning_header_lvls <- x$table_styling$spanning_header$level |> append(0L) |> max()
   df_footnote_header <-
-    .number_footnotes(x, "footnote_header") |>
-    tidyr::nest(df_location = c("column", "column_id")) |>
+    dplyr::bind_rows(
+      x$table_styling$footnote_header |> dplyr::mutate(level = 0L),
+      x$table_styling$footnote_spanning_header
+    ) |>
+    dplyr::mutate(
+      row_numbers = .env$spanning_header_lvls - .data$level + 1L
+    ) %>%
+    .number_footnotes(x, type = .) |>
+    tidyr::nest(df_location = c("column", "column_id", "row_numbers")) |>
     dplyr::mutate(
+      row_numbers = map(.data$df_location, ~ getElement(.x, "row_numbers")),
       column_id = map(.data$df_location, ~ getElement(.x, "column_id"))
     )
-  header_i_index <- ifelse(any_spanning_header == TRUE, 2L, 1L)
 
   flextable_calls[["footnote_header"]] <-
     map(
       seq_len(nrow(df_footnote_header)),
       ~ expr(
         flextable::footnote(
-          i = !!header_i_index,
+          i = !!df_footnote_header$row_numbers[[.x]],
           j = !!df_footnote_header$column_id[[.x]],
           value = flextable::as_paragraph(!!df_footnote_header$footnote[[.x]]),
           part = "header",
@@ -231,7 +248,7 @@ table_styling_to_flextable_calls <- function(x, ...) {
 
   # footnote_body --------------------------------------------------------------
   df_footnote_body <-
-    .number_footnotes(x, "footnote_body", start_with = nrow(df_footnote_header)) |>
+    .number_footnotes(x, type = x$table_styling$footnote_body, start_with = nrow(df_footnote_header)) |>
     tidyr::nest(df_location = c("column", "column_id", "row_numbers")) |>
     dplyr::mutate(
       row_numbers = map(.data$df_location, ~ getElement(.x, "row_numbers")),
@@ -252,7 +269,6 @@ table_styling_to_flextable_calls <- function(x, ...) {
       )
     )
 
-
   # abbreviation ---------------------------------------------------------------
   flextable_calls[["abbreviations"]] <-
     case_switch(

diff --git a/R/as_gt.R b/R/as_gt.R
@@ -234,6 +234,25 @@ table_styling_to_gt_calls <- function(x, ...) {
         expr(gt::cols_label_with(fn = function(x) gsub(x = x, pattern = "\\n(?!\\\\)", replacement = "", fixed = FALSE, perl = TRUE)))
     )
 
+  # spanning_header ------------------------------------------------------------
+  gt_calls[["tab_spanner"]] <-
+    case_switch(
+      nrow(x$table_styling$spanning_header) > 0L ~
+        x$table_styling$spanning_header |>
+        dplyr::group_by(.data$level, .data$spanning_header, .data$text_interpret) |>
+        dplyr::group_map(
+          \(.x, .y) {
+            expr(gt::tab_spanner(
+              columns = !!.x$column,
+              label = !!call2(parse_expr(.y$text_interpret), .y$spanning_header),
+              level = !!.y$level,
+              id = !!paste0("level ", .y$level, "; ", .x$column[1]),
+              gather = FALSE
+            ))
+          }
+        ),
+      .default = list()
+    )
 
   # tab_footnote ---------------------------------------------------------------
   gt_calls[["tab_footnote"]] <-
@@ -270,32 +289,27 @@ table_styling_to_gt_calls <- function(x, ...) {
             )
           )
         }
-      )
-    )
-
-  # spanning_header ------------------------------------------------------------
-  df_spanning_header <-
-    x$table_styling$header |>
-    dplyr::select("column", "interpret_spanning_header", "spanning_header") |>
-    dplyr::filter(!is.na(.data$spanning_header)) |>
-    tidyr::nest(cols = "column") |>
-    dplyr::mutate(
-      spanning_header = map2(
-        .data$interpret_spanning_header, .data$spanning_header,
-        ~ call2(parse_expr(.x), .y)
       ),
-      cols = map(.data$cols, ~ dplyr::pull(.x))
-    ) |>
-    dplyr::select("spanning_header", "cols")
-
-  gt_calls[["tab_spanner"]] <-
-    map(
-      seq_len(nrow(df_spanning_header)),
-      ~ expr(gt::tab_spanner(
-        columns = !!df_spanning_header$cols[[.x]],
-        label = gt::md(!!df_spanning_header$spanning_header[[.x]]),
-        gather = FALSE
-      ))
+      # spanning header footnotes
+      map(
+        seq_len(nrow(x$table_styling$footnote_spanning_header)),
+        function(i) {
+          expr(
+            gt::tab_footnote(
+              footnote =
+                !!call2(
+                  parse_expr(x$table_styling$footnote_spanning_header$text_interpret[i]),
+                  x$table_styling$footnote_spanning_header$footnote[i]
+                ),
+              locations =
+                gt::cells_column_spanners(
+                  spanners = !!paste0("level ", x$table_styling$footnote_spanning_header$level[i], "; ", x$table_styling$footnote_spanning_header$column[i]),
+                  levels = !!x$table_styling$footnote_spanning_header$level[i]
+                )
+            )
+          )
+        }
+      )
     )
 
   # horizontal_line ------------------------------------------------------------

diff --git a/R/as_hux_table.R b/R/as_hux_table.R
@@ -187,8 +187,9 @@ table_styling_to_huxtable_calls <- function(x, ...) {
   # footnote -------------------------------------------------------------------
   vct_footnote <-
     dplyr::bind_rows(
-      .number_footnotes(x, "footnote_header"),
-      .number_footnotes(x, "footnote_body")
+      .number_footnotes(x, x$table_styling$footnote_spanning_header),
+      .number_footnotes(x, x$table_styling$footnote_header),
+      .number_footnotes(x, x$table_styling$footnote_body)
     ) |>
     dplyr::pull("footnote") %>%
     unique()
@@ -331,30 +332,35 @@ table_styling_to_huxtable_calls <- function(x, ...) {
     expr(huxtable::insert_row(after = 0, !!!col_labels))
   )
 
-  any_spanning_header <- sum(!is.na(x$table_styling$header$spanning_header)) > 0
-  if (any_spanning_header) {
-    header_content <- x$table_styling$header$spanning_header[x$table_styling$header$hide == FALSE]
-    huxtable_calls[["insert_row"]] <- append(
-      huxtable_calls[["insert_row"]],
-      expr(huxtable::insert_row(after = 0, !!!header_content))
-    )
-
-    header_colspans <- rle(header_content)$lengths
-    header_colspan_cols <- cumsum(c(
-      1,
-      header_colspans[-length(header_colspans)]
-    ))
-    huxtable_calls[["insert_row"]] <- append(
-      huxtable_calls[["insert_row"]],
-      expr(
-        huxtable::set_colspan(
-          row = 1, col = !!header_colspan_cols,
-          value = !!header_colspans
-        )
+  if (nrow(x$table_styling$spanning_header) > 0L) {
+    huxtable_calls[["insert_row"]] <-
+      huxtable_calls[["insert_row"]] |>
+      append(
+        tidyr::expand_grid(
+          level = unique(x$table_styling$spanning_header$level),
+          column = x$table_styling$header$column[!x$table_styling$header$hide]
+        ) |>
+          dplyr::left_join(
+            x$table_styling$spanning_header[c("level", "column", "spanning_header")],
+            by = c("level", "column")
+          ) |>
+          dplyr::group_by(.data$level) |>
+          dplyr::group_map(
+            \(df_values, df_group) {
+              header_content <-  df_values$spanning_header
+              header_colspans <- rle(header_content)$lengths
+              header_colspan_cols <- cumsum(c(1, header_colspans[-length(header_colspans)]))
+
+              list(
+                expr(huxtable::insert_row(after = 0, !!!header_content)),
+                expr(huxtable::set_colspan(row = 1, col = !!header_colspan_cols, value = !!header_colspans))
+              )
+            }
+          )
       )
-    )
   }
-  header_bottom_row <- if (any_spanning_header) 2 else 1
+
+  header_bottom_row <- length(unique(x$table_styling$spanning_header$level)) + 1L
   huxtable_calls[["insert_row"]] <- append(
     huxtable_calls[["insert_row"]],
     expr(
@@ -366,7 +372,7 @@ table_styling_to_huxtable_calls <- function(x, ...) {
   )
 
   # set_markdown ---------------------------------------------------------------
-  header_rows <- switch(any_spanning_header, 1:2) %||% 1L # styler: off
+  header_rows <- seq_len(length(unique(x$table_styling$spanning_header$level)) + 1L) # styler: off
   huxtable_calls[["set_markdown"]] <-
     list(
       set_markdown =