Scda test reversedependency

.Rbuildignore

@@ -41,7 +41,7 @@ pkgdown
 ^cran-comments\.md$
 ^\.covrignore$
 ^\.idea$
-^lint_results.txt$
+^dev$
 
 # output
 ^output$

.github/workflows/release.yaml

@@ -0,0 +1,42 @@
+---
+name: release 🕰️
+
+on:
+  pull_request:
+    types:
+      - opened
+      - ready_for_review
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+    inputs:
+      chosen-workflow:
+        description: |
+          Select which workflow you'd like to run
+        required: true
+        type: choice
+        default: rhub
+        options:
+          - rhub
+          - revdepcheck
+
+jobs:
+  revdepcheck:
+    if: >
+      github.event_name == 'release' || (
+        github.event_name == 'workflow_dispatch' &&
+        inputs.chosen-workflow == 'revdepcheck'
+      )
+    name: revdepcheck ↩️
+    uses: johnsonandjohnson/junco/.github/workflows/revdepcheck.yaml@scda_test_reversedependency
+  rhub:
+    if: >
+      github.event_name == 'release' || (
+        github.event_name == 'workflow_dispatch' &&
+        inputs.chosen-workflow == 'rhub'
+      )
+    name: R-hub 🌐
+    uses: johnsonandjohnson/junco/.github/workflows/rhub.yaml@main

.github/workflows/revdepcheck.yaml

@@ -0,0 +1,101 @@
+---
+name: revdepcheck ⏪
+
+on:
+  workflow_dispatch:
+  workflow_call:
+    secrets:
+      REPO_GITHUB_TOKEN:
+        description: |
+          Github token with read access to repositories, required for dependencies installation
+        required: false
+    inputs:
+      additional-env-vars:
+        description: |
+          Extra environment variables, as a 'key=value' pair, with each pair on a new line.
+          Example usage:
+          additional-env-vars: |
+            ABC=123
+            XYZ=456
+        required: false
+        default: ""
+        type: string
+      lookup-refs:
+        description: |
+          Passed to setup-r-dependencies action.
+        required: false
+        default: ""
+        type: string
+
+jobs:
+  revdepcheck:
+    name: revdepcheck ⏪
+    runs-on: ubuntu-latest
+    if: >
+      !contains(github.event.commits[0].message, '[skip revdepcheck]')
+       && github.event.pull_request.draft == false
+    container:
+      image: ghcr.io/insightsengineering/rstudio:latest
+
+    steps:
+      - name: Setup token 🔑
+        id: github-token
+        run: |
+          if [ "${{ secrets.REPO_GITHUB_TOKEN }}" == "" ]; then
+            echo "REPO_GITHUB_TOKEN is empty. Substituting it with GITHUB_TOKEN."
+            echo "token=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
+          else
+            echo "Using REPO_GITHUB_TOKEN."
+            echo "token=${{ secrets.REPO_GITHUB_TOKEN }}" >> $GITHUB_OUTPUT
+          fi
+        shell: bash
+
+      - name: Get branch names 🌿
+        id: branch-name
+        uses: tj-actions/branch-names@v9.0.0
+
+      - name: Checkout repo 🛎
+        uses: actions/checkout@v4.1.1
+        with:
+          ref: ${{ steps.branch-name.outputs.current_branch }}
+          fetch-depth: 1
+
+      - name: Restore cache 💰
+        uses: actions/cache@v4
+        with:
+          key: revdepcheck-${{ runner.os }}-${{ github.event.repository.name }}
+          path: |
+            ~/.cache/R/pkgcache/pkg
+            ~/.cache/R-crancache
+
+      - name: Check commit message 💬
+        run: |
+          git config --global --add safe.directory $(pwd)
+          export head_commit_message="$(git show -s --format=%B | tr '\r\n' ' ' | tr '\n' ' ')"
+          echo "head_commit_message = $head_commit_message"
+          if [[ $head_commit_message == *"$SKIP_INSTRUCTION"* ]]; then
+            echo "Skip instruction detected - cancelling the workflow."
+            exit 1
+          fi
+        shell: bash
+        env:
+          SKIP_INSTRUCTION: "[skip revdepcheck]"
+
+      - name: revdepcheck 🔄
+        id: revdepcheck
+        uses: insightsengineering/r-revdepcheck-action@main
+        with:
+          github-token: ${{ steps.github-token.outputs.token }}
+          additional-env-vars: ${{ inputs.additional-env-vars }}
+
+      - name: Prepare revdep artifact 🎁
+        run: |
+          rm -rf revdep/library.noindex
+          rm -rf revdep/library
+        shell: bash
+
+      - name: Upload artifact ⬆
+        uses: actions/upload-artifact@v4
+        with:
+          name: revdep
+          path: revdep/

.revdeprefs.yaml

@@ -0,0 +1,2 @@
+- insightsengineering/teal.modules.clinical
+- insightsengineering/scda.test

CHANGELOG.md

@@ -5,22 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [0.1.4] - Unreleased
+## [0.1.4.9] - Unreleased
+
+### Added and Removed
+- Added new behavior for nested `countsource` in h_a_freq_dataprep `altdf_subset` (#200)
+- Add `geom_boxplot_j()` to be able to draw boxplots whose statistics follow SAS quantile(type =2)
+
+
+## [0.1.4] - 2026-02-02
 
 ### Fixed
 - "caption" paragraph style in the docx exporter is now handled by flextable (#182)
 - Fixed `tt_to_tlgrtf()`, when exporting an empty listing do not lose Title and Footers
+- Fixed `tt_to_tlgrtf()` argument `label_width_ins` which was not applying the change in the row label column width (#166).
 
 ### Changed
 - Reinstate rbmi as dependency
 
 
-## [0.1.3.9.1] - 2026-02-02
-
-### Fixed
-- Fixed `tt_to_tlgrtf()` argument `label_width_ins` which was not applying the change in the row label column width (#166).
-
-
 ## [0.1.3] - 2026-01-12
 
 ### Changed

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: junco
 Title: Create Common Tables and Listings Used in Clinical Trials
-Version: 0.1.4
-Date: 2026-01-12
+Version: 0.1.4.9
+Date: 2026-03-11
 Authors@R: c(
     person("Gabriel", "Becker", , "gabembecker@gmail.com", role = c("cre", "aut"),
            comment = "Original creator of the package, and author of included formatters functions"),

NAMESPACE

@@ -49,6 +49,7 @@ export(find_missing_chg_after_avisit)
 export(fit_ancova)
 export(fit_mmrm_j)
 export(format_stats)
+export(geom_boxplot_j)
 export(get_mmrm_lsmeans)
 export(get_ref_info)
 export(get_titles_from_file)
@@ -137,6 +138,11 @@ import(tidytlg)
 importFrom(assertthat,assert_that)
 importFrom(formatters,wrap_string_ttype)
 importFrom(generics,tidy)
+importFrom(ggplot2,GeomBoxplot)
+importFrom(ggplot2,Stat)
+importFrom(ggplot2,ggproto)
+importFrom(ggplot2,layer)
+importFrom(stats,quantile)
 importFrom(stats,setNames)
 importFrom(survival,Surv)
 importFrom(survival,coxph)

NEWS.md

@@ -1,12 +1,5 @@
-# junco 0.1.4
+# junco 0.1.4.9
 
 
-### Fixed
-- "caption" paragraph style in the docx exporter is now handled by flextable (#182)
-- Fixed `tt_to_tlgrtf()`, when exporting an empty listing do not lose Title and Footers
-- Fixed `tt_to_tlgrtf()` argument `label_width_ins` which was not applying the change in the row label column width (#166).
-
-### Changed
-- Reinstate rbmi as dependency
 
 

R/a_freq_j.R

@@ -33,8 +33,10 @@
 #' It is a data frame in the higher row-space than the current input df
 #' (which underwent row-splitting by the rtables splitting machinery).
 #'
-#' @param countsource Either `df` or `alt_df`.\cr
-#' When `alt_df` the counts will be based upon the alternative dataframe `alt_df`.\cr
+#' @param countsource Either `df`, `altdf`, or `altdf_subset`.\cr
+#' When `altdf` the counts will be based upon the alternative dataframe `alt_df`.\cr
+#' When `altdf_subset` the counts will be based upon `alt_df` but first restricted\cr
+#' to the levels/values of the current row split for `.var` (or to `val` when provided).\cr
 #' This is useful for subgroup processing,
 #' to present counts of subjects in a subgroup from the alternative dataframe.
 #'
@@ -86,15 +88,15 @@ s_freq_j <- function(
   id = "USUBJID",
   denom = c("n_df", "n_altdf", "N_col", "n_rowdf", "n_parentdf"),
   .N_col,
-  countsource = c("df", "altdf")
+  countsource = c("df", "altdf", "altdf_subset")
 ) {
   if (is.na(.var) || is.null(.var)) {
     stop("Argument .var cannot be NA or NULL.")
   }
 
   countsource <- match.arg(countsource)
 
-  if (countsource == "altdf") {
+  if (countsource %in% c("altdf", "altdf_subset")) {
     df <- alt_df
   }
 
@@ -630,7 +632,7 @@ a_freq_j <- function(
   extrablanklineafter = NULL,
   restr_columns = NULL,
   colgroup = NULL,
-  countsource = c("df", "altdf")
+  countsource = c("df", "altdf", "altdf_subset")
 ) {
   denom <- match.arg(denom)
   method <- match.arg(method)
@@ -679,7 +681,8 @@ a_freq_j <- function(
     label_map = label_map,
     .alt_df_full = .alt_df_full,
     denom_by = denom_by,
-    .stats = .stats
+    .stats = .stats,
+    countsource = countsource
   )
   # res_dataprep is list with elements
   # df .df_row val