Hotfix pipeline broken

.Rbuildignore

@@ -41,13 +41,9 @@ pkgdown
 ^cran-comments\.md$
 ^\.covrignore$
 ^\.idea$
-^lint_results.txt$
-
-# output
+^\.vscode$
+^air\.toml$
 ^output$
-^junco_tlg_template_scripts$
 ^[^/]*\.R$
-^\.vscode$
-^[.]?air[.]toml$
 ^CHANGELOG\.md$
-^air\.toml$
+^dev$

.github/workflows/hotfix.yml

@@ -0,0 +1,83 @@
+name: Hotfix Tests
+
+on:
+  push:
+    branches:
+      - 'feature/hotfix-*'
+  pull_request:
+    branches: [main, CRAN]
+  workflow_dispatch:
+
+jobs:
+  test-hotfix:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: '4.5.0'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::devtools
+            any::testthat
+
+      - name: Install Local Junco
+        shell: Rscript {0}
+        run: |
+          devtools::install(".", upgrade = FALSE, quick = TRUE)
+
+      - name: Execute tests with hotfixes
+        shell: Rscript {0}
+        run: |
+          project_root <- getwd()
+          hotfix_file <- file.path(project_root, "dev", "junco_hotfix.R")
+
+          devtools::load_all(project_root)
+
+          # Inject the Hotfix 
+          if (file.exists(hotfix_file)) {
+            message(">>> Injecting Hotfix: ", hotfix_file)
+            source(hotfix_file, local = FALSE)
+          } else {
+            stop("Hotfix file not found at ", hotfix_file)
+          }
+
+          #  Run tests in the current environment
+          library(testthat)
+          options(rgl.useNULL = TRUE)
+          options(testthat.progress.max_reports = 10)
+          testthat::set_max_fails(Inf)
+
+          reporter <- testthat::ListReporter$new()
+          try({
+            testthat::test_dir("tests/testthat", reporter = reporter)
+          }, silent = FALSE)
+          results <- reporter$get_results()
+
+          # Exit with error code if any tests failed
+          if (!testthat:::all_passed(results)) {
+            stop("Tests failed with the current hotfix applied.")
+          }
+
+
+

CHANGELOG.md

@@ -5,22 +5,23 @@ 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
+- 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/geom_j.R

@@ -0,0 +1,124 @@
+#' Boxplot statistics with configurable quantile type
+#'
+#' `StatBoxplotQuantile` computes boxplot statistics using a configurable
+#' quantile definition. By default, quartiles use `quantile(type = 2)` to follow
+#' `PCTLDEF = 5` (SAS default). It computes quartiles, whiskers, and outliers.
+#'
+#' Required aesthetics: `x`, `y`.
+#'
+#' Computed variables (per group):
+#' - `ymin`: lower whisker (min value within lower fence)
+#' - `lower`: first quartile (Q1)
+#' - `middle`: median (Q2)
+#' - `upper`: third quartile (Q3)
+#' - `ymax`: upper whisker (max value within upper fence)
+#' - `outliers`: list-column of values outside whiskers
+#' - `x`: x position (first value in group)
+#' - `width`: box width used by `GeomBoxplot`
+#'
+#' @section Quantile details:
+#' By default, quartiles are computed with `quantile(type = 2)` to follow
+#' `PCTLDEF = 5` (SAS default). You can change this via the `quantile_type` argument. Fences
+#' are defined as `Q1 - coef * IQR` and `Q3 + coef * IQR` where `IQR = Q3 - Q1` and `coef`
+#' defaults to `1.5`.
+#'
+#' @keywords internal
+#' @importFrom ggplot2 ggproto Stat
+#' @importFrom stats quantile
+StatBoxplotQuantile <- ggproto(
+  "StatBoxplotQuantile", Stat,
+  required_aes = c("x", "y"),
+  dropped_aes = c("x", "y", "weight"),
+  compute_group = function(
+    data,
+    scales,
+    width = NULL,
+    na.rm = FALSE,
+    coef = 1.5,
+    quantile_type = 2
+  ) {
+    vec <- data$y
+    if (length(vec) == 0) {
+      return(data.frame())
+    }
+
+    # Quantiles controlled by quantile_type (default 2 = PCTLDEF=5)
+    qs <- quantile(vec, probs = c(0, 0.25, 0.5, 0.75, 1), type = quantile_type, na.rm = na.rm)
+    iqr <- qs[4] - qs[2]
+
+    lower_fence <- qs[2] - (coef * iqr)
+    upper_fence <- qs[4] + (coef * iqr)
+
+    ymin <- min(vec[vec >= lower_fence], na.rm = na.rm)
+    ymax <- max(vec[vec <= upper_fence], na.rm = na.rm)
+
+    outliers <- vec[vec < ymin | vec > ymax]
+
+    data.frame(
+      ymin = ymin,
+      lower = qs[2],
+      middle = qs[3],
+      upper = qs[4],
+      ymax = ymax,
+      outliers = I(list(outliers)),
+      x = data$x[1],
+      width = if (is.null(width)) 0.75 else width
+    )
+  }
+)
+
+#'  Draws boxplots with configurable quantile type
+#'
+#' `geom_boxplot_j()` draws boxplots whose statistics can follow different
+#'  percentile definitions for quartiles. By default it uses
+#'  `quantile(type = 2)` to follow `PCTLDEF = 5` (SAS default). You can override
+#'  the quantile definition via `quantile_type`. It uses `StatBoxplotQuantile`
+#'  then renders with `GeomBoxplot`.
+#'
+#' @param mapping,data,position,... Standard ggplot2 layer arguments passed to
+#'   `layer()`/`GeomBoxplot`.
+#' @param coef Numeric multiplier for the IQR to compute fences. Defaults to 1.5
+#'   (Tukey).
+#' @param quantile_type Integer in 1:9 passed to `stats::quantile(type = ...)` to
+#'   compute quartiles. Defaults to 2 (follows PCTLDEF = 5).
+#' @param na.rm Logical; if `TRUE`, silently removes `NA` values.
+#' @param show.legend,inherit.aes See `ggplot2::layer()`.
+#'
+#' @return A ggplot2 layer that produces boxplots using the chosen quantile type.
+#'
+#' @examples
+#' library(ggplot2)
+#' library(pharmaverseadamjnj)
+#' ggplot(advs, aes(AVISIT, AVAL, fill = TRT01A)) +
+#'   geom_boxplot_j(position = position_dodge2(preserve = "single"), na.rm = TRUE) +
+#'   theme(axis.text.x = element_text(angle = 45, hjust = 1))
+#'
+#' @export
+#' @importFrom ggplot2 layer GeomBoxplot
+geom_boxplot_j <- function(
+  mapping = NULL,
+  data = NULL,
+  position = "dodge2",
+  ...,
+  coef = 1.5,
+  quantile_type = 2,
+  na.rm = FALSE,
+  show.legend = NA,
+  inherit.aes = TRUE
+) {
+  layer(
+    data = data,
+    mapping = mapping,
+    stat = StatBoxplotQuantile,
+    geom = GeomBoxplot,
+    position = position,
+    show.legend = show.legend,
+    inherit.aes = inherit.aes,
+    params = list(
+      na.rm = na.rm,
+      coef = coef,
+      quantile_type = quantile_type,
+      ...
+    )
+  )
+}

_pkgdown.yml

@@ -124,11 +124,16 @@ reference:
   - title: junco Miscellaneous Functions
     desc: The following functions are other miscellaneous junco functions used to create common table layouts.
     contents:
-    - remove_col_count
-    - rm_levels
-    - get_mmrm_lsmeans
-    - get_ref_info
-    - get_visit_levels
+      - remove_col_count
+      - rm_levels
+      - get_mmrm_lsmeans
+      - get_ref_info
+      - get_visit_levels
+
+  - title: junco Geoms
+    desc: ggplot2 geoms provided by junco.
+    contents:
+      - geom_boxplot_j
 
   - title: internal
     desc: The following are additional junco functions.