Merge branch 'main' into 37-ard-for-moods-test

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,60 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+
+          - {os: windows-latest, r: 'release'}
+          # use 4.1 to check with rtools40's older compiler
+          # - {os: windows-latest, r: '4.1'}
+
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          # - {os: ubuntu-latest,   r: 'oldrel-2'}
+          # - {os: ubuntu-latest,   r: 'oldrel-3'}
+          # - {os: ubuntu-latest,   r: 'oldrel-4'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - 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::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/test-coverage.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -5,14 +5,16 @@ Authors@R: c(
     person("Daniel", "Sjoberg", , "[email protected]", role = c("aut", "cre")),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
-Description: R Package to Supplement ARD Functions Found in {cards}.
+Description: Extra Analysis Results Data (ARD) functions. The package
+    supplements the ARD functions from the 'cards' package, exporting
+    functions to put statistical results in the ARD format.
 License: Apache License 2.0
 URL: https://github.com/insightsengineering/cardx
 BugReports: https://github.com/insightsengineering/cardx/issues
 Depends:
     R (>= 4.1)
 Imports:
-    cards (>= 0.0.0.9039),
+    cards (>= 0.0.0.9044),
     cli (>= 3.6.1),
     dplyr (>= 1.1.2),
     glue (>= 1.6.2),

R/ard_ttest.R

@@ -62,7 +62,7 @@ ard_ttest <- function(data, by, variable, ...) {
     variable = variable,
     lst_tidy =
       cards::eval_capture_conditions(
-        stats::t.test(data[[variable]] ~ data[[by]], paired = FALSE, ...) |>
+        stats::t.test(data[[variable]] ~ data[[by]], ...) |>
           broom::tidy()
       ),
     paired = FALSE,

R/ard_wilcoxtest.R

@@ -62,7 +62,7 @@ ard_wilcoxtest <- function(data, by, variable, ...) {
     variable = variable,
     lst_tidy =
       cards::eval_capture_conditions(
-        stats::wilcox.test(data[[variable]] ~ data[[by]], paired = FALSE, ...) |>
+        stats::wilcox.test(data[[variable]] ~ data[[by]], ...) |>
           broom::tidy()
       ),
     paired = FALSE,