v2.0 to main branch (#1778)

* progress * Bridge updates (#1570) * progress * Update NEWS.md * Update NEWS.md * small updates * Selecting updates (#1573) * in progress * progress * GH Action workflow updates (#1574) * updates * more updates * Update test-coverage.yaml * Update pull_request_template.md * updates * updates * Update NEWS.md * Assign digits (#1575) * in progress * progress * Dynamic column headers (#1576) * in progress * progress * progress * Update DESCRIPTION * progress * Update tbl_summary.R * Updating with the `tbl_summary(sort)` argument (#1583) * in progress * Update tbl_summary.R * moving indentation to its own table styling enttry (#1584) * moving indentation to its own table styling enttry * Update NEWS.md * check updates * Update DESCRIPTION * Adding `tbl_summary(percent)` argument (#1585) * updates * updates * progress (#1595) * doc updates * adding default stat labels * progress * Update tbl_summary.R * Update bridge_summary.R * style * Update README.Rmd * dichotomous variable updates * Update test-tbl_summary.R * checks updates * forcats shim update * purrr shim update * Update test-tbl_summary.R * new checks file * lil updates * Adding more `tbl_summary()` tests and organizing snapshot tests (#1604) * data arg update * by arg update for snaps * snap updates for label argument * snaps sort arg * more updates * trucking along * Update tbl_summary.md * more testing * doc update * messaging update * Update .Rbuildignore * updates * updates after cards rename * adding ARDs as lists inside tbl_summary * Create import-standalone-tibble.R * selecting updates (#1611) * rename column summary_type to var_type (#1612) * Adding v2 `add_p.tbl_summary()` (#1615) * in progress * in progress * Update style_sigfig.R * in progress * progress * progress * progress * progress * progress * updates * progress * progress * Update test-add_p.tbl_summary.R * updates * Update R-CMD-check.yaml * Update R-CMD-check.yaml * Update R-CMD-check.yaml * Update R-CMD-check.yaml * more updates * Update test-coverage.yaml * more updates * progress * Update R-CMD-check-as-cran.yaml * Update R-CMD-check-as-cran.yaml * progress * updates * Update R-CMD-check.yaml * more updates * Update add_p.R * more updates * Adding `add_difference.tbl_summary()` to v2 branch (#1634) * more progress * more updates * Update DESCRIPTION * Update DESCRIPTION * Update DESCRIPTION * Update DESCRIPTION * idk what's going on * Update DESCRIPTION * Update test-add_difference.tbl_summary.R * Update DESCRIPTION * emmeans updates * emmeans updates * Update DESCRIPTION * updates * Update utils-add_p_tests.R * First draft of `card_summary()` (#1636) * first draft of `card_summary()` * Update card_summary.R * adding some unit tests * more tests * styler * Generalizing `brdg_summary()` and supporting `pier_*()` functions (#1642) * brdg updates! * updates * v2.0 Adding `add_n.tbl summary()` (#1645) * adding add_n.tbl_summary() * Update add_n.R * Update add_n.R * lil updates * progress * Adding v2.0 `tbl_regression()` (#1648) * progress * doc updates * updates * Update DESCRIPTION * Update test-tbl_regression.R * bridge rename (#1661) * Adding `add_q()` (#1662) * v2.0 `add_overall.tbl summary()` (#1663) * progress * progress * styler * progress (#1664) * V2.0 adding pkgdown (#1665) * adding pkgdown yaml * doc update * doc updates related to pkgdown * v2.0 Adding `add_stat()` (#1667) * progress * Update add_stat.md * lil updates * Update _pkgdown.yml * v2.0 `add_stat_label.tbl_summary()` (#1669) * progress * progress * doc updates * Update add_stat_label.R * v2.0 `modify_table_styling()` (#1672) * progress * progress * progress (#1673) * v2.0 `modify_header()`, `modify_spanning_header()`, `modify_footnote()`, `modify_caption()` (#1676) * progress * progress * Create test-modify_spanning_header.R * progress (#1677) * v2.0 `modify_column_hide()`, `modify_column_unhide()`, `modify_column_alignment()`, `modify_column_indent()` (#1678) * in progress * progress * progress * v2.0 `modify_fmt_fun()` (#1679) * progress * Update DESCRIPTION * Update DESCRIPTION * v2.0 bold and italicize labels and levels (#1680) * progress * Update _pkgdown.yml * v2.0 `bold_p()` (#1686) * progress * progress * progress * v2.0 Migrating themes (#1685) * progress * progress * Update DESCRIPTION * progress * Update test-theme_gtsummary.R * Update _pkgdown.yml * v2.0 `style_*()` migration (#1688) * in progress * style updates * progress * v2.0 language translations (#1682) * in progress * Update sysdata.rda * progress * V2.0 `tbl_stack()` (#1694) * adding function * lil updates * Update utils-add_p_tests.R * v2.0 `tbl_uvregression()` (#1692) * progress * updates * updates * progress * in progress * progress * progress * Update tbl_uvregression.Rd * progress * Update DESCRIPTION * V2.0 `separate_p_footnotes()` (#1695) * progress * progress * updates * Update _pkgdown.yml * V2.0 `tbl_custom_summary()` (#1698) * progress * progress * progress * Update _pkgdown.yml * progress (#1700) * v2.0 regression tidiers + S3 methods (#1701) * progress * updates * docs * updates * trying to get pkgdown to work * updates * v2.0 `add_global_p()` (#1706) * progress * Update R-CMD-check.yaml * progress (#1707) * V2.0 `add_vif()` (#1708) * progress * Update _pkgdown.yml * Update _pkgdown.yml * progress (#1709) * V2.0 `tbl_butcher()` (#1711) * progress * Update NEWS.md * progress (#1710) * v2.0 Adding `add ci.tbl summary()` (#1666) * in progress * doc updates * Update add_ci.R * progress * progress * progress * Update _pkgdown.yml * Update NEWS.md * Update NEWS.md * Update DESCRIPTION * doc update * Update add_ci.R * V2.0 `add_nevent.tbl uvregression()` (#1713) * progress * doc updates * V2.0 `add_p.tbl continuous()` (#1717) * progress * Update _pkgdown.yml * lil gt updates (#1718) * V2.0 `as_tibble()` (#1719) * progress * redoc * progress (#1721) * V2.0 standalone updates (#1722) * update standalone scripts * Update tbl_summary.R * v2.0 `tbl_merge()` (#1703) * progress * Update test-tbl_uvregression.R * remove deps * v2.0 `tbl_crosss()`, `add_p.tbl_cross()` (#1702) * progress * doc updates * updates * V2.0 `add_glance_*()` (#1724) * in progress * glancing * V2.0 more selectors (#1726) * adding selectors * update * V2.0 `tbl_survfit()` (#1728) * in progress * progress * progress * progress * Update DESCRIPTION * Update DESCRIPTION * Update _pkgdown.yml * v2.0 Add unit tests for `as_tibble` and `as.data.frame` (#1723) * Add tests * Add unit tests for as_tibble * Remove comment * Update tbl_stack.R * Use base R pipe * Add test for column grouping * A bit of clean up * Comment code * Remove some snapshot tests * Add test for as.data.frame --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * V2.0 `as_kable()` (#1729) * progress * Update import-standalone-stringr.R * V2.0 add unit tests for `add_n` and `add_nevent` to `tbl_uvregression()` (#1725) * add test for add_n.tbl_uvregression() * all tests added and styler * forgot a skip_if_not * adopt feedback * adopt feedback * V2.0 `as_flex_table()` (#1731) * in progress * in progress * stringr updates * Update add_q.R * adding kabel extra output (#1732) * V2.0 as kable extra (#1733) * adding kabel extra output * adding indent * V2.0 `as_hux_table()` (#1735) * in progress * progress * progress * renaming label_style function (#1737) * progress (#1738) * data update * progress (#1739) * progress (#1742) * adding a few tests * V2.0 rename card functions (#1744) * rename some functions * Update _pkgdown.yml * snap updates * progress (#1745) * progress (#1746) * more tests * progress (#1747) * progress * v2.0 Add unit tests for `as_gt` (#1727) * Add tests for as_gt * Fix * Fix * Fix * Test * Test * Rearrange existing * Add tests for as_gt * Update footnotes test * Simplify interpreter test * Add footnotes test * Clean up * Add test for bold/italics * Add test for missing symbols * Add test for column merging * Simplify tests * Add test for missing values * Add tests for formatting functions --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * v2.0 Add unit tests for `as_flex_table` (#1752) * Initialize * Add tests * Test for formatting functions * Test for glance statistics * Test tbl_merge * Added explicit test for markdown syntax in headers * V2.0 `tbl_wide_summary()` (#1749) * progress * Update NEWS.md * Update _pkgdown.yml * docs * doc update --------- Co-authored-by: Melkiades <davide.garolini@roche.com> * V2.0 `tbl_ard_wide_summary()` (#1750) * progress * Update NEWS.md * Update _pkgdown.yml * docs * doc update * progress --------- Co-authored-by: Melkiades <davide.garolini@roche.com> * v2.0 Add unit tests for `tbl_merge` (#1754) * Add tests for tbl_merge * Add more tests * Message test * Update test-tbl_merge.R --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * V2.0 `inline_text()` (#1751) * Update inline_text.R * in progress * in progress * progress * Update _pkgdown.yml * Update NEWS.md * closes #1755 (#1757) * updates (#1761) * adding tests (#1762) * Create test-select_helpers.R (#1763) * v2.0 Add unit tests for `tbl_stack` (#1756) * Initialize * Reorder * Wrong file * Add tests * Add snapshot * Fix pkg check * Update tbl_stack.md * Add test for mismatched number of columns error * fix --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * Update print.R * V2.0 add stat.tbl continuous tests (#1759) * raise attention * need at least this to get old tests working * how to use include for formula formation? * should work * as a fun exercise * add comments * nvm found the issue * DS review updates * move the tests and take in feedback * remove unncessary comments and return tbl_continuous back to original shape * use native pipe only --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * Update DESCRIPTION * adding show header fn * website updates * progress * v2.0 Add unit tests for `as_kable` (#1760) * init * Add tests * Updates after review * Fix failing test * Adding `tbl_svysummary()` (#1764) * progress * in progress * in progress * Update DESCRIPTION * progress * V2.0 `add_p.tbl_svysummary()` (#1766) * progress * progress * Update _pkgdown.yml * lil updates * doc updates * V2.0 `add_difference.tbl_svysummary()` (#1768) * Create add_difference.tbl_svysummary.R * progress * Update _pkgdown.yml * progress * V2.0 `add_n.tbl_svysummary()` (#1769) * progress * progress * progress * v2.0 Add unit tests for `as_kable_extra` (#1770) * Add tests * Add test * Clean up * v2.0 additional tests for `tbl uvregression()` (#1730) * there's preexisting add_global_p() tests? * add basic plot test * remove purrr dependencies * swap in tests for each argument * styler and fix errors * adopt feedback * accidentally pushed one * add geepack * new snap * make sure p-values match properly * avoid using example geepack uses * adopt feedback * forgot to push new snap --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> * progress (#1772) * V2.0 vignettes (#1773) * making progress * progress * updates * V2.0 todo (#1776) * doc updates * snap updates * progress * progress * V2.0 workflows (#1777) * mostly workflow updates * Update test-coverage.yaml * Removing archive of old package version --------- Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> Co-authored-by: Melkiades <davide.garolini@roche.com>
ddsjoberg · Jun 29, 2024 · 2596514 · 2596514
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -18,6 +18,7 @@
 ^revdep$
 ^CRAN-RELEASE$
 ^\.covrignore$
+^\.DS_Store$
 ^lastMiKTeXException$
 ^bench$
 ^benchmark$
@@ -37,3 +38,4 @@
 ^CRAN-SUBMISSION$
 ^man-images$
 ^vignettes/articles$
+^_archive$
diff --git a/.Rprofile b/.Rprofile
diff --git a/.github/pull_request_template.md → .github/PULL_REQUEST_TEMPLATE.md b/.github/pull_request_template.md → .github/PULL_REQUEST_TEMPLATE.md
@@ -8,20 +8,16 @@
 
 Reviewer Checklist (if item does not apply, mark is as complete)
 
-- [ ] Ensure all package dependencies are installed by running `renv::install()`
-- [ ] PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
-- [ ] If an update was made to `tbl_summary()`, was the same change implemented for `tbl_svysummary()`?
-- [ ] If a new function was added, function included in `_pkgdown.yml`
-- [ ] If a bug was fixed, a unit test was added for the bug check
+- [ ] Ensure all package dependencies are installed: `renv::install()`
+- [ ] PR branch has pulled the most recent updates from master branch: `usethis::pr_merge_main()`
+- [ ] If a bug was fixed, a unit test was added.
 - [ ] Run `pkgdown::build_site()`. Check the R console for errors, and review the rendered website.
-- [ ] Code coverage is suitable for any new functions/features. Review coverage with `withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report())`. Begin in a fresh R session without any packages loaded. 
-- [ ] R CMD Check runs without errors, warnings, and notes
+- [ ] Code coverage is suitable for any new functions/features: `devtools::test_coverage()`
 - [ ] `usethis::use_spell_check()` runs with no spelling errors in documentation
 
 When the branch is ready to be merged into master:
 - [ ] Update `NEWS.md` with the changes from this pull request under the heading "`# gtsummary (development version)`". If there is an issue associated with the pull request, reference it in parentheses at the end update (see `NEWS.md` for examples).
 - [ ] Increment the version number using `usethis::use_version(which = "dev")` 
-- [ ] Run `codemetar::write_codemeta()`
 - [ ] Run `usethis::use_spell_check()` again
 - [ ] Approve Pull Request
 - [ ] Merge the PR. Please use "Squash and merge".

diff --git a/.github/R-version b/.github/R-version
diff --git a/.github/workflows/R-CMD-check-historic-R-versions.yaml b/.github/workflows/R-CMD-check-historic-R-versions.yaml
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -1,9 +1,5 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
@@ -12,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -22,24 +20,20 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-
-          # Use older ubuntu to maximise backward compatibility
-          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {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@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -51,24 +45,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update -y
-          sudo apt-get install -y texlive-fonts-extra
+          extra-packages: any::rcmdcheck
+          needs: check
 
       - uses: r-lib/actions/check-r-package@v2
-
-      - name: Show testthat output
-        if: always()
-        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
-        shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/close.yaml b/.github/workflows/close.yaml
diff --git a/.github/workflows/continuous-benchmarks.txt b/.github/workflows/continuous-benchmarks.txt
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -19,8 +21,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -39,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages

diff --git a/.github/workflows/pr-commands.yaml b/.github/workflows/pr-commands.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
   issue_comment:
@@ -8,13 +8,13 @@ name: Commands
 
 jobs:
   document:
-    if: startsWith(github.event.comment.body, '/document')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
     name: document
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -26,10 +26,12 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: roxygen2
+          extra-packages: any::roxygen2
+          needs: pr-document
 
       - name: Document
-        run: Rscript -e 'roxygen2::roxygenise()'
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
 
       - name: commit
         run: |
@@ -43,13 +45,13 @@ jobs:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
   style:
-    if: startsWith(github.event.comment.body, '/style')
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
     name: style
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -58,10 +60,12 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
 
       - name: Install dependencies
-        run: Rscript -e 'install.packages("styler")'
+        run: install.packages("styler")
+        shell: Rscript {0}
 
       - name: Style
-        run: Rscript -e 'styler::style_pkg()'
+        run: styler::style_pkg()
+        shell: Rscript {0}
 
       - name: commit
         run: |