Merge pull request #1 from epinowcast/add-skeleton-from-primary-censored

.Rbuildignore

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+^LICENSE\.md$
+^\.devcontainer$
+^data-raw$
+^README\.Rmd$
+^\.github$
+^\.pre-commit-config\.yaml$
+^\.lintr$
+^\.Rprofile
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^vignettes/cache$
+^.*\.Rproj$
+^\.Rproj\.user$
+^codemeta\.json$
+^inst/make_hexsticker\.R$
+^inst/scripts$
+^vignettes/precompile\.R$
+^vignettes/chunks$
+^doc$
+^Meta$
+^\.vscode$
+^CITATION\.cff$
+^vignettes/using-stan-tools\.Rmd$
+^touchstone$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

.github/.gitignore

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+*.html

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

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+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+  schedule:
+    - cron: '5 4 * * 1'
+  pull_request:
+    branches:
+      - main
+  merge_group:
+  workflow_dispatch:
+
+name: R-CMD-check
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+jobs:
+  R-CMD-check:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+      NOT_CRAN: true
+
+    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 }}
+          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/codemeta.yaml

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+on:
+  push:
+    paths:
+      - DESCRIPTION
+      - .github/workflows/codemeta.yml
+  workflow_dispatch:
+
+name: Render codemeta
+
+jobs:
+  render:
+    runs-on: ubuntu-latest
+    if: "!contains(github.event.head_commit.message, 'cm-skip')"
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::codemetar
+          needs: codemeta
+
+      - name: Render codemeta
+        run: codemetar::write_codemeta()
+        shell: Rscript {0}
+
+      - name: Create Pull Request
+        if: github.ref == 'refs/heads/main'
+        uses: peter-evans/create-pull-request@v7
+        with:
+          commit-message: "Update codemeta.json"
+          title: "Update codemeta.json"
+          body: "This is an automated pull request to update the codemeta.json file."
+          branch: "update-codemeta-${{ github.run_number }}"
+          labels: "metadata"
+          reviewers: seabbs
+          add-paths: |
+            codemeta.json
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/lint-changed-files.yaml

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+# 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:
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+name: lint-changed-files
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+          needs: check
+
+      - name: Add lintr options
+        run: |
+          cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("GET https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+          changed_files <- purrr::map_chr(files, "filename")
+          all_files <- list.files(recursive = TRUE)
+          exclusions_list <- as.list(setdiff(all_files, changed_files))
+          lintr::lint_package(exclusions = exclusions_list)
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main]
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref }}
+  cancel-in-progress: true
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Upload website
+        uses: actions/upload-artifact@v4
+        with:
+          name: website
+          retention-days: 5
+          path: docs
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.7.2
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/pr-commands.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: Commands
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: roxygen2
+
+      - name: Document
+        run: Rscript -e 'roxygen2::roxygenise()'
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: Rscript -e 'install.packages(c("styler", "roxygen2"))'
+
+      - name: Style
+        run: Rscript -e 'styler::style_pkg()'
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add \*.R
+          git commit -m 'Style'
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  update_wordlist:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/update_wordlist') }}
+    name: update_wordlist
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: |
+          install.packages(c("spelling"))
+        shell: Rscript {0}
+
+      - name: Update wordlist
+        run: |
+          spelling::update_wordlist(confirm = TRUE)
+        shell: Rscript {0}
+
+      - name: Commit changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+          git add inst/WORDLIST
+          git commit -m 'Update wordlist' || echo "No changes to commit"
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}