Initial commit

.Rbuildignore

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+^LICENSE\.md$
+^\.github$
+^README\.Rmd$
+^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.lintr$
+^.*\.Rproj$
+^\.Rproj\.user$
+^CITATION\.cff$
+^tools$
+^doc$
+^Meta$

.gitattributes

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+*.bib -linguist-detectable

.github/.gitignore

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+*.html

.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/settings.yml

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+repository:
+  # https://probot.github.io/apps/settings/
+  allow_merge_commit: false
+  allow_rebase_merge: true
+  allow_squash_merge: true
+  default_branch: main
+  delete_branch_on_merge: true
+  # has_discussions: false
+  has_issues: true
+  # has_projects: false
+  # has_wiki: false
+  # private: false
+branches:
+  - name: main
+    # https://docs.github.com/en/rest/reference/repos#update-branch-protection
+    protection:
+      required_pull_request_reviews:
+        required_approving_review_count: 0 # (1-6; optionally 0)
+        dismiss_stale_reviews: true
+        require_code_owner_reviews: false
+      required_status_checks:
+        strict: true

.github/workflows/R-CMD-check.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
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::rcmdcheck", "."), dependencies = "Config/Needs/check")
+# rcmdcheck::rcmdcheck()
+# ```
+on:
+  push:
+    branches: [main, master]
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
+  merge_group:
+  pull_request:
+    paths:
+      - 'data/**'
+      - 'R/**'
+      - 'inst/**'
+      - 'man/**'
+      - 'src/**'
+      - 'tests/**'
+      - 'vignettes/**'
+      - 'DESCRIPTION'
+      - 'NAMESPACE'
+      - 'LICENSE'
+      - '.Rbuildignore'
+      - '.github/workflows/R-CMD-check.yaml'
+
+name: R-CMD-check
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+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'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    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::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        id: rcmdcheck
+        with:
+          upload-snapshots: true
+          error-on: '"note"'
+
+      # fail-fast but only if rcmdcheck step fails
+      - name: Manual fail-fast
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        if: always() && steps.rcmdcheck.outcome == 'failure'
+        run: gh run cancel ${{ github.run_id }}

.github/workflows/dependency-change.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:
+    paths:
+      - 'DESCRIPTION'
+
+name: Analyze dependency changes
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  pull-requests: write
+
+jobs:
+  dependency-changes:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: any::pak, glue, gh
+
+      - name: Analyze dependency changes
+        shell: Rscript {0}
+        run: |
+          deps_base <- pak::pkg_deps("${{ github.repository }}@${{ github.base_ref }}", dependencies = TRUE) |>
+            subset(!directpkg) |>
+            subset(is.na(priority))
+          # We install from PR number rather than branch to deal with the case
+          # of PR coming from forks
+          deps_head <- pak::pkg_deps("${{ github.repository }}#${{ github.event.number }}", dependencies = TRUE) |>
+            subset(!directpkg) |>
+            subset(is.na(priority))
+
+          deps_added <- deps_head |>
+            subset(!ref %in% deps_base$ref)
+
+          deps_removed <- deps_base |>
+            subset(!ref %in% deps_head$ref)
+
+          if (nrow(deps_added) + nrow(deps_removed) > 0) {
+
+            message("Dependencies have changed! Analyzing...")
+
+            msg <- glue::glue(
+              .sep = "\n",
+              "This pull request:",
+              "- Adds {nrow(deps_added)} new dependencies (direct and indirect)",
+              "- Adds {length(unique(deps_added$sysreqs))} new system dependencies",
+              "- Removes {nrow(deps_removed)} existing dependencies (direct and indirect)",
+              "- Removes {length(unique(deps_removed$sysreqs))} existing system dependencies",
+              "",
+              "(Note that results may be inacurrate if you branched from an outdated version of the target branch.)"
+            )
+
+            message("Posting results as a pull request comment.")
+
+            gh::gh(
+              "POST /repos/{repo}/issues/{issue_number}/comments",
+              repo = "${{ github.repository }}",
+              issue_number = "${{ github.event.number }}",
+              body = msg
+            )
+
+          }

.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:
+  workflow_dispatch:
+  pull_request:
+    branches: [main, master]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - '**/.lintr'
+      - '**/.lintr.R'
+
+name: lint-changed-files
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+            epiverse-trace/etdev
+          needs: check
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("/repos/${{ 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/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# Reproduce locally by running:
+# ```r
+# pak::pak(c("any::pkgdown", "."), dependencies = "Config/Needs/website")
+# pkgdown::build_site()
+# ```
+on:
+  push:
+    branches: [main, master]
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
+  merge_group:
+  pull_request:
+    paths:
+      - 'README.Rmd'
+      - 'README.md'
+      - 'index.Rmd'
+      - 'index.md'
+      - 'man/**'
+      - 'vignettes/**'
+      - '_pkgdown.yml'
+      - 'pkgdown/**'
+      - 'DESCRIPTION'
+      - '.Rbuildignore'
+      - '.github/**'
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: write
+
+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: Check website links
+        uses: untitaker/[email protected]
+        with:
+          args: docs/
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          # We clean on releases because we want to remove old vignettes,
+          # figures, etc. that have been deleted from the `main` branch.
+          # But we clean ONLY on releases because we want to be able to keep
+          # both the 'stable' and 'dev' websites.
+          # Also discussed in https://github.com/r-lib/actions/issues/484
+          clean: ${{ github.event_name == 'release' }}
+          branch: gh-pages
+          folder: docs