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Merge branch 'main' into 25-update-vignettes-to-use-mrbayestrees
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‎.github/workflows/R-CMD-check.yml‎

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- "**.json"
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- "**.md"
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- "**.yml"
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- "!**R-cmd-check.yml"
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- "!**R-CMD-check.yml"
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- "**.R[dD]ata"
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- "**.Rpro*"
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pull_request:
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- "**.json"
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- "**.md"
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- "**.yml"
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- "!**R-cmd-check.yml"
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- "!**R-CMD-check.yml"
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- "**.R[dD]ata"
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- "**.Rpro*"
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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submodules: true
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- name: Install system dependencies (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update -y
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sudo apt-get install -y libpoppler-glib-dev bwidget libavfilter-dev libtesseract-dev gdal-bin proj-bin libgdal-dev libproj-dev tesseract-ocr-eng libleptonica-dev tcl libgtk2.0-dev libgtk-3-dev
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sudo pkg-config --libs poppler-glib
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sudo pkg-config --cflags poppler-glib
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Query dependencies
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if: runner.os != 'macOS'
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run: |
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install.packages('remotes')
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saveRDS(
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remotes::dev_package_deps(dependencies = c("soft",
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"Config/Needs/github-actions")), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor),
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".github/R-version")
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shell: Rscript {0}
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- name: Query dependencies (macOS)
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if: runner.os == 'macOS'
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run: |
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install.packages('remotes')
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saveRDS(
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remotes::dev_package_deps(dependencies = c("soft",
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"Config/Needs/coverage", "Config/Needs/github-actions"))
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, ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor),
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".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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if: runner.os != 'Windows'
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uses: actions/cache@v3
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uses: actions/cache@v4
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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- name: Install system dependencies (Linux)
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update -y
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sudo apt-get install -y libpoppler-glib-dev bwidget libavfilter-dev libtesseract-dev gdal-bin proj-bin libgdal-dev libproj-dev tesseract-ocr-eng libleptonica-dev tcl libgtk2.0-dev libgtk-3-dev
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sudo pkg-config --libs poppler-glib
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sudo pkg-config --cflags poppler-glib
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while read -r cmd
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do
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eval sudo $cmd
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done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
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- name: Install system dependencies (macOS)
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if: runner.os == 'macOS'
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run: |
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brew install libgit2 xquartz
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- name: Install callr (Windows)
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- name: Set up R dependencies (Windows)
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if: runner.os == 'Windows'
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run: |
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remotes::install_cran("callr")
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shell: Rscript {0}
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- name: Install dependencies
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run: |
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remotes::install_deps(dependencies = c("soft", "Config/Needs/github-actions"))
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shell: Rscript {0}
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- name: Install coverage dependencies
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if: runner.os == 'macOS'
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run: |
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remotes::install_deps(dependencies = 'Config/Needs/coverage')
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shell: Rscript {0}
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- name: Check
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env:
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_R_CHECK_CRAN_INCOMING_REMOTE_: false
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run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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shell: Rscript {0}
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# - name: Upload check results
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# if: failure()
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# uses: actions/upload-artifact@main
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# with:
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# name: ${{ runner.os }}-r${{ matrix.config.r }}-results
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# path: check
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: callr
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needs: |
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check
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coverage
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github-actions
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- name: Set up R dependencies (Non-Windows)
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if: runner.os != 'Windows'
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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needs: |
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check
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github-actions
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extra-packages: |
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phangorn=?ignore-before-r=4.1.0
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- name: Check package
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uses: r-lib/actions/check-r-package@v2
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- name: Test coverage
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if: runner.os == 'macOS'
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if: runner.os == 'Windows'
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run: |
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covr::codecov()
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shell: Rscript {0}
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- name: Notify on failure
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if: failure() && github.event_name == 'schedule'
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uses: actions/github-script@v7
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with:
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github-token: ${{ secrets.GITHUB_TOKEN }}
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script: |
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github.rest.issues.createComment({
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owner: context.repo.owner,
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repo: context.repo.repo,
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issue_number: 31,
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body: 'Scheduled workflow has failed: https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}'
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});
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‎.github/workflows/RcppDeepState.yml‎

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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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with:
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submodules: true
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‎.github/workflows/codemeta.yml‎

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RSPM: ${{ matrix.config.rspm }}
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

‎.github/workflows/memcheck.yml‎

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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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submodules: true
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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uses: actions/cache@v4
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

‎.github/workflows/pkgdown.yml‎

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R_COMPILE_AND_INSTALL_PACKAGES: 'never'
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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submodules: true
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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uses: actions/cache@v4
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with:
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

‎.github/workflows/revdepcheck.yml‎

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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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- uses: actions/checkout@v2
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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uses: actions/cache@v4
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path: ${{ env.R_LIBS_USER }}
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}

‎.github/workflows/update-csl.yml‎

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name: Update CSL file
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on:
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schedule:
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- cron: '0 0 * * 1' # Runs weekly on Monday at 00:00 UTC
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workflow_dispatch: # Allows manual triggering
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jobs:
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update-csl:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- name: Download latest CSL file
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run: |
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curl -o inst/apa-old-doi-prefix.csl https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
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- name: Check for changes
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id: changes
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run: |
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if git diff --quiet inst/apa-old-doi-prefix.csl; then
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echo "::set-output name=changed::false"
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echo "No changes to commit"
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else
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echo "::set-output name=changed::true"
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fi
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- name: Commit and push
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if: steps.changes.outputs.changed == 'true'
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run: |
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git config --local user.email "[email protected]"
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git config --local user.name "GitHub Actions"
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git add inst/apa-old-doi-prefix.csl
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git commit -m "Update CSL file from upstream"
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git push

‎CONTRIBUTING.md‎

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* We use the Oxford ending of 'ize' (not 'ise'), and UK spelling (e.g. 'colour')
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where it is not possible to avoid the distinction (e.g. by shortening to 'col')
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* We use [roxygen2](https://cran.r-project.org/package=roxygen2) to build
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documentation.
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documentation.
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* We use [testthat](https://cran.r-project.org/package=testthat). Contributions
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with test cases included are easier to accept.
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with test cases included are easier to accept.
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* We use [semantic versioning](https://semver.org/).
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* For user-facing changes, add a bullet to the top of `NEWS.md` below the
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current development version header describing the changes made followed by your
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GitHub username, and links to relevant issue(s)/PR(s).
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### Contributor license agreement
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Contributors agree to reassign the copyright of their contributions to the
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maintainers of the package.
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### Code of Conduct
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Please note that the project is released with a

‎DESCRIPTION‎

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Package: Rogue
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Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
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Version: 2.1.6.9001
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Version: 2.1.6.9000
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Authors@R: c(person("Martin R.", 'Smith',
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email = "[email protected]",
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role = c("aut", "cre", "cph"),
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Encoding: UTF-8
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Language: en-GB
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VignetteBuilder: knitr
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RoxygenNote: 7.2.3
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RoxygenNote: 7.3.1
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Roxygen: list(markdown = TRUE)

‎NEWS.md‎

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# Rogue v2.1.6.9001 (development)
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# Rogue v2.1.6.9000 (2025-04-14)
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- Simplify vignette with new `TreeTools::ReadMrBayesTrees()`.
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- Improve tip instability calculation in identical tree sets
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([#29](https://github.com/ms609/Rogue/issues/29)).
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# Rogue v2.1.6
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# Rogue v2.1.6 (2023-11-29)
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- Legend annotations in documentation.
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- Disable parallel evaluation by default in `TipInstability()`,
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adding `parallel` parameter to allow user to override.
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- Use format string in REprintf().
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# Rogue v2.1.5
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# Rogue v2.1.5 (2023-03-20)
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- Call C functions using symbols, not strings.
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# Rogue v2.1.4
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# Rogue v2.1.4 (2023-01-16)
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- C2X compliant function prototypes.
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- Remove unused `sprintf()` calls.
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# Rogue v2.1.3
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# Rogue v2.1.3 (2022-09-26)
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- `ColByStability()` gains `pal` argument to allow specification of custom
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palettes.
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# Rogue v2.1.2
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# Rogue v2.1.2 (2022-08-16)
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- Faster rogue detection when edge lengths provided, per report by Joe Keating.
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- Don't list `neverDrop` in `QuickRogue(fullSeq = TRUE)`.
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# Rogue v2.1.1
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# Rogue v2.1.1 (2022-07-20)
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- Handle `ColByStability(trees = NULL)`.
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# Rogue v2.1.0
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# Rogue v2.1.0 (2022-01-13)
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- Early termination of `QuickRogue()` when no further improvement possible.
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- New vignette detailing rogue detection with Bayesian tree samples.
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# Rogue v2.0.0
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# Rogue v2.0.0 (2021-09-13)
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- Information theoretic rogue detection (per Smith, 2022).
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# Rogue v1.0.0
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# Rogue v1.0.0 (2021-06-28)
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- R interface to RogueNaRok.

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