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Commitd80d596

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Merge pull request#44 from alwinw/fix-gh-workflows
Fix GitHub Workflows
2 parents9c3d077 +4f03dfe commitd80d596

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+2704
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15 files changed

+2704
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‎.Rprofile‎

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source("renv/activate.R")

‎.cz.toml‎

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[tool.commitizen]
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version ="0.9.9"
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name ="cz_conventional_commits"
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version_scheme ="semver"
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tag_format ="v$version"
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update_changelog_on_bump =false
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changelog_incremental =false
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use_shortcuts =true
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major_version_zero =true
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version ="0.9.9"
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version_files = ["DESCRIPTION:Version"]

‎.github/workflows/R-CMD-check.yaml‎

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push:
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branches:[main, master]
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pull_request:
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branches:[main, master]
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name:R-CMD-check.yaml
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‎.github/workflows/lint.yaml‎

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push:
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branches:[main, master]
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pull_request:
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branches:[main, master]
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name:lint.yaml
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‎.github/workflows/pkgdown.yaml‎

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push:
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branches:[main, master]
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pull_request:
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branches:[main, master]
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release:
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types:[published]
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workflow_dispatch:
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name:pkgdown
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name:pkgdown.yaml
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permissions:read-all
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jobs:
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pkgdown:
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group:pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT:${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents:write
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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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-uses:r-lib/actions/setup-pandoc@v2
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-name:Deploy to GitHub pages 🚀
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if:github.event_name != 'pull_request'
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uses:JamesIves/github-pages-deploy-action@v4.4.1
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uses:JamesIves/github-pages-deploy-action@v4.5.0
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with:
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clean:false
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branch:gh-pages

‎.github/workflows/render-rmarkdown.yaml‎

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-uses:r-lib/actions/setup-pandoc@v2
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-uses:r-lib/actions/setup-r@v2
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with:
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r-version:renv
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-uses:r-lib/actions/setup-renv@v2
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‎.github/workflows/style.yaml‎

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with:
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use-public-rspm:true
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-name:Installdependencies
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-name:Installstyler and roxygen2
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uses:r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages:any::styler, any::roxygen2
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needs:styler
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packages:styler, roxygen2
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-name:Enable styler cache
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run:styler::cache_activate()

‎.github/workflows/test-coverage.yaml‎

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push:
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branches:[main, master]
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pull_request:
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branches:[main, master]
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name:test-coverage.yaml
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell:Rscript {0}
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-uses:codecov/codecov-action@v4
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-uses:codecov/codecov-action@v5
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with:
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fail_ci_if_error:${{ github.event_name != 'pull_request' && true || false }}
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file:./cobertura.xml
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plugin:noop
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error:${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files:./cobertura.xml
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plugins:noop
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disable_search:true
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token:${{ secrets.CODECOV_TOKEN }}
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‎.gitignore‎

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# Custom
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#---------------------------------------------------------------------------------------
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# Custom.gitignore
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#---------------------------------------------------------------------------------------
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resources/
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renv/
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renv.lock
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docs
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.Rprofile
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CRAN-RELEASE
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CRAN-SUBMISSION
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check/
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#---------------------------------------------------------------------------------------
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# Archives.gitignore
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#---------------------------------------------------------------------------------------
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# It's better to unpack these files and commit the raw source because
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# git has its own built in compression methods.
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*.7z
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*.jar
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*.rar
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*.zip
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*.gz
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*.gzip
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*.tgz
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*.bzip
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*.bzip2
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*.bz2
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*.xz
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*.lzma
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*.cab
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*.xar
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*.zst
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*.tzst
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# Packing-only formats
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*.iso
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*.tar
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# Package management formats
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*.dmg
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*.xpi
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*.gem
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*.egg
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*.deb
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*.rpm
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*.msi
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*.msm
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*.msp
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*.txz
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#---------------------------------------------------------------------------------------
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# Backup.gitignore
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#---------------------------------------------------------------------------------------
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*.bak
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*.gho
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*.ori
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*.orig
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*.tmp
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#---------------------------------------------------------------------------------------
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# Images.gitignore
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#---------------------------------------------------------------------------------------
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# JPEG
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*.jpg
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*.jpeg
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*.jpe
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*.jif
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*.jfif
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*.jfi
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# JPEG 2000
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*.jp2
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*.j2k
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*.jpf
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*.jpx
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*.jpm
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*.mj2
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# JPEG XR
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*.jxr
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*.hdp
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*.wdp
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# Graphics Interchange Format
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*.gif
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# RAW
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*.raw
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# Web P
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*.webp
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# Portable Network Graphics
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*.png
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# Animated Portable Network Graphics
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*.apng
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# Multiple-image Network Graphics
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*.mng
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# Tagged Image File Format
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*.tiff
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*.tif
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# Scalable Vector Graphics
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*.svg
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*.svgz
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# Portable Document Format
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*.pdf
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# X BitMap
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*.xbm
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# BMP
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*.bmp
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*.dib
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# ICO
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*.ico
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# 3D Images
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*.3dm
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*.max
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#---------------------------------------------------------------------------------------
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# Linux.gitignore
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#---------------------------------------------------------------------------------------
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*~
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# temporary files which can be created if a process still has a handle open of a deleted file
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.fuse_hidden*
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# KDE directory preferences
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.directory
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# Linux trash folder which might appear on any partition or disk
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.Trash-*
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# .nfs files are created when an open file is removed but is still being accessed
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.nfs*
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#---------------------------------------------------------------------------------------
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# macOS.gitignore
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#---------------------------------------------------------------------------------------
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# General
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.DS_Store
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.AppleDouble
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.LSOverride
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# Icon must end with two \r
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Icon
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# Thumbnails
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._*
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# Files that might appear in the root of a volume
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.DocumentRevisions-V100
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.fseventsd
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.Spotlight-V100
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.TemporaryItems
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.Trashes
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.VolumeIcon.icns
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.com.apple.timemachine.donotpresent
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# Directories potentially created on remote AFP share
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.AppleDB
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.AppleDesktop
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NetworkTrashFolder
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TemporaryItems
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.apdisk
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#---------------------------------------------------------------------------------------
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# MicrosoftOffice.gitignore
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#---------------------------------------------------------------------------------------
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*.tmp
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# Word temporary
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~$*.doc*
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# Word Auto Backup File
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Backupof*.doc*
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# Excel temporary
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~$*.xls*
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# Excel Backup File
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*.xlk
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# PowerPoint temporary
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~$*.ppt*
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# Visio autosave temporary files
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*.~vsd*
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#---------------------------------------------------------------------------------------
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# R.gitignore
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#---------------------------------------------------------------------------------------
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# History files
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.Rhistory
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.Rapp.history
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# Session Data files
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.RData
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.RDataTmp
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# User-specific files
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.Ruserdata
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# R Environment Variables
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.Renviron
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.Rproj.user
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inst/doc
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# pkgdown site
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docs/
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# translation temp files
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po/*~
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# RStudio Connect folder
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rsconnect/
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#---------------------------------------------------------------------------------------
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# VSCode.gitignore
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#---------------------------------------------------------------------------------------
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.vscode/*
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!.vscode/settings.json
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!.vscode/tasks.json
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!.vscode/launch.json
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!.vscode/extensions.json
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!.vscode/*.code-snippets
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# Local History for Visual Studio Code
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.history/
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# Built Visual Studio Code Extensions
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*.vsix

‎DESCRIPTION‎

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person(given = "Davis",
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family = "Vaughan",
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role = "ctb",
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email = "davis@rstudio.com"))
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email = "davis@rstudio.com"),
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person(given = "olivroy",
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role = "ctb"))
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Description: Clinical coding and diagnosis of patients with kidney using
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clinical practice guidelines. The guidelines used are the evidence-based
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KDIGO guidelines, see <https://kdigo.org/guidelines/> for more information.

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