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new workflow files
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78
.github/workflows/check-pr.yaml
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78
.github/workflows/check-pr.yaml
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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on:
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pull_request:
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# run in each PR in this repo
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branches: '**'
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name: R-code-check-PR
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jobs:
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R-code-check-PR:
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macOS-latest, r: 'devel', allowfail: true}
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: ubuntu-latest, r: 'devel', allowfail: true}
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- {os: ubuntu-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: 'release', allowfail: false}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v3
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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: ${{ matrix.config.r }}
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# use RStudio Package Manager to quickly install packages
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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env:
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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4
.github/workflows/check.yaml
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4
.github/workflows/check.yaml
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@ -48,6 +48,7 @@ jobs:
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config:
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# test all systems against all released versions of R >= 3.0, we support them all!
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- {os: macOS-latest, r: 'devel', allowfail: true}
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- {os: macOS-latest, r: '4.2', allowfail: false}
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- {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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@ -63,6 +64,7 @@ jobs:
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- {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: windows-latest, r: 'devel', allowfail: true}
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- {os: windows-latest, r: '4.2', allowfail: false}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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@ -72,7 +74,7 @@ jobs:
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R_REPOSITORIES: "https://cran.rstudio.com"
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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9
.github/workflows/codecovr.yaml
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9
.github/workflows/codecovr.yaml
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on:
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push:
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branches:
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- development
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- main
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branches: '**'
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pull_request:
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branches:
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- main
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branches: '**'
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name: code-coverage
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@ -40,7 +37,7 @@ jobs:
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env:
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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@v3
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- uses: r-lib/actions/setup-r@v2
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with:
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9
.github/workflows/lintr.yaml
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9
.github/workflows/lintr.yaml
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on:
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push:
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branches:
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- development
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- main
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branches: '**'
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pull_request:
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branches:
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- main
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branches: '**'
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name: lintr
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@ -40,7 +37,7 @@ jobs:
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env:
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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@v3
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- uses: r-lib/actions/setup-r@v2
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.1.9029
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Version: 1.8.1.9030
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Date: 2022-08-26
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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