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new setup unit tests
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16
.github/workflows/check-old.yaml
vendored
16
.github/workflows/check-old.yaml
vendored
@ -50,24 +50,14 @@ jobs:
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fail-fast: false
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matrix:
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config:
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# test all old versions of R >= 3.0, we support them all!
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# (for R-release and R-devel, see check-current.yaml)
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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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- {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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# R 3.5 returns a strange GC error when running examples, omit the checks for that
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# - {os: ubuntu-22.04, r: '3.5', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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# Test all old versions of R >= 3.0, we support them all!
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# For recent R versions, see check-recent.yaml (r-lib supports the latest 5 major versions)
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- {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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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: '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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env:
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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RSPM: ${{ matrix.config.rspm }}
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@ -38,7 +38,7 @@ on:
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# this is to check that all dependencies are still available (see R/zzz.R)
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- cron: '0 1 * * *'
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name: check-current
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name: check-recent
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jobs:
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R-code-check:
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@ -52,15 +52,30 @@ jobs:
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fail-fast: false
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matrix:
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config:
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# current development version:
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- {os: macOS-latest, r: 'devel', allowfail: false}
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- {os: macOS-latest, r: 'release', allowfail: false}
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- {os: ubuntu-latest, r: 'devel', allowfail: false}
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- {os: ubuntu-latest, r: 'release', allowfail: false}
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- {os: windows-latest, r: 'devel', allowfail: false}
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- {os: windows-latest, r: 'release', allowfail: false}
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- {os: ubuntu-latest, r: 'devel', allowfail: false}
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# current 'release' version:
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- {os: macOS-latest, r: '4.2', allowfail: false}
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- {os: windows-latest, r: '4.2', allowfail: false}
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- {os: ubuntu-latest, r: '4.2', allowfail: false}
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# older versions:
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- {os: macOS-latest, r: '4.1', allowfail: false}
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- {os: windows-latest, r: '4.1', allowfail: false}
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- {os: ubuntu-latest, r: '4.1', allowfail: false}
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- {os: macOS-latest, r: '4.0', allowfail: false}
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- {os: windows-latest, r: '4.0', allowfail: false}
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- {os: ubuntu-latest, r: '4.0', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: ubuntu-latest, r: '3.6', allowfail: false}
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- {os: windows-latest, r: '3.6', allowfail: false}
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- {os: ubuntu-latest, r: '3.6', allowfail: false}
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- {os: macOS-latest, r: '3.5', allowfail: false}
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- {os: windows-latest, r: '3.5', allowfail: false}
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- {os: ubuntu-latest, r: '3.5', allowfail: false}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.2.9078
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Version: 1.8.2.9079
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Date: 2023-01-05
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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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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9078
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# AMR 1.8.2.9079
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -51,13 +51,13 @@ expect_identical(
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)
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expect_equal(
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mean_amr_distance(data.frame(vctr_mic, vctr_rsi, vctr_disk)),
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mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_rsi, TOB = vctr_disk)),
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c(-1.10603655, -0.74968823, -0.39333990, -0.03699158, 0.96485397, 1.32120229),
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tolerance = 0.00001
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)
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expect_equal(
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mean_amr_distance(data.frame(vctr_mic, vctr_rsi, vctr_disk), 2:3),
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mean_amr_distance(data.frame(AMX = vctr_mic, GEN = vctr_rsi, TOB = vctr_disk), 2:3),
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c(-0.9909017, -0.7236405, -0.4563792, -0.1891180, 1.0463891, 1.3136503),
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tolerance = 0.00001
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)
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