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https://github.com/msberends/AMR.git
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2
Commits
| Author | SHA1 | Date | |
|---|---|---|---|
 dr. M.S. (Matthijs) Berends
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743479d460 | ||
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dr. M.S. (Matthijs) Berends
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d2252b1062 |
@@ -31,11 +31,13 @@ on:
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pull_request:
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pull_request:
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# run in each PR in this repo
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# run in each PR in this repo
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branches: '**'
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branches: '**'
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push:
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branches: '**'
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name: R-code-check-PR
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name: check-devel
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jobs:
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jobs:
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R-code-check-PR:
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R-code-check:
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runs-on: ${{ matrix.config.os }}
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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continue-on-error: ${{ matrix.config.allowfail }}
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@@ -47,11 +49,8 @@ jobs:
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matrix:
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matrix:
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config:
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config:
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- {os: macOS-latest, r: 'devel', allowfail: true}
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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: '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: 'devel', allowfail: true}
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- {os: windows-latest, r: 'release', allowfail: false}
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env:
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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@@ -36,7 +36,7 @@ on:
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# this is to check that all dependencies are still available (see R/zzz.R)
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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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- cron: '0 1 * * *'
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name: R-code-check
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name: check-release
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jobs:
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jobs:
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R-code-check:
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R-code-check:
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@@ -50,24 +50,21 @@ jobs:
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fail-fast: false
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fail-fast: false
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matrix:
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matrix:
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config:
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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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# test 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: '4.2', allowfail: false}
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- {os: macOS-latest, r: '4.1', 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: '4.0', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: macOS-latest, r: '3.6', allowfail: false}
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- {os: ubuntu-22.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '4.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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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: '4.1', 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: '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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- {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.5.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.5', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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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: '3.4', 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: '3.3', 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: '3.2', 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: '3.1', 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: 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: '4.2', allowfail: false}
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- {os: windows-latest, r: '4.1', 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: '4.0', allowfail: false}
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+1
-1
@@ -1,5 +1,5 @@
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Package: AMR
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Package: AMR
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Version: 1.8.2.9031
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Version: 1.8.2.9033
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Date: 2022-10-05
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Date: 2022-10-05
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Title: Antimicrobial Resistance Data Analysis
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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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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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@@ -1,4 +1,4 @@
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# AMR 1.8.2.9031
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# AMR 1.8.2.9033
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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This version will eventually become v2.0! We're happy to reach a new major milestone soon!
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@@ -164,7 +164,7 @@
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#' as.rsi() # automatically determines urine isolates
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#' as.rsi() # automatically determines urine isolates
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#'
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#'
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#' df %>%
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#' df %>%
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#' mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
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#' mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
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#' }
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#' }
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#'
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#'
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#' # For CLEANING existing R/SI values ------------------------------------
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#' # For CLEANING existing R/SI values ------------------------------------
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+1
-1
@@ -229,7 +229,7 @@ if (require("dplyr")) {
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as.rsi() # automatically determines urine isolates
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as.rsi() # automatically determines urine isolates
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df \%>\%
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df \%>\%
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mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
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mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
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}
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}
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# For CLEANING existing R/SI values ------------------------------------
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# For CLEANING existing R/SI values ------------------------------------
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