.github/workflows/check-pr.yaml

@@ -31,13 +31,11 @@ on:
   pull_request:
     # run in each PR in this repo
     branches: '**'
-  push:
-    branches: '**'
 
-name: check-devel
+name: R-code-check-PR
 
 jobs:
-  R-code-check:
+  R-code-check-PR:
     runs-on: ${{ matrix.config.os }}
 
     continue-on-error: ${{ matrix.config.allowfail }}
@@ -49,8 +47,11 @@ jobs:
       matrix:
         config:
           - {os: macOS-latest,   r: 'devel',   allowfail: true}
+          - {os: macOS-latest,   r: 'release', allowfail: false}
           - {os: ubuntu-latest,  r: 'devel',   allowfail: true}
+          - {os: ubuntu-latest,  r: 'release', allowfail: false}
           - {os: windows-latest, r: 'devel',   allowfail: true}
+          - {os: windows-latest, r: 'release', allowfail: false}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -65,7 +66,7 @@ jobs:
         with:
           r-version: ${{ matrix.config.r }}
           # use RStudio Package Manager to quickly install packages
-          use-public-rspm: true
+          use-public-rspm: true      
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/check.yaml

@@ -36,7 +36,7 @@ on:
     # this is to check that all dependencies are still available (see R/zzz.R)
     - cron:  '0 1 * * *'
 
-name: check-release
+name: R-code-check
 
 jobs:
   R-code-check:
@@ -50,21 +50,24 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # test all released versions of R >= 3.0, we support them all!
+          # test all systems against all released versions of R >= 3.0, we support them all!
+          - {os: macOS-latest,   r: 'devel',   allowfail: true}
           - {os: macOS-latest,   r: '4.2',     allowfail: false}
           - {os: macOS-latest,   r: '4.1',     allowfail: false}
           - {os: macOS-latest,   r: '4.0',     allowfail: false}
           - {os: macOS-latest,   r: '3.6',     allowfail: false}
+          - {os: ubuntu-22.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '4.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
-          - {os: ubuntu-22.04,   r: '3.5',     allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: ubuntu-22.04,   r: '3.5.0',   allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
           - {os: ubuntu-22.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
+          - {os: windows-latest, r: 'devel',   allowfail: true}
           - {os: windows-latest, r: '4.2',     allowfail: false}
           - {os: windows-latest, r: '4.1',     allowfail: false}
           - {os: windows-latest, r: '4.0',     allowfail: false}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9033
+Version: 1.8.2.9031
 Date: 2022-10-05
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.2.9033
+# AMR 1.8.2.9031
 
 This version will eventually become v2.0! We're happy to reach a new major milestone soon!
 

R/rsi.R

@@ -164,7 +164,7 @@
 #'     as.rsi() # automatically determines urine isolates
 #'
 #'   df %>%
-#'     mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
+#'     mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
 #' }
 #'
 #' # For CLEANING existing R/SI values ------------------------------------

man/as.rsi.Rd

@@ -229,7 +229,7 @@ if (require("dplyr")) {
     as.rsi() # automatically determines urine isolates
 
   df \%>\%
-    mutate_at(vars(AMP:TOB), as.rsi, mo = "E. coli", uti = TRUE)
+    mutate_at(vars(AMP:NIT), as.rsi, mo = "E. coli", uti = TRUE)
 }
 
 # For CLEANING existing R/SI values ------------------------------------