(v3.0.0.9022) postpone new features - we like a clearly focussed bugfix release first

(v3.0.0.9021) checkouts
new umcg logo and old CHECKOUT update
2025-09-03 18:49:43 +02:00 · 2025-09-03 15:39:44 +02:00 · 2025-09-03 12:12:05 +02:00 · 2025-09-03 11:49:10 +02:00 · 2025-09-01 16:56:55 +02:00 · 2025-08-07 16:23:47 +02:00
41 changed files with 305 additions and 4321 deletions
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -40,3 +40,4 @@
 ^CRAN-SUBMISSION$
 ^PythonPackage$
 ^README\.Rmd$
+\.no_include$
--- a/.github/prehooks/pre-commit
+++ b/.github/prehooks/pre-commit
@@ -68,49 +68,56 @@ echo ""
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 echo "Updating semantic versioning and date..."

-# Get tags from remote and remove tags not on remote
-git fetch origin --prune --prune-tags --quiet
-currenttagfull=$(git describe --tags --abbrev=0)
-currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
-
-# Assume main branch to be 'main' or 'master'
-defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
-if [ "$currenttag" = "" ]; then
-  currenttag="0.0.1"
-  currentcommit=$(git rev-list --count ${defaultbranch})
-  echo "- No git tags found, creating one in format 'v(x).(y).(z)' - currently ${currentcommit} previous commits in '${defaultbranch}'"
+current_branch=$(git rev-parse --abbrev-ref HEAD)
+if [ "$current_branch" != "main" ]; then
+  echo "- Current branch is '$current_branch'; skipping version/date update (only runs on 'main')"
 else
-  currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
-  echo "- Latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
-fi
-
-# Combine tag and commit number
-currentversion="$currenttag.$((currentcommit + 9001))"
-echo "- ${currentpkg} pkg version set to ${currentversion}"
-
-# Update version number and date in DESCRIPTION
-sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
-sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
-echo "- Updated version number and date in ./DESCRIPTION"
-rm -f DESCRIPTION--
-git add DESCRIPTION
-
-# Update version number in NEWS.md
-if [ -e "NEWS.md" ]; then
-  if [ "$currentpkg" = "your" ]; then
-    currentpkg=""
+  # Version update logic begins here
+  
+  # Get tags from remote and remove tags not on remote
+  git fetch origin --prune --prune-tags --quiet
+  currenttagfull=$(git describe --tags --abbrev=0)
+  currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
+  
+  # Assume main branch to be 'main' or 'master'
+  defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
+  if [ "$currenttag" = "" ]; then
+    currenttag="0.0.1"
+    currentcommit=$(git rev-list --count ${defaultbranch})
+    echo "- No git tags found, creating one in format 'v(x).(y).(z)' - currently ${currentcommit} previous commits in '${defaultbranch}'"
+  else
+    currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+    echo "- Latest tag is '${currenttagfull}', with ${currentcommit} previous commits in '${defaultbranch}'"
  fi
-  sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
-  echo "- Updated version number in ./NEWS.md"
-  rm -f NEWS.md--
-  git add NEWS.md
-else
-  echo "- No NEWS.md found!"
+  
+  # Combine tag and commit number
+  currentversion="$currenttag.$((currentcommit + 9001))"
+  echo "- ${currentpkg} pkg version set to ${currentversion}"
+  
+  # Update version number and date in DESCRIPTION
+  sed -i -- "s/^Version: .*/Version: ${currentversion}/" DESCRIPTION
+  sed -i -- "s/^Date: .*/Date: $(date '+%Y-%m-%d')/" DESCRIPTION
+  echo "- Updated version number and date in ./DESCRIPTION"
+  rm -f DESCRIPTION--
+  git add DESCRIPTION
+  
+  # Update version number in NEWS.md
+  if [ -e "NEWS.md" ]; then
+    if [ "$currentpkg" = "your" ]; then
+      currentpkg=""
+    fi
+    sed -i -- "1s/.*/# ${currentpkg} ${currentversion}/" NEWS.md
+    echo "- Updated version number in ./NEWS.md"
+    rm -f NEWS.md--
+    git add NEWS.md
+  else
+    echo "- No NEWS.md found!"
+  fi
+  echo ""
+  
+  # Save the version number for use in the commit-msg hook
+  echo "${currentversion}" > .git/commit_version.tmp
 fi
-echo ""
-
-# Save the version number for use in the commit-msg hook
-echo "${currentversion}" > .git/commit_version.tmp

 git add data-raw/*
 git add data/*
--- a/.github/workflows/check-old-tinytest.yaml
+++ b/.github/workflows/check-old-tinytest.yaml
@@ -50,17 +50,24 @@ jobs:
          # For these old versions, dependencies and vignettes will not be checked.
          # For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R releases).
          - {os: ubuntu-latest, r: '3.6', allowfail: false}
-          # - {os: windows-latest, r: '3.5', allowfail: true} # always fails, horrible with UTF-8
-          - {os: ubuntu-latest, r: '3.4', allowfail: false}
-          - {os: ubuntu-latest, r: '3.3', allowfail: false}
-          - {os: ubuntu-latest, r: '3.2', allowfail: false}
-          - {os: ubuntu-latest, r: '3.1', allowfail: false}
+          # - {os: windows-latest, r: '3.5', allowfail: false} # always fails, horrible with UTF-8
+          # - {os: ubuntu-latest, r: '3.4', allowfail: false}  # 3.1-3.4 now always fails with Error in grep(warn_re, lines, invert = TRUE, value = TRUE) attempt to set index 46/46 in SET_STRING_ELT
+          # - {os: ubuntu-latest, r: '3.3', allowfail: false}
+          # - {os: ubuntu-latest, r: '3.2', allowfail: false}
+          # - {os: ubuntu-latest, r: '3.1', allowfail: false}
          - {os: ubuntu-latest, r: '3.0', allowfail: false}

    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      LANG: en_US.UTF-8
+      LC_ALL: en_US.UTF-8

    steps:
+      - name: Set up locales
+        run: |
+          sudo locale-gen en_US.UTF-8
+          sudo update-locale LANG=en_US.UTF-8
+
      - uses: actions/checkout@v4

      - uses: r-lib/actions/setup-r@v2
@@ -69,9 +76,14 @@ jobs:

      - uses: r-lib/actions/setup-pandoc@v2

-      - name: Install tinytest from CRAN
+      - name: Install suggested pkgs (and tinytest) from CRAN
        run: |
-          install.packages("tinytest", repos = "https://cran.r-project.org")
+          desc_lines <- readLines('DESCRIPTION')
+          suggests <- readLines('DESCRIPTION')[grepl("^(Suggests:|  )", readLines('DESCRIPTION'))]
+          suggests <- suggests[(which(grepl("^Suggests", suggests)) + 1):length(suggests)]
+          suggests <- gsub("[ ,]", "", suggests)
+          pkgs <- unique(c(suggests, "tinytest"))
+          for (p in pkgs) try(install.packages(p, repos = "https://cran.r-project.org"), silent = TRUE)
        shell: Rscript {0}

      - name: Show session info
--- a/.github/workflows/publish-to-pypi.yml
+++ b/.github/workflows/publish-to-pypi.yml
@@ -39,7 +39,7 @@ jobs:
    runs-on: ubuntu-latest
    
    env:
-      PYPI_PAT: ${{ secrets.PYPI_PAT }}
+      GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
    
    steps:
      - name: Checkout code
@@ -78,6 +78,7 @@ jobs:
          cd PythonPackage/AMR
          python -m twine upload --repository-url https://test.pypi.org/legacy/ dist/*

+      # TODO - Support Miniconda and Anaconda too
      # - name: Set up Miniconda
      #   continue-on-error: true
      #   uses: conda-incubator/setup-miniconda@v2
@@ -117,7 +118,7 @@ jobs:
          rm -rf PythonPackage

          git init
-          git remote add origin https://$PYPI_PAT@github.com/msberends/AMR
+          git remote add origin https://$GH_REPO_SCOPE@github.com/msberends/AMR
          git checkout --orphan python-wrapper
          git config user.name "github-actions[bot]"
          git config user.email "github-actions[bot]@users.noreply.github.com"
@@ -125,4 +126,4 @@ jobs:
          git rm -rf . || true
          git add .
          git commit -m "Python wrapper update"
-          git push https://$PYPI_PAT@github.com/msberends/AMR.git python-wrapper --force
+          git push https://$GH_REPO_SCOPE@github.com/msberends/AMR.git python-wrapper --force
--- a/.github/workflows/renew-gpt-training-data.yml
+++ b/.github/workflows/renew-gpt-training-data.yml
@@ -39,7 +39,7 @@ jobs:
    runs-on: ubuntu-latest
    
    env:
-      PYPI_PAT: ${{ secrets.PYPI_PAT }}
+      GH_REPO_SCOPE: ${{ secrets.GH_REPO_SCOPE }}
    
    steps:
      - name: Checkout code
@@ -63,4 +63,4 @@ jobs:
          git config user.email "github-actions[bot]@users.noreply.github.com"
          git add latest_training_data.txt
          git commit -m "GPT training data update"
-          git push https://$PYPI_PAT@github.com/msberends/amr-for-r-assistant.git main --force
+          git push https://$GH_REPO_SCOPE@github.com/msberends/amr-for-r-assistant.git main --force
--- a/.github/workflows/todo-tracker.yml
+++ b/.github/workflows/todo-tracker.yml
@@ -18,7 +18,7 @@
 # This R package is free software; you can freely use and distribute   #
 # it for both personal and commercial purposes under the terms of the  #
 # GNU General Public License version 2.0 (GNU GPL-2), as published by  #
-# the Free Software Foundation.
+# the Free Software Foundation.                                        #
 # We created this package for both routine data analysis and academic  #
 # research and it was publicly released in the hope that it will be    #
 # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
@@ -29,57 +29,47 @@

 on:
  push:
-    branches: '**'
-  pull_request:
-    branches: '**'
+    # only on main
+    branches: "main"

-name: lintr
+name: Update TODO Tracker

 jobs:
-  lintr:
+  update-todo:
    runs-on: ubuntu-latest
-    env:
-      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
    steps:
      - uses: actions/checkout@v4

-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: release
-          # use RStudio Package Manager to quickly install packages
-          use-public-rspm: true
-
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: |
-            any::lintr
-            any::cyclocomp
-            any::roxygen2
-            any::devtools
-            any::usethis
-            
-      - name: Remove unneeded folders
+      - name: Generate TODO list from R/
        run: |
-          # do not check these folders
-          rm -rf data-raw
-          rm -rf tests
-          rm -rf vignettes
-          
-      - name: Lint
-        run: |
-          # get ALL linters, not just default ones
-          linters <- getNamespaceExports(asNamespace("lintr"))
-          linters <- sort(linters[grepl("_linter$", linters)])
-          # lose deprecated
-          linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator|consecutive_stopifnot|no_tab|single_quotes|unnecessary_nested_if|unneeded_concatenation)_linter$", linters)]
-          linters <- linters[linters != "linter"]
-          # and the ones we find unnnecessary
-          linters <- linters[!grepl("^(commented_code|extraction_operator|implicit_integer|indentation|line_length|namespace|nonportable_path|object_length|object_name|object_usage|is)_linter$", linters)]
-          # put the functions in a list
-          linters_list <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
-          names(linters_list) <- linters
-          # run them all!
-          lintr::lint_package(linters = linters_list, exclusions = list("R/aa_helper_pm_functions.R"))
-        shell: Rscript {0}
+          echo "## TODO Report" > todo.md
+          echo "" >> todo.md
+          echo "_This issue is automatically updated on each push to `main`._" >> todo.md
+          echo "" >> todo.md
+          todos=$(find R/ -type f ! -name "sysdata.rda" -exec grep -nH "TODO" {} + || true)
+          if [ -z "$todos" ]; then
+            echo "✅ No TODOs found." >> todo.md
+          else
+            echo "$todos" | awk -F: '
+              {
+                file = $1
+                line = $2
+                text = substr($0, index($0,$3))
+                if (file != last_file) {
+                  if (last_file != "") print ""
+                  print "### " file
+                  last_file = file
+                }
+                printf "L%s: %s\n", line, text
+              }
+            ' >> todo.md
+          fi
+
+      - name: Update GitHub issue
+        uses: peter-evans/create-or-update-comment@v4
+        with:
+          token: ${{ secrets.GH_REPO_SCOPE }}
+          issue-number: 231
+          body-file: todo.md
+          edit-mode: replace
--- a/.github/workflows/website.yaml
+++ b/.github/workflows/website.yaml
@@ -42,16 +42,15 @@ jobs:
    runs-on: ubuntu-latest
    steps:

-      - uses: actions/checkout@v4
+      - name: checkout
+        uses: actions/checkout@v4
        with:
          # this is to keep timestamps, the default fetch-depth: 1 gets the timestamps of the moment of cloning
          # we need this for the download page on our website - dates must be of the files, not of the latest git push
          fetch-depth: 0

-      - name: Preserve timestamps
-        run: |
-          sudo apt install git-restore-mtime
-          git restore-mtime
+      - name: restore timestamps
+        uses: chetan/git-restore-mtime-action@v2

      - uses: r-lib/actions/setup-pandoc@v2

--- a/4
+++ b/4
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9012
-Date: 2025-07-17
+Version: 3.0.0.9022
+Date: 2025-09-03
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
  data analysis and to work with microbial and antimicrobial properties by
--- a/14
+++ b/14
@@ -106,8 +106,6 @@ S3method(print,mo_uncertainties)
 S3method(print,pca)
 S3method(print,sir)
 S3method(print,sir_log)
-S3method(print,step_mic_log2)
-S3method(print,step_sir_numeric)
 S3method(quantile,mic)
 S3method(rep,ab)
 S3method(rep,av)
@@ -161,10 +159,6 @@ export(administrable_per_os)
 export(age)
 export(age_groups)
 export(all_antimicrobials)
-export(all_mic)
-export(all_mic_predictors)
-export(all_sir)
-export(all_sir_predictors)
 export(aminoglycosides)
 export(aminopenicillins)
 export(amr_class)
@@ -358,8 +352,6 @@ export(sir_df)
 export(sir_interpretation_history)
 export(sir_predict)
 export(skewness)
-export(step_mic_log2)
-export(step_sir_numeric)
 export(streptogramins)
 export(sulfonamides)
 export(susceptibility)
@@ -396,12 +388,6 @@ if(getRversion() >= "3.0.0") S3method(pillar::type_sum, av)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mic)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mo)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, sir)
-if(getRversion() >= "3.0.0") S3method(recipes::bake, step_mic_log2)
-if(getRversion() >= "3.0.0") S3method(recipes::bake, step_sir_numeric)
-if(getRversion() >= "3.0.0") S3method(recipes::prep, step_mic_log2)
-if(getRversion() >= "3.0.0") S3method(recipes::prep, step_sir_numeric)
-if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
-if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,11 +1,6 @@
-# AMR 3.0.0.9012
+# AMR 3.0.0.9022

-This is primarily a bugfix release, though we added one nice feature too.
-
-### New
-* Integration with the **tidymodels** framework to allow seamless use of MIC and SIR data in modelling pipelines via `recipes`
-  - `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
-  - New `tidyselect` helpers: `all_mic()`, `all_mic_predictors()`, `all_sir()`, `all_sir_predictors()`
+This is a bugfix release following the release of v3.0.0 in June 2025.

 ### Changed
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
@@ -15,10 +10,16 @@ This is primarily a bugfix release, though we added one nice feature too.
 * Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
 * Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
 * Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
+* Fixed a bug the `antimicrobials` data set to remove statins (#229)
+* Fixed a bug in `mdro()` to make sure all genes specified in arguments are acknowledged
+* Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (#230)
 * Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
 * Fixed some specific Dutch translations for antimicrobials
+* Added all reasons in verbose output of `mdro()` (#227)
 * Added `names` to `age_groups()` so that custom names can be given (#215)
 * Added note to `as.sir()` to make it explicit when higher-level taxonomic breakpoints are used (#218)
+* Added antibiotic codes from the Comprehensive Antibiotic Resistance Database (CARD) to the `antimicrobials` data set (#225)
+* Updated Fosfomycin to be of antibiotic class 'Phosphonics' (#225)
 * Updated `random_mic()` and `random_disk()` to set skewedness of the distribution and allow multiple microorganisms


--- a/R/aa_globals.R
+++ b/R/aa_globals.R
@@ -233,6 +233,7 @@ globalVariables(c(
  "uti_index",
  "value",
  "varname",
+  "where",
  "x",
  "xvar",
  "y",
--- a/R/data.R
+++ b/R/data.R
@@ -362,14 +362,14 @@
 #' dosage
 "dosage"

-#' Data Set with `r format(nrow(esbl_isolates), big.mark = " ")` ESBL Isolates
-#'
-#' A data set containing `r format(nrow(esbl_isolates), big.mark = " ")` microbial isolates with MIC values of common antibiotics and a binary `esbl` column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with [tidymodels](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
-#' @format A [tibble][tibble::tibble] with `r format(nrow(esbl_isolates), big.mark = " ")` observations and `r ncol(esbl_isolates)` variables:
-#' - `esbl`\cr Logical indicator if the isolate is ESBL-producing
-#' - `genus`\cr Genus of the microorganism
-#' - `AMC:COL`\cr MIC values for 17 antimicrobial agents, transformed to class [`mic`] (see [as.mic()])
-#' @details See our [tidymodels integration][amr-tidymodels] for an example using this data set.
-#' @examples
-#' esbl_isolates
-"esbl_isolates"
+# TODO #' Data Set with `r format(nrow(esbl_isolates), big.mark = " ")` ESBL Isolates
+# TODO #'
+# TODO #' A data set containing `r format(nrow(esbl_isolates), big.mark = " ")` microbial isolates with MIC values of common antibiotics and a binary `esbl` column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with [tidymodels](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
+# TODO #' @format A [tibble][tibble::tibble] with `r format(nrow(esbl_isolates), big.mark = " ")` observations and `r ncol(esbl_isolates)` variables:
+# TODO #' - `esbl`\cr Logical indicator if the isolate is ESBL-producing
+# TODO #' - `genus`\cr Genus of the microorganism
+# TODO #' - `AMC:COL`\cr MIC values for 17 antimicrobial agents, transformed to class [`mic`] (see [as.mic()])
+# TODO #' @details See our [tidymodels integration][amr-tidymodels] for an example using this data set.
+# TODO #' @examples
+# TODO #' esbl_isolates
+# TODO "esbl_isolates"
--- a/R/ggplot_sir.R
+++ b/R/ggplot_sir.R
@@ -177,8 +177,8 @@ ggplot_sir <- function(data,
                       nrow = NULL,
                       colours = c(
                         S = "#3CAEA3",
-                         SI = "#3CAEA3",
                         SDD = "#8FD6C4",
+                         SI = "#3CAEA3",
                         I = "#F6D55C",
                         IR = "#ED553B",
                         R = "#ED553B"
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -41,7 +41,7 @@
 #' @inheritParams eucast_rules
 #' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
 #' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
-#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
+#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
 #' @details
 #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
 #'
@@ -174,48 +174,23 @@ mdro <- function(x = NULL,
  }

  # get gene values as TRUE/FALSE
-  if (is.character(esbl)) {
-    meet_criteria(esbl, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    esbl <- x[[esbl]]
-    meet_criteria(esbl, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(esbl) == 1) {
-    esbl <- rep(esbl, NROW(x))
-  }
-  if (is.character(carbapenemase)) {
-    meet_criteria(carbapenemase, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    carbapenemase <- x[[carbapenemase]]
-    meet_criteria(carbapenemase, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(carbapenemase) == 1) {
-    carbapenemase <- rep(carbapenemase, NROW(x))
-  }
-  if (is.character(mecA)) {
-    meet_criteria(mecA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    mecA <- x[[mecA]]
-    meet_criteria(mecA, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(mecA) == 1) {
-    mecA <- rep(mecA, NROW(x))
-  }
-  if (is.character(mecC)) {
-    meet_criteria(mecC, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    mecC <- x[[mecC]]
-    meet_criteria(mecC, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(mecC) == 1) {
-    mecC <- rep(mecC, NROW(x))
-  }
-  if (is.character(vanA)) {
-    meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanA <- x[[vanA]]
-    meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(vanA) == 1) {
-    vanA <- rep(vanA, NROW(x))
-  }
-  if (is.character(vanB)) {
-    meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanB <- x[[vanB]]
-    meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
-  } else if (length(vanB) == 1) {
-    vanB <- rep(vanB, NROW(x))
+  resolve_gene_var <- function(x, gene, varname) {
+    if (is.character(gene)) {
+      meet_criteria(gene, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
+      gene <- x[[gene]]
+      meet_criteria(gene, allow_class = "logical", allow_NA = TRUE)
+    } else if (length(gene) == 1) {
+      gene <- rep(gene, NROW(x))
+    }
+    x[[varname]] <- gene
+    x
  }
+  x <- resolve_gene_var(x, esbl, "esbl")
+  x <- resolve_gene_var(x, carbapenemase, "carbapenemase")
+  x <- resolve_gene_var(x, mecA, "mecA")
+  x <- resolve_gene_var(x, mecC, "mecC")
+  x <- resolve_gene_var(x, vanA, "vanA")
+  x <- resolve_gene_var(x, vanB, "vanB")

  info.bak <- info
  # don't throw info's more than once per call
@@ -772,7 +747,7 @@ mdro <- function(x = NULL,
        )
      }
      x[rows_to_change, "MDRO"] <<- to
-      x[rows_to_change, "reason"] <<- reason
+      x[rows_to_change, "reason"] <<- paste0(x[rows_to_change, "reason", drop = TRUE], "; ", reason)
      x[rows_not_to_change, "reason"] <<- "guideline criteria not met"
    }
  }
@@ -854,7 +829,7 @@ mdro <- function(x = NULL,
  x <- left_join_microorganisms(x, by = col_mo)
  x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
  x$row_number <- seq_len(nrow(x))
-  x$reason <- NA_character_
+  x$reason <- ""
  x$all_nonsusceptible_columns <- ""

  if (guideline$code == "cmi2012") {
@@ -1498,7 +1473,7 @@ mdro <- function(x = NULL,
    }
    trans_tbl(
      3, # positive
-      rows = which(x$order == "Enterobacterales" & esbl == TRUE),
+      rows = which(x$order == "Enterobacterales" & x$esbl == TRUE),
      cols = "any",
      any_all = "any",
      reason = "Enterobacterales: ESBL"
@@ -1519,7 +1494,7 @@ mdro <- function(x = NULL,
    )
    trans_tbl(
      3,
-      rows = which(x$order == "Enterobacterales" & carbapenemase == TRUE),
+      rows = which(x$order == "Enterobacterales" & x$carbapenemase == TRUE),
      cols = "any",
      any_all = "any",
      reason = "Enterobacterales: carbapenemase"
@@ -1557,14 +1532,14 @@ mdro <- function(x = NULL,
    )
    trans_tbl(
      2, # unconfirmed
-      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(carbapenemase)),
+      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & is.na(x$carbapenemase)),
      cols = carbapenems,
      any_all = "any",
      reason = "A. baumannii-calcoaceticus complex: potential carbapenemase"
    )
    trans_tbl(
      3,
-      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & carbapenemase == TRUE),
+      rows = which(x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"] & x$carbapenemase == TRUE),
      cols = carbapenems,
      any_all = "any",
      reason = "A. baumannii-calcoaceticus complex: carbapenemase"
@@ -1574,6 +1549,7 @@ mdro <- function(x = NULL,
    x$psae <- 0
    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R") | NA_as_FALSE(col_values(x, AMK) == "R"), 1, 0)
    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R") | NA_as_FALSE(col_values(x, MEM) == "R"), 1, 0)
+    x$psae <- x$psae + ifelse(NA_as_FALSE(x$carbapenemase), 1, 0)
    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R") | NA_as_FALSE(col_values(x, TZP) == "R"), 1, 0)
    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R") | NA_as_FALSE(col_values(x, CZA) == "R"), 1, 0)
    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R") | NA_as_FALSE(col_values(x, NOR) == "R") | NA_as_FALSE(col_values(x, LVX) == "R"), 1, 0)
@@ -1602,7 +1578,7 @@ mdro <- function(x = NULL,
    )
    trans_tbl(
      3,
-      rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (vanA == TRUE | vanB == TRUE)),
+      rows = which(x$genus == "Enterococcus" & x$species == "faecium" & (x$vanA == TRUE | x$vanB == TRUE)),
      cols = c(PEN, AMX, AMP, VAN),
      any_all = "any",
      reason = "E. faecium: vanA/vanB gene + penicillin group"
@@ -1611,14 +1587,14 @@ mdro <- function(x = NULL,
    # Staphylococcus aureus complex (= aureus, argenteus or schweitzeri)
    trans_tbl(
      2,
-      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(mecA) | is.na(mecC))),
+      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (is.na(x$mecA) | is.na(x$mecC))),
      cols = c(AMC, TZP, FLC, OXA, FOX, FOX1),
      any_all = "any",
      reason = "S. aureus complex: potential MRSA"
    )
    trans_tbl(
      3,
-      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (mecA == TRUE | mecC == TRUE)),
+      rows = which(x$genus == "Staphylococcus" & x$species %in% c("aureus", "argenteus", "schweitzeri") & (x$mecA == TRUE | x$mecC == TRUE)),
      cols = "any",
      any_all = "any",
      reason = "S. aureus complex: mecA/mecC gene"
@@ -1899,6 +1875,10 @@ mdro <- function(x = NULL,
    # fill in empty reasons
    x$reason[is.na(x$reason)] <- "not covered by guideline"
    x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)")
+    # starting semicolons must be removed
+    x$reason <- trimws(gsub("^;", "", x$reason))
+    # if criteria were not met initially, but later they were, then they have a following semicolon; remove the initial lack of meeting criteria
+    x$reason <- trimws(gsub("guideline criteria not met;", "", x$reason, fixed = TRUE))
    # format data set
    colnames(x)[colnames(x) == col_mo] <- "microorganism"
    x$microorganism <- mo_name(x$microorganism, language = NULL)
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -90,6 +90,10 @@
 #'   autoplot(some_mic_values, mo = "Escherichia coli", ab = "cipro")
 #' }
 #' if (require("ggplot2")) {
+#'   autoplot(some_mic_values, mo = "Staph aureus", ab = "Ceftaroline", guideline = "CLSI")
+#' }
+#'
+#' if (require("ggplot2")) {
 #'   # support for 27 languages, various guidelines, and many options
 #'   autoplot(some_disk_values,
 #'     mo = "Escherichia coli", ab = "cipro",
@@ -146,7 +150,7 @@
 #'     aes(group, mic)
 #'   ) +
 #'     geom_boxplot() +
-#'     geom_violin(linetype = 2, colour = "grey", fill = NA) +
+#'     geom_violin(linetype = 2, colour = "grey30", fill = NA) +
 #'     scale_y_mic()
 #' }
 #' if (require("ggplot2")) {
@@ -158,7 +162,7 @@
 #'     aes(group, mic)
 #'   ) +
 #'     geom_boxplot() +
-#'     geom_violin(linetype = 2, colour = "grey", fill = NA) +
+#'     geom_violin(linetype = 2, colour = "grey30", fill = NA) +
 #'     scale_y_mic(mic_range = c(NA, 0.25))
 #' }
 #'
@@ -191,7 +195,7 @@
 #'     aes(x = group, y = mic, colour = sir)
 #'   ) +
 #'     theme_minimal() +
-#'     geom_boxplot(fill = NA, colour = "grey") +
+#'     geom_boxplot(fill = NA, colour = "grey30") +
 #'     geom_jitter(width = 0.25)
 #'
 #'   plain
@@ -377,12 +381,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
  args <- list(...)
  args[c("value", "labels", "limits")] <- NULL

-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 4)
-  } else if (length(colours_SIR) == 3) {
-    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
-  }
-  colours_SIR <- unname(colours_SIR)
+  colours_SIR <- expand_SIR_colours(colours_SIR, unname = FALSE)

  if (identical(aesthetics, "x")) {
    ggplot_fn <- ggplot2::scale_x_discrete
@@ -392,24 +391,19 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
      args,
      list(
        aesthetics = aesthetics,
-        values = c(
-          S = colours_SIR[1],
-          SDD = colours_SIR[2],
-          I = colours_SIR[3],
-          R = colours_SIR[4],
-          NI = "grey30"
-        )
+        values = c(colours_SIR, NI = "grey30")
      )
    )
  }
  scale <- do.call(ggplot_fn, args)

  scale$labels <- function(x) {
-    stop_ifnot(all(x %in% c(levels(NA_sir_), NA)),
+    stop_ifnot(all(x %in% c(levels(NA_sir_), "SI", "IR", NA)),
      "Apply `scale_", aesthetics[1], "_sir()` to a variable of class 'sir', see `?as.sir`.",
      call = FALSE
    )
-    x <- as.character(as.sir(x))
+    x <- as.character(x)
+    x[!x %in% c("SI", "IR")] <- as.character(as.sir(x[!x %in% c("SI", "IR")]))
    if (!is.null(language)) {
      x[x == "S"] <- "(S) Susceptible"
      x[x == "SDD"] <- "(SDD) Susceptible dose-dependent"
@@ -419,6 +413,8 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
        x[x == "I"] <- "(I) Intermediate"
      }
      x[x == "R"] <- "(R) Resistant"
+      x[x == "SI"] <- "(S/I) Susceptible"
+      x[x == "IR"] <- "(I/R) Non-susceptible"
      x[x == "NI"] <- "(NI) Non-interpretable"
      x <- translate_AMR(x, language = language)
    }
@@ -426,7 +422,7 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
  }
  scale$limits <- function(x, ...) {
    # force SIR in the right order
-    as.character(sort(factor(x, levels = levels(NA_sir_))))
+    as.character(sort(factor(x, levels = c(levels(NA_sir_), "SI", "IR"))))
  }

  scale
@@ -536,6 +532,7 @@ plot.mic <- function(x,

  x <- as.mic(x) # make sure that currently implemented MIC levels are used
  main <- gsub(" +", " ", paste0(main, collapse = " "))
+  colours_SIR <- expand_SIR_colours(colours_SIR)

  x <- plotrange_as_table(x, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
@@ -683,6 +680,8 @@ autoplot.mic <- function(object,
    title <- gsub(" +", " ", paste0(title, collapse = " "))
  }

+  colours_SIR <- expand_SIR_colours(colours_SIR)
+
  object <- as.mic(object) # make sure that currently implemented MIC levels are used
  x <- plotrange_as_table(object, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
@@ -702,12 +701,14 @@ autoplot.mic <- function(object,
  colnames(df) <- c("mic", "count")
  df$cols <- cols_sub$cols
  df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
-  df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
-  df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
+  df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
+  df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
+  df$cols[df$cols == colours_SIR[4]] <- "(R) Resistant"
  df$cols <- factor(translate_into_language(df$cols, language = language),
    levels = translate_into_language(
      c(
        "(S) Susceptible",
+        "(SDD) Susceptible dose-dependent",
        paste("(I)", plot_name_of_I(cols_sub$guideline)),
        "(R) Resistant"
      ),
@@ -721,10 +722,10 @@ autoplot.mic <- function(object,
    vals <- c(
      "(S) Susceptible" = colours_SIR[1],
      "(SDD) Susceptible dose-dependent" = colours_SIR[2],
-      "(I) Susceptible, incr. exp." = colours_SIR[2],
-      "(I) Intermediate" = colours_SIR[2],
-      "(R) Resistant" = colours_SIR[3],
-      "(NI) Non-interpretable" = "grey"
+      "(I) Susceptible, incr. exp." = colours_SIR[3],
+      "(I) Intermediate" = colours_SIR[3],
+      "(R) Resistant" = colours_SIR[4],
+      "(NI) Non-interpretable" = "grey30"
    )
    names(vals) <- translate_into_language(names(vals), language = language)
    p <- p +
@@ -790,6 +791,7 @@ plot.disk <- function(x,
  meet_criteria(expand, allow_class = "logical", has_length = 1)

  main <- gsub(" +", " ", paste0(main, collapse = " "))
+  colours_SIR <- expand_SIR_colours(colours_SIR)

  x <- plotrange_as_table(x, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
@@ -935,6 +937,8 @@ autoplot.disk <- function(object,
    title <- gsub(" +", " ", paste0(title, collapse = " "))
  }

+  colours_SIR <- expand_SIR_colours(colours_SIR)
+
  x <- plotrange_as_table(object, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
    x = x,
@@ -952,10 +956,10 @@ autoplot.disk <- function(object,
  df <- as.data.frame(x, stringsAsFactors = TRUE)
  colnames(df) <- c("disk", "count")
  df$cols <- cols_sub$cols
-
  df$cols[df$cols == colours_SIR[1]] <- "(S) Susceptible"
-  df$cols[df$cols == colours_SIR[2]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
-  df$cols[df$cols == colours_SIR[3]] <- "(R) Resistant"
+  df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
+  df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
+  df$cols[df$cols == colours_SIR[4]] <- "(R) Resistant"
  df$cols <- factor(translate_into_language(df$cols, language = language),
    levels = translate_into_language(
      c(
@@ -973,10 +977,10 @@ autoplot.disk <- function(object,
    vals <- c(
      "(S) Susceptible" = colours_SIR[1],
      "(SDD) Susceptible dose-dependent" = colours_SIR[2],
-      "(I) Susceptible, incr. exp." = colours_SIR[2],
-      "(I) Intermediate" = colours_SIR[2],
-      "(R) Resistant" = colours_SIR[3],
-      "(NI) Non-interpretable" = "grey"
+      "(I) Susceptible, incr. exp." = colours_SIR[3],
+      "(I) Intermediate" = colours_SIR[3],
+      "(R) Resistant" = colours_SIR[4],
+      "(NI) Non-interpretable" = "grey30"
    )
    names(vals) <- translate_into_language(names(vals), language = language)
    p <- p +
@@ -1093,12 +1097,7 @@ barplot.sir <- function(height,
  language <- validate_language(language)
  meet_criteria(expand, allow_class = "logical", has_length = 1)

-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 4)
-  } else if (length(colours_SIR) == 3) {
-    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
-  }
-  colours_SIR <- unname(colours_SIR)
+  colours_SIR <- expand_SIR_colours(colours_SIR)

  # add SDD and N to colours
  colours_SIR <- c(colours_SIR, "grey30")
@@ -1148,12 +1147,7 @@ autoplot.sir <- function(object,
    title <- gsub(" +", " ", paste0(title, collapse = " "))
  }

-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 4)
-  } else if (length(colours_SIR) == 3) {
-    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
-  }
-  colours_SIR <- unname(colours_SIR)
+  colours_SIR <- expand_SIR_colours(colours_SIR)

  df <- as.data.frame(table(object), stringsAsFactors = TRUE)
  colnames(df) <- c("x", "n")
@@ -1252,13 +1246,6 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f

  guideline <- get_guideline(guideline, AMR::clinical_breakpoints)

-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 4)
-  } else if (length(colours_SIR) == 3) {
-    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
-  }
-  colours_SIR <- unname(colours_SIR)
-
  # store previous interpretations to backup
  sir_history <- AMR_env$sir_interpretation_history
  # and clear previous interpretations
@@ -1382,11 +1369,7 @@ scale_sir_colours <- function(...,
    colours_SIR <- list(...)$colours
  }

-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 4)
-  } else if (length(colours_SIR) == 3) {
-    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
-  }
+  colours_SIR <- expand_SIR_colours(colours_SIR, unname = FALSE)

  # behaviour when coming from ggplot_sir()
  if ("colours" %in% names(list(...))) {
@@ -1502,3 +1485,39 @@ labels_sir_count <- function(position = NULL,
    }
  )
 }
+
+expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
+  sir_order <- c("S", "SDD", "I", "R", "SI", "IR")
+
+  if (is.null(names(colours_SIR))) {
+    if (length(colours_SIR) == 1) {
+      colours_SIR <- rep(colours_SIR, 4)
+    } else if (length(colours_SIR) == 3) {
+      # old method for AMR < 3.0.1 which allowed for 3 colours
+      # fill in green for SDD as extra colour
+      colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
+    }
+    if (length(colours_SIR) == 4) {
+      # add colours for SI (same as S) and IR (same as R)
+      colours_SIR <- c(colours_SIR[1:4], colours_SIR[1], colours_SIR[4])
+    }
+    names(colours_SIR) <- sir_order
+  } else {
+    # named input: match and reorder
+    stop_ifnot(
+      all(names(colours_SIR) %in% sir_order),
+      "Unknown names in `colours_SIR`. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
+    )
+    if (length(colours_SIR) == 4) {
+      # add colours for SI (same as S) and IR (same as R)
+      colours_SIR <- c(colours_SIR[1:4], SI = unname(colours_SIR[1]), IR = unname(colours_SIR[4]))
+    }
+    colours_SIR <- colours_SIR[sir_order]
+  }
+
+  if (unname) {
+    colours_SIR <- unname(colours_SIR)
+  }
+
+  return(colours_SIR)
+}
--- a/R/sysdata.rda
+++ b/R/sysdata.rda
--- a/R/tidymodels.R.no_include
+++ b/R/tidymodels.R.no_include
--- a/data-raw/ab.md5
+++ b/data-raw/ab.md5
@@ -1 +1 @@
-228840b3941753c4adee2b781d901590
+d12f1c78feaecbb4d1631f9c735ad49b
--- a/data-raw/datasets/antimicrobials.dta
+++ b/data-raw/datasets/antimicrobials.dta
--- a/data-raw/datasets/antimicrobials.feather
+++ b/data-raw/datasets/antimicrobials.feather
--- a/data-raw/datasets/antimicrobials.parquet
+++ b/data-raw/datasets/antimicrobials.parquet
--- a/data-raw/datasets/antimicrobials.rds
+++ b/data-raw/datasets/antimicrobials.rds
--- a/data-raw/datasets/antimicrobials.sav
+++ b/data-raw/datasets/antimicrobials.sav
--- a/data-raw/datasets/antimicrobials.txt
+++ b/data-raw/datasets/antimicrobials.txt
@@ -116,7 +116,7 @@
 "CSU"	68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"	"NA"			"NA"	"cefsulmid,cefsumido,cefsumidum"					"NA"
 "CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02,QJ01DI02"			"ceftar,cfro"	"ceftaroine,teflaro,zinforo"					"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
 "CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"	"NA"			"NA"	"NA"					"73604-1,73626-4,73649-6"
-"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
+"CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cef,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
 "CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"			"cfav"	"avycaz,zavicefta"			6	"g"	"101483-6,73603-3,73625-6,73648-8,87734-0"
 "CCV"	9575352	"Ceftazidime/clavulanic acid"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"czcl,tazcla,xtzl"	"NA"			6	"g"	"NA"
 "CEM"	6537431	"Cefteram"	"Cephalosporins (3rd gen.)"	"J01DD18,QJ01DD18"			"cefter"	"cefterame,cefteramum,ceftetrame"	0.4	"g"			"100047-0,76144-5"
@@ -162,7 +162,7 @@
 "CYC"	6234	"Cycloserine"	"Oxazolidinones"	"J04AB01,QJ04AB01"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"cycl,cyclos"	"cicloserina,closina,cyclorin,cycloserin,cycloserinum,farmiserina,levcicloserina,levcycloserine,levcycloserinum,micoserina,miroserina,miroseryn,novoserin,oxamicina,oxamycin,seromycin,tebemicina,wasserina"	0.75	"g"			"16702-3,18914-2,212-1,213-9,214-7,215-4,23608-3,25207-2,25208-0,25209-8,25251-0,3519-6,55667-0"
 "DAL"	23724878	"Dalbavancin"	"Glycopeptides"	"J01XA04,QJ01XA04"	"Other antibacterials"	"Glycopeptide antibacterials"	"dalb,dalbav"	"dalbavancina,dalvance,xydalba,zeven"			1.5	"g"	"41688-3,41689-1,41690-9,41734-5"
 "DAN"	71335	"Danofloxacin"	"Fluoroquinolones"	"QJ01MA92"			"danofl"	"advocin,danofloxacine,danofloxacino,danofloxacinum"					"73601-7,73623-1,73646-2"
-"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02,QD10AX05,QJ04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"NA"	"aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac"	50	"mg"			"51698-9,9747-7"
+"DPS"	2955	"Dapsone"	"Other antibacterials"	"D10AX05,J04BA02,QD10AX05,QJ04BA02"	"Drugs for treatment of lepra"	"Drugs for treatment of lepra"	"dao"	"aczone,atrisone,avlosulfon,avlosulfone,avlosulphone,benzenamide,benzenamine,bissulfone,bissulphone,croysulfone,croysulphone,dapson,dapsona,dapsonum,daspone,diaphenylsulfon,diaphenylsulfone,diaphenylsulphon,diaphenylsulphone,diphenasone,diphone,disulfone,disulone,disulphone,dubronax,dumitone,eporal,medapsol,novophone,servidapson,sulfadione,sulfona,sulfonyldianiline,sulphadione,sulphonyldianiline,tarimyl,udolac,undolac"	50	"mg"			"51698-9,9747-7"
 "DAP"	16134395	"Daptomycin"	"Other antibacterials"	"J01XX09,QJ01XX09"	"Other antibacterials"	"Other antibacterials"	"dap,dapt,dapt25,dapt50,daptom"	"cidecin,cubicin,dapcin,daptomicina,daptomycine,daptomycinum,deptomycin"			0.28	"g"	"35787-1,35788-9,35789-7,41691-7"
 "DFX"	487101	"Delafloxacin"	"Fluoroquinolones"	"J01MA23,QJ01MA23"			"NA"	"baxdela,delafloxacinum,quofenix"	0.9	"g"	0.6	"g"	"88885-9,90447-4,93790-4"
 "DLM"	6480466	"Delamanid"	"Antimycobacterials"	"J04AK06,QJ04AK06"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"dela"	"deltyba"	0.2	"g"			"93851-4,96109-4"
@@ -184,7 +184,7 @@
 "ERV"	54726192	"Eravacycline"	"Tetracyclines"	"J01AA13,QJ01AA13"	"Tetracyclines"	"Tetracyclines"	"erav"	"xerava"			0.14	"g"	"100049-6,85423-2,93767-2"
 "ETP"	150610	"Ertapenem"	"Carbapenems"	"J01DH03,QJ01DH03"	"Other beta-lactam antibacterials"	"Carbapenems"	"erta,ertape,etp"	"ertapenemsalt,invanz"			1	"g"	"101486-9,35799-6,35800-2,35801-0,35802-8"
 "ERY"	12560	"Erythromycin"	"Macrolides/lincosamides"	"D10AF02,J01FA01,QD10AF02,QJ01FA01,QJ51FA01,QS01AA17,S01AA17"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"e,em,ery,ery32,eryt,eryth"	"abboticin,abomacetin,acneryne,acnesol,aknemycin,aknin,benzamycin,derimer,deripil,dotycin,dumotrycin,emgel,emuvin,emycin,endoeritrin,erecin,erisone,eritomicina,eritrocina,eritromicina,ermycin,eryacne,eryacnen,erycen,erycette,erycinum,eryderm,erydermer,erygel,eryhexal,erymax,erymed,erysafe,erytab,erythro,erythroderm,erythrogran,erythroguent,erythromast,erythromid,erythromycine,erythromycinum,erytop,erytrociclin,ilocaps,ilosone,iloticina,ilotycin,inderm,latotryd,lederpax,mephamycin,mercina,oftamolets,pantoderm,pantodrin,pantomicina,pharyngocin,primacine,propiocine,proterytrin,retcin,robimycin,sansac,spotex,staticin,stiemicyn,stiemycin,tiprocin,torlamicina,wemid"	2	"g"	1	"g"	"100050-4,11576-6,12298-6,16829-4,16830-2,18919-1,18920-9,20380-2,232-9,233-7,234-5,235-2,236-0,23633-1,237-8,238-6,239-4,25224-7,25275-9,3597-2,7009-4"
-"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02,QJ04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"etha,ethamb"	"aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
+"ETH"	14052	"Ethambutol"	"Antimycobacterials"	"J04AK02,QJ04AK02"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"emb,etha,ethamb"	"aethambutolum,dadibutol,diambutol,etambutol,etambutolo,ethambutolum,myambutol,purderal,servambutol,tibutol"	1.2	"g"	1.2	"g"	"100051-2,16841-9,18921-7,20381-0,23625-7,240-2,241-0,242-8,243-6,25187-6,25194-2,25195-9,25230-4,25404-5,3607-9,42645-2,42646-0,55154-9,55674-6,56025-0,7010-2,89491-5"
 "ETI"	456476	"Ethambutol/isoniazid"	"Antimycobacterials"	"J04AM03,QJ04AM03"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
 "ETI1"	2761171	"Ethionamide"	"Antimycobacterials"	"J04AD03,QJ04AD03"	"Drugs for treatment of tuberculosis"	"Thiocarbamide derivatives"	"ethi,ethion"	"aethionamidum,aetina,aetiva,amidazin,amidazine,atina,ethimide,ethina,ethinamide,ethionamidum,ethioniamide,ethylisothiamide,ethyonomide,etimid,etiocidan,etionamid,etionamida,etionamide,etioniamid,etionid,etionizin,etionizina,etionizine,fatoliamid,iridocin,iridozin,isothin,isotiamida,itiocide,nicotion,nisotin,nizotin,rigenicid,sertinon,teberus,thianid,thianide,thioamide,thiodine,thiomid,thioniden,tianid,tiomid,trecator,trekator,trescatyl,trescazide,tubenamide,tubermin,tuberoid,tuberoson"	0.75	"g"			"16099-4,16845-0,18922-5,20382-8,23617-4,25183-5,25196-7,25198-3,25231-2,41693-3,42647-8,42648-6,7011-0,96110-2"
 "ETO"	6034	"Ethopabate"	"Other antibacterials"	"QP51AX17"			"NA"	"ethopabat"					"NA"
@@ -202,7 +202,7 @@
 "FLM"	3374	"Flumequine"	"Quinolones"	"J01MB07,QJ01MB07"	"Quinolone antibacterials"	"Other quinolones"	"flumeq"	"apurone,fantacin,flumequina,flumequino,flumequinum,flumigal,flumiquil,flumisol,flumix,imequyl"	1.2	"g"			"55675-3,55676-1,55677-9,55678-7"
 "FLR1"	71260	"Flurithromycin"	"Macrolides/lincosamides"	"J01FA14,QJ01FA14"	"Macrolides, lincosamides and streptogramins"	"Macrolides"	"NA"	"abbot,beritromicina,berythromycin,berythromycine,berythromycinum,flurithromycine,flurithromycinum,fluritromicina,fluritromycinum,flurizic,mizar"	0.75	"g"			"NA"
 "FFL"	214356	"Fosfluconazole"	"Antifungals/antimycotics"	"NA"			"NA"	"fosfluconazol,procif,prodif"					"NA"
-"FOS"	446987	"Fosfomycin"	"Other antibacterials"	"J01XX01,QJ01XX01,QS02AA17,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf,fosfom,fosmyc"	"fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
+"FOS"	446987	"Fosfomycin"	"Phosphonics"	"J01XX01,QJ01XX01,QS02AA17,S02AA17"	"Other antibacterials"	"Other antibacterials"	"ff,fm,fo,fof,fos,fosf,fosfom,fosmyc"	"fosfocina,fosfomicin,fosfomicina,fosfomycine,fosfomycinum,fosfonomycin,infectophos,phosphonemycin,phosphonomycin,veramina"	3	"g"	8	"g"	"25596-8,25653-7,35809-3,35810-1"
 "FMD"	572	"Fosmidomycin"	"Other antibacterials"	"NA"			"NA"	"fosmidomicina,fosmidomycina,fosmidomycine,fosmidomycinsalt,fosmidomycinum"					"NA"
 "FRM"	8378	"Framycetin"	"Aminoglycosides"	"D09AA01,QD09AA01,QJ01GB91,QR01AX08,QS01AA07,R01AX08,S01AA07"			"fram,framyc"	"actilin,actiline,antibiotique,bycomycin,enterfram,fradiomycin,fradiomycinum,framicetina,framidal,framycetine,framycetinum,framycin,framygen,francetin,jernadex,myacyne,mycerin,mycifradin,neobrettin,neolate,neomas,neomcin,neomicina,neomin,neomycine,neomycinum,nivemycin,soframycin,soframycine"					"18926-6,257-6,258-4,259-2,260-0,55679-5"
 "FUR"	6870646	"Furazidin"	"Other antibacterials"	"J01XE03,QJ01XE03"	"Other antibacterials"	"Nitrofuran derivatives"	"NA"	"akritoin,furagin,furaginum,furamag,furazidine,hydantoin"	0.3	"g"			"NA"
@@ -268,7 +268,7 @@
 "MET"	6087	"Meticillin"	"Beta-lactams/penicillins"	"J01CF03,QJ01CF03,QJ51CF03"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"methic,meti"	"belfacillin,celbenin,celpilline,cinopenil,dimocillin,estafcilina,flabelline,lucopenin,metacillin,methcillin,methicillin,methicillinanhydrous,methicillinhydrate,methicillinsalt,methicillinum,methycillin,meticilina,meticillina,meticilline,meticillinsalt,meticillinum,penaureus,penysol,staficyn,staphcillin,synticillin"			4	"g"	"NA"
 "MTP"	68590	"Metioprim"	"Other antibacterials"	"NA"			"NA"	"methioprim,metioprima,metioprime,metioprimum"					"NA"
 "MXT"	3047729	"Metioxate"	"Fluoroquinolones"	"NA"			"NA"	"metioxato,metioxatum"					"NA"
-"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01"	"Other antibacterials"	"Imidazole derivatives"	"metr,metron,mnz"	"acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
+"MTR"	4173	"Metronidazole"	"Other antibacterials"	"A01AB17,D06BX01,G01AF01,J01XD01,P01AB01,QA01AB17,QD06BX01,QG01AF01,QJ01XD01,QP51CA01"	"Other antibacterials"	"Imidazole derivatives"	"metr,metron,mnz,mtz"	"acromona,anagiardil,arilin,atrivyl,bexon,clont,danizol,deflamon,donnan,efloran,elyzol,entizol,eumin,flagemona,flagesol,flagil,flagyl,flazol,flegyl,florazole,fossyol,giatricol,gineflavir,givagil,hydroxydimetridazole,hydroxymetronidazole,izoklion,klion,klont,mepagyl,meronidal,metric,metrolag,metrolyl,metromidol,metronidazolo,metronidazolum,metroplex,metrotop,mexibol,monagyl,monasin,nalox,nidagyl,noritate,novonidazol,nuvessa,orvagil,polibiotic,protostat,rathimed,rosaced,rosased,sanatrichom,satric,takimetol,trichazol,trichex,trichobrol,trichocide,trichomol,trichopal,trichopol,tricocet,tricom,trikacide,trikamon,trikhopol,trikojol,trikozol,trimeks,trivazol,vagilen,vagimid,vandazole,vertisal,wagitran,zadstat,zidoval"	2	"g"	1.5	"g"	"10991-8,18946-4,326-9,327-7,328-5,329-3,7031-8"
 "MEZ"	656511	"Mezlocillin"	"Beta-lactams/penicillins"	"J01CA10,QJ01CA10"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"mez,mezl,mezlo,mz"	"baycipen,baypen,mezlin,mezlocilina,mezlocilline,mezlocillinsalt,mezlocillinum,multocillin"			6	"g"	"18947-2,330-1,331-9,332-7,333-5,3820-8,41702-2,54194-6,54195-3,54196-1"
 "MSU"		"Mezlocillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			"mezsul"	"NA"					"54194-6,54195-3,54196-1"
 "MIF"	477468	"Micafungin"	"Antifungals/antimycotics"	"J02AX05,QJ02AX05"	"Antimycotics for systemic use"	"Other antimycotics for systemic use"	"mica,micafu"	"fungard,funguard,micafungina,micafunginsalt,mycamine"			0.1	"g"	"53812-4,58418-5,65340-2,85048-7"
@@ -339,7 +339,7 @@
 "PMR"	5284447	"Pimaricin"	"Antifungals/antimycotics"	"NA"			"natamycin"	"delvocid,delvolan,delvopos,mycophyt,myprozine,natacyn,natafucin,natajen,natamatrix,natamax,natamicina,natamycin,natamycine,natamycinum,pimafucin,pimaracin,pimaricine,pimarizin,synogil,tennecetin"					"NA"
 "PPA"	4831	"Pipemidic acid"	"Quinolones"	"J01MB04,QJ01MB04"	"Quinolone antibacterials"	"Other quinolones"	"pipaci,pipz,pizu"	"deblaston,dolcol,filtrax,karunomazin,memento,nuril,palin,pipedac,pipemid,pipemidate,pipemidic,pipemidicacid,pipram,pipurin,tractur,uromidin,urosten,uroval"	0.8	"g"			"NA"
 "PIP"	43672	"Piperacillin"	"Beta-lactams/penicillins"	"J01CA12,QJ01CA12"	"Beta-lactam antibacterials, penicillins"	"Penicillins with extended spectrum"	"pi,pip,pipc,pipe,pipera,pp"	"penmalin,pentcillin,peperacillin,peracin,piperacilina,piperacillina,piperacilline,piperacillinhydrate,piperacillinum,pipercillin,pipracil,tazocin"			14	"g"	"101490-1,101491-9,18969-6,18970-4,25268-4,3972-7,407-7,408-5,409-3,410-1,411-9,412-7,413-5,414-3,54197-9,54198-7,54199-5,55704-1,7043-3,7044-1"
-"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"J01CR05,QJ01CR05"			"NA"	"NA"			14	"g"	"54197-9,54198-7,54199-5,55704-1"
+"PIS"		"Piperacillin/sulbactam"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"			14	"g"	"54197-9,54198-7,54199-5,55704-1"
 "TZP"	461573	"Piperacillin/tazobactam"	"Beta-lactams/penicillins"	"J01CR05,QJ01CR05"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"p/t,piptaz,piptazo,pit,pita,pt,ptc,ptz,tzp"	"piptazobactam,tazonam,zobactin,zosyn"			14	"g"	"101491-9,18970-4,411-9,412-7,413-5,414-3,7044-1"
 "PRC"	71978	"Piridicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"NA"					"NA"
 "PRL"	157385	"Pirlimycin"	"Macrolides/lincosamides"	"QJ51FF90"			"pirlim"	"pirlimycina,pirlimycine,pirlimycinum,pirsue"					"35829-1,35830-9,35831-7"
@@ -370,7 +370,7 @@
 "RBC"	44631912	"Ribociclib"	"Antifungals/antimycotics"	"L01EF02,QL01EF02"	"Antimycotics for systemic use"	"Triazole derivatives"	"ribo"	"kisqali"	0.45	"g"			"NA"
 "RST"	33042	"Ribostamycin"	"Aminoglycosides"	"J01GB10,QJ01GB10"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"NA"	"exaluren,hetangmycin,ribastamin,ribostamicina,ribostamycine,ribostamycinum,vistamycin,xylostatin"			1	"g"	"NA"
 "RID1"	16659285	"Ridinilazole"	"Other antibacterials"	"NA"			"NA"	"ridinilazol"					"NA"
-"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04,QJ04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"ansamy,rifb"	"alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
+"RIB"	135398743	"Rifabutin"	"Antimycobacterials"	"J04AB04,QJ04AB04"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"ansamy,rfb,rifb"	"alfacid,ansamicin,ansamycins,ansatipin,ansatipine,assatipin,mycobutin,rifabutinum"	0.15	"g"			"100699-8,16100-0,16386-5,16387-3,19149-4,20386-9,23630-7,24032-5,25199-1,25200-7,25201-5,42655-1,42656-9,54183-9,96113-6"
 "RIF"	135398735	"Rifampicin"	"Antimycobacterials"	"J04AB02,QJ04AB02,QJ54AB02"	"Drugs for treatment of tuberculosis"	"Antibiotics"	"rifa,rifamp"	"abrifam,archidyn,arficin,arzide,benemicin,doloresum,eremfat,famcin,fenampicin,rifadin,rifadine,rifagen,rifaldazin,rifaldazine,rifaldin,rifam,rifamor,rifampicina,rifampicine,rifampicinum,rifampin,rifamsolin,rifapiam,rifaprodin,rifcin,rifinah,rifobac,rifoldin,rifoldine,riforal,rimactan,rimactane,rimactazid,rimactizid,rimazid,sinerdol,tubocin"	0.6	"g"	0.6	"g"	"NA"
 "REI"	135483893	"Rifampicin/ethambutol/isoniazid"	"Antimycobacterials"	"J04AM07,QJ04AM07"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"isonarif,rifamate,rifamazid"					"NA"
 "RFI"		"Rifampicin/isoniazid"	"Antimycobacterials"	"J04AM02,QJ04AM02"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
@@ -391,7 +391,6 @@
 "SRC"	54681908	"Sarecycline"	"Tetracyclines"	"J01AA14,QJ01AA14"	"Tetracyclines"	"Tetracyclines"	"NA"	"sareciclina,seysara"	0.1	"g"			"NA"
 "SRX"	9933415	"Sarmoxicillin"	"Beta-lactams/penicillins"	"NA"			"NA"	"sarmoxillina,sarmoxilline,sarmoxillinum"					"NA"
 "SEC"	71815	"Secnidazole"	"Other antibacterials"	"P01AB07"			"NA"	"flagentyl,secnidal,secnidazolum,secnil,sindose,solosec"	2	"g"			"NA"
-"SMF"		"Simvastatin/fenofibrate"	"Antimycobacterials"	"C10BA04,QC10BA04"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"simv"	"NA"					"NA"
 "SIS"	36119	"Sisomicin"	"Aminoglycosides"	"J01GB08,QJ01GB08"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"siso,sisomy"	"rickamicin,salvamina,sisomicina,sisomicine,sisomicinum,sisomin,sisomycin,sissomicin,sizomycin"			0.24	"g"	"18979-5,447-3,448-1,449-9,450-7,55714-0"
 "SIT"	461399	"Sitafloxacin"	"Fluoroquinolones"	"J01MA21,QJ01MA21"			"sitafl"	"gracevit"	0.1	"g"			"NA"
 "SDA"	2724368	"Sodium aminosalicylate"	"Antimycobacterials"	"J04AA02,QJ04AA02"	"Drugs for treatment of tuberculosis"	"Aminosalicylic acid and derivatives"	"NA"	"bactylan,lepasen,monopas,tubersan"	14	"g"	14	"g"	"NA"
@@ -495,4 +494,4 @@
 "VOR"	71616	"Voriconazole"	"Antifungals/antimycotics"	"J02AC03,QJ02AC03"	"Antimycotics for systemic use"	"Triazole derivatives"	"vori,vorico,vrc"	"vfend,voriconazol,voriconazolum,voriconzole,vorikonazole"	0.4	"g"	0.4	"g"	"32379-0,35862-2,35863-0,38370-3,41199-1,41200-7,53902-3,73676-9,80553-1,80651-3"
 "XBR"	72144	"Xibornol"	"Other antibacterials"	"J01XX02,QJ01XX02"	"Other antibacterials"	"Other antibacterials"	"NA"	"bactacine,bracen,nanbacine,xibornolo,xibornolum"					"NA"
 "ZID"	77846445	"Zidebactam"	"Other antibacterials"	"NA"			"NA"	"zidebactamsalt"					"NA"
-"ZFD"		"Zoliflodacin"		"NA"			"NA"	"NA"					"NA"
+"ZFD"		"Zoliflodacin"		"NA"			"zol"	"NA"					"NA"
--- a/data-raw/datasets/antimicrobials.xlsx
+++ b/data-raw/datasets/antimicrobials.xlsx
--- a/data/antibiotics.rda
+++ b/data/antibiotics.rda
--- a/data/antimicrobials.rda
+++ b/data/antimicrobials.rda
--- a/data/esbl_isolates.rda.no_include
+++ b/data/esbl_isolates.rda.no_include
--- a/index.Rmd
+++ b/index.Rmd
@@ -133,7 +133,7 @@ ggplot(data.frame(mic = some_mic_values,
                  sir = interpretation),
       aes(x = group, y = mic, colour = sir)) +
  theme_minimal() +
-  geom_boxplot(fill = NA, colour = "grey") +
+  geom_boxplot(fill = NA, colour = "grey30") +
  geom_jitter(width = 0.25) +
  
  # NEW scale function: plot MIC values to x, y, colour or fill
--- a/index.md
+++ b/index.md
@@ -171,14 +171,14 @@ example_isolates %>%
  select(bacteria,
         aminoglycosides(),
         carbapenems())
-#> ℹ Using column 'mo' as input for mo_fullname()
-#> ℹ Using column 'mo' as input for mo_is_gram_negative()
-#> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()
+#> ℹ Using column 'mo' as input for `mo_fullname()`
+#> ℹ Using column 'mo' as input for `mo_is_gram_negative()`
+#> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`
 #> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
 #>   Phenotypes' v1.2 (2023). This note will be shown once per session.
-#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
 #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
+#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
 #> # A tibble: 35 × 7
 #>    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  
 #>    <chr>                        <sir> <sir> <sir> <sir> <sir> <sir>
@@ -215,9 +215,9 @@ output format automatically (such as markdown, LaTeX, HTML, etc.).
 ``` r
 antibiogram(example_isolates,
            antimicrobials = c(aminoglycosides(), carbapenems()))
-#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
 #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)
+#> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)
 ```

 | Pathogen | Amikacin | Gentamicin | Imipenem | Kanamycin | Meropenem | Tobramycin |
@@ -289,7 +289,7 @@ ggplot(data.frame(mic = some_mic_values,
                  sir = interpretation),
       aes(x = group, y = mic, colour = sir)) +
  theme_minimal() +
-  geom_boxplot(fill = NA, colour = "grey") +
+  geom_boxplot(fill = NA, colour = "grey30") +
  geom_jitter(width = 0.25) +
  
  # NEW scale function: plot MIC values to x, y, colour or fill
@@ -340,15 +340,15 @@ out <- example_isolates %>%
  # calculate AMR using resistance(), over all aminoglycosides and polymyxins:
  summarise(across(c(aminoglycosides(), polymyxins()),
            resistance))
-#> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'
+#> ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'
 #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)
-#> ℹ For polymyxins() using column 'COL' (colistin)
+#> ℹ For `polymyxins()` using column 'COL' (colistin)
 #> Warning: There was 1 warning in `summarise()`.
 #> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
 #> ℹ In group 3: `ward = "Outpatient"`.
 #> Caused by warning:
 #> ! Introducing NA: only 23 results available for KAN in group: ward =
-#> "Outpatient" (minimum = 30).
+#> "Outpatient" (`minimum` = 30).
 out
 #> # A tibble: 3 × 6
 #>   ward         GEN   TOB   AMK   KAN   COL
--- a/man/amr-tidymodels.Rd
+++ b/man/amr-tidymodels.Rd
@@ -1,125 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/tidymodels.R
-\name{amr-tidymodels}
-\alias{amr-tidymodels}
-\alias{all_mic}
-\alias{all_mic_predictors}
-\alias{all_sir}
-\alias{all_sir_predictors}
-\alias{step_mic_log2}
-\alias{step_sir_numeric}
-\title{AMR Extensions for Tidymodels}
-\usage{
-all_mic()
-
-all_mic_predictors()
-
-all_sir()
-
-all_sir_predictors()
-
-step_mic_log2(recipe, ..., role = NA, trained = FALSE, columns = NULL,
-  skip = FALSE, id = recipes::rand_id("mic_log2"))
-
-step_sir_numeric(recipe, ..., role = NA, trained = FALSE, columns = NULL,
-  skip = FALSE, id = recipes::rand_id("sir_numeric"))
-}
-\arguments{
-\item{recipe}{A recipe object. The step will be added to the sequence of
-operations for this recipe.}
-
-\item{...}{One or more selector functions to choose variables for this step.
-See \code{\link[recipes:selections]{selections()}} for more details.}
-
-\item{role}{Not used by this step since no new variables are created.}
-
-\item{trained}{A logical to indicate if the quantities for preprocessing have
-been estimated.}
-
-\item{skip}{A logical. Should the step be skipped when the recipe is baked by
-\code{\link[recipes:bake]{bake()}}? While all operations are baked when \code{\link[recipes:prep]{prep()}} is run, some
-operations may not be able to be conducted on new data (e.g. processing the
-outcome variable(s)). Care should be taken when using \code{skip = TRUE} as it
-may affect the computations for subsequent operations.}
-
-\item{id}{A character string that is unique to this step to identify it.}
-}
-\description{
-This family of functions allows using AMR-specific data types such as \verb{<mic>} and \verb{<sir>} inside \code{tidymodels} pipelines.
-}
-\details{
-You can read more in our online \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{AMR with tidymodels introduction}.
-
-Tidyselect helpers include:
-\itemize{
-\item \code{\link[=all_mic]{all_mic()}} and \code{\link[=all_mic_predictors]{all_mic_predictors()}} to select \verb{<mic>} columns
-\item \code{\link[=all_sir]{all_sir()}} and \code{\link[=all_sir_predictors]{all_sir_predictors()}} to select \verb{<sir>} columns
-}
-
-Pre-processing pipeline steps include:
-\itemize{
-\item \code{\link[=step_mic_log2]{step_mic_log2()}} to convert MIC columns to numeric (via \code{as.numeric()}) and apply a log2 transform, to be used with \code{\link[=all_mic_predictors]{all_mic_predictors()}}
-\item \code{\link[=step_sir_numeric]{step_sir_numeric()}} to convert SIR columns to numeric (via \code{as.numeric()}), to be used with \code{\link[=all_sir_predictors]{all_sir_predictors()}}: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. Keep this in mind for further processing, especially if the model does not allow for \code{NA} values.
-}
-
-These steps integrate with \code{recipes::recipe()} and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
-}
-\examples{
-if (require("tidymodels")) {
-
-  # The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703
-  # Presence of ESBL genes was predicted based on raw MIC values.
-
-
-  # example data set in the AMR package
-  esbl_isolates
-
-  # Prepare a binary outcome and convert to ordered factor
-  data <- esbl_isolates \%>\%
-    mutate(esbl = factor(esbl, levels = c(FALSE, TRUE), ordered = TRUE))
-
-  # Split into training and testing sets
-  split <- initial_split(data)
-  training_data <- training(split)
-  testing_data <- testing(split)
-
-  # Create and prep a recipe with MIC log2 transformation
-  mic_recipe <- recipe(esbl ~ ., data = training_data) \%>\%
-
-    # Optionally remove non-predictive variables
-    remove_role(genus, old_role = "predictor") \%>\%
-
-    # Apply the log2 transformation to all MIC predictors
-    step_mic_log2(all_mic_predictors()) \%>\%
-
-    # And apply the preparation steps
-    prep()
-
-  # View prepped recipe
-  mic_recipe
-
-  # Apply the recipe to training and testing data
-  out_training <- bake(mic_recipe, new_data = NULL)
-  out_testing <- bake(mic_recipe, new_data = testing_data)
-
-  # Fit a logistic regression model
-  fitted <- logistic_reg(mode = "classification") \%>\%
-    set_engine("glm") \%>\%
-    fit(esbl ~ ., data = out_training)
-
-  # Generate predictions on the test set
-  predictions <- predict(fitted, out_testing) \%>\%
-    bind_cols(out_testing)
-
-  # Evaluate predictions using standard classification metrics
-  our_metrics <- metric_set(accuracy, kap, ppv, npv)
-  metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
-
-  # Show performance
-  metrics
-}
-}
-\seealso{
-\code{\link[recipes:recipe]{recipes::recipe()}}, \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.sir]{as.sir()}}
-}
-\keyword{internal}
--- a/man/antimicrobial_selectors.Rd
+++ b/man/antimicrobial_selectors.Rd
@@ -181,7 +181,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)
 \item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin (AMX) and ampicillin (AMP)
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)
-\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
+\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)
 \item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)
 \item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)
 \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)
--- a/man/antimicrobials.Rd
+++ b/man/antimicrobials.Rd
@@ -5,9 +5,9 @@
 \alias{antimicrobials}
 \alias{antibiotics}
 \alias{antivirals}
-\title{Data Sets with 617 Antimicrobial Drugs}
+\title{Data Sets with 616 Antimicrobial Drugs}
 \format{
-\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 497 observations and 14 variables:}{
+\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 496 observations and 14 variables:}{
 \itemize{
 \item \code{ab}\cr antimicrobial ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. \emph{\strong{This is a unique identifier.}}
 \item \code{cid}\cr Compound ID as found in PubChem. \emph{\strong{This is a unique identifier.}}
@@ -50,7 +50,7 @@ LOINC:
 }
 }

-An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 496 rows and 14 columns.

 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
 }
--- a/man/custom_eucast_rules.Rd
+++ b/man/custom_eucast_rules.Rd
@@ -103,7 +103,7 @@ These 35 antimicrobial groups are allowed in the rules (case-insensitive) and ca
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
 \item aminopenicillins\cr(amoxicillin and ampicillin)
 \item antifungals\cr(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)
-\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
+\item antimycobacterials\cr(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)
 \item betalactams\cr(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)
 \item betalactams_with_inhibitor\cr(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)
 \item carbapenems\cr(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)
--- a/man/custom_mdro_guideline.Rd
+++ b/man/custom_mdro_guideline.Rd
@@ -99,7 +99,7 @@ All 35 antimicrobial selectors are supported for use in the rules:
 \item \code{\link[=aminoglycosides]{aminoglycosides()}} can select: \cr amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high
 \item \code{\link[=aminopenicillins]{aminopenicillins()}} can select: \cr amoxicillin and ampicillin
 \item \code{\link[=antifungals]{antifungals()}} can select: \cr amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole
-\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
+\item \code{\link[=antimycobacterials]{antimycobacterials()}} can select: \cr 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin
 \item \code{\link[=betalactams]{betalactams()}} can select: \cr amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam
 \item \code{\link[=betalactams_with_inhibitor]{betalactams_with_inhibitor()}} can select: \cr amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid
 \item \code{\link[=carbapenems]{carbapenems()}} can select: \cr biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem
--- a/man/esbl_isolates.Rd
+++ b/man/esbl_isolates.Rd
@@ -1,27 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/data.R
-\docType{data}
-\name{esbl_isolates}
-\alias{esbl_isolates}
-\title{Data Set with 500 ESBL Isolates}
-\format{
-A \link[tibble:tibble]{tibble} with 500 observations and 19 variables:
-\itemize{
-\item \code{esbl}\cr Logical indicator if the isolate is ESBL-producing
-\item \code{genus}\cr Genus of the microorganism
-\item \code{AMC:COL}\cr MIC values for 17 antimicrobial agents, transformed to class \code{\link{mic}} (see \code{\link[=as.mic]{as.mic()}})
-}
-}
-\usage{
-esbl_isolates
-}
-\description{
-A data set containing 500 microbial isolates with MIC values of common antibiotics and a binary \code{esbl} column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{tidymodels}.
-}
-\details{
-See our \link[=amr-tidymodels]{tidymodels integration} for an example using this data set.
-}
-\examples{
-esbl_isolates
-}
-\keyword{datasets}
--- a/man/ggplot_sir.Rd
+++ b/man/ggplot_sir.Rd
@@ -9,7 +9,7 @@ ggplot_sir(data, position = NULL, x = "antibiotic",
  fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
  limits = NULL, translate_ab = "name", combine_SI = TRUE,
  minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S
-  = "#3CAEA3", SI = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", IR = "#ED553B",
+  = "#3CAEA3", SDD = "#8FD6C4", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B",
  R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5,
  datalabels.colour = "grey15", title = NULL, subtitle = NULL,
  caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...)
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@@ -57,7 +57,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),

 \item{combine_SI}{A \link{logical} to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{\link[=mdro]{mdro()}} function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.}

-\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
+\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}

 \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}

--- a/man/plot.Rd
+++ b/man/plot.Rd
@@ -210,6 +210,10 @@ if (require("ggplot2")) {
  # when providing the microorganism and antibiotic, colours will show interpretations:
  autoplot(some_mic_values, mo = "Escherichia coli", ab = "cipro")
 }
+if (require("ggplot2")) {
+  autoplot(some_mic_values, mo = "Staph aureus", ab = "Ceftaroline", guideline = "CLSI")
+}
+
 if (require("ggplot2")) {
  # support for 27 languages, various guidelines, and many options
  autoplot(some_disk_values,
@@ -267,7 +271,7 @@ if (require("ggplot2")) {
    aes(group, mic)
  ) +
    geom_boxplot() +
-    geom_violin(linetype = 2, colour = "grey", fill = NA) +
+    geom_violin(linetype = 2, colour = "grey30", fill = NA) +
    scale_y_mic()
 }
 if (require("ggplot2")) {
@@ -279,7 +283,7 @@ if (require("ggplot2")) {
    aes(group, mic)
  ) +
    geom_boxplot() +
-    geom_violin(linetype = 2, colour = "grey", fill = NA) +
+    geom_violin(linetype = 2, colour = "grey30", fill = NA) +
    scale_y_mic(mic_range = c(NA, 0.25))
 }

@@ -312,7 +316,7 @@ if (require("ggplot2")) {
    aes(x = group, y = mic, colour = sir)
  ) +
    theme_minimal() +
-    geom_boxplot(fill = NA, colour = "grey") +
+    geom_boxplot(fill = NA, colour = "grey30") +
    geom_jitter(width = 0.25)

  plain
--- a/pkgdown/assets/logo_umcg.svg
+++ b/pkgdown/assets/logo_umcg.svg
--- a/pkgdown/extra.css
+++ b/pkgdown/extra.css
@@ -190,6 +190,15 @@ this shows on top of every sidebar to the right
  }
 }

+.template-reference-topic h3,
+.template-reference-topic h3 code {
+  color: var(--amr-green-dark) !important;
+}
+.template-reference-topic h3 {
+  font-weight: normal;
+  margin-top: 2rem;
+}
+
 /* replace 'Developers' with 'Maintainers' */
 .developers h2 {
  display: none;
Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	3ba1b8a10a	(v3.0.0.9022) postpone new features - we like a clearly focussed bugfix release first	2025-09-03 15:39:44 +02:00
dr. M.S. (Matthijs) Berends	0744c6feee	(v3.0.0.9021) checkouts	2025-09-03 12:12:05 +02:00
dr. M.S. (Matthijs) Berends	eca638529c	new umcg logo and old CHECKOUT update	2025-09-03 11:49:10 +02:00
dr. M.S. (Matthijs) Berends	60bd631e1a	(v3.0.0.9019) Fixes #229 , #230 , #227 , #225	2025-09-01 16:56:55 +02:00
dr. M.S. (Matthijs) Berends	9b07a8573a	(v3.0.0.9018) keep all reasons in mdro(), fixed #227	2025-08-07 16:23:47 +02:00
dr. M.S. (Matthijs) Berends	fc72cf9324	(v3.0.0.9017) semantic versioning only on branch `main`	2025-07-28 12:24:52 +02:00
dr. M.S. (Matthijs) Berends	2f866985c9	(v3.0.0.9016) fix for plotting	2025-07-23 22:05:20 +02:00
github-actions[bot]	6cb724a208	(v3.0.0.9015) plotting fix	2025-07-19 14:06:36 +02:00
dr. M.S. (Matthijs) Berends	49274f010b	(v3.0.0.9014) fix plot colours	2025-07-18 15:57:48 +02:00
github-actions[bot]	8da0f525b5	set lang for R<3.5	2025-07-17 22:58:34 +02:00