eucast_rules(): add add_if_missing argument to control NA imputation (#259)

When `add_if_missing = FALSE`, rules are only applied to cells that already
contain an SIR value; `NA` cells are left untouched. This is useful with
`overwrite = TRUE` to update reported results without imputing values for
drugs that were not tested.

https://claude.ai/code/session_01Nucc8nXGLqNUjtuC9GrhTc

CLAUDE.md

@@ -146,21 +146,37 @@ Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
 - Stable CRAN releases drop the dev suffix (e.g., `3.0.1`)
 - `NEWS.md` uses sections **New**, **Fixes**, **Updates** with GitHub issue references (`#NNN`)
 
-### Version bump required for every PR
+### Version and date bump required for every PR
 
-Before opening a pull request, always increment the four-digit dev counter by 1 in **both** of these files:
+All PRs are **squash-merged**, so each PR lands as exactly **one commit** on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore **exactly one version bump is allowed per PR**, regardless of how many intermediate commits are made on the branch.
 
-1. **`DESCRIPTION`** — the `Version:` field:
+#### Computing the correct version number
-   ```
-   Version: 3.0.1.9021  →  Version: 3.0.1.9022
-   ```
 
-2. **`NEWS.md`** — the top-level heading:
+Run the following from the repo root to determine the version string to use:
-   ```
-   # AMR 3.0.1.9021  →  # AMR 3.0.1.9022
-   ```
 
-Read the current version from `DESCRIPTION`, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.
+```bash
+currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
+currenttagfull=$(git describe --tags --abbrev=0)
+defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
+currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
+echo "$currentversion"
+```
+
+The `+ 1` accounts for the fact that this PR's squash commit is not yet on the default branch. Set **both** of these files to the resulting version string (and only once per PR, even across multiple commits):
+
+1. **`DESCRIPTION`** — the `Version:` field
+2. **`NEWS.md`** — the top-level heading `# AMR <version>`
+
+If `git describe` fails (e.g. no tags exist in the environment), fall back to reading the current version from `DESCRIPTION` and adding 1 to the last numeric component — but only if no bump has already been made in this PR.
+
+#### Date field
+
+The `Date:` field in `DESCRIPTION` must reflect the date of the **last commit to the PR** (not the first), in ISO format. Update it with every commit so it is always current:
+
+```
+Date: 2026-03-07
+```
 
 ## Internal State
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9022
+Version: 3.0.1.9034
-Date: 2026-03-03
+Date: 2026-03-09
 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

NAMESPACE

@@ -133,8 +133,10 @@ export("%like%")
 export("%like_case%")
 export("%unlike%")
 export("%unlike_case%")
+export(NA_ab_)
 export(NA_disk_)
 export(NA_mic_)
+export(NA_mo_)
 export(NA_sir_)
 export(ab_atc)
 export(ab_atc_group1)
@@ -246,6 +248,7 @@ export(glycopeptides)
 export(guess_ab_col)
 export(inner_join_microorganisms)
 export(interpretive_rules)
+export(ionophores)
 export(is.ab)
 export(is.av)
 export(is.disk)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9022
+# AMR 3.0.1.9034
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -8,29 +8,35 @@
     - `all_mic()`, `all_mic_predictors()`
     - `all_disk()`, `all_disk_predictors()`
 * Data set `esbl_isolates` to practise with AMR modelling
-* AMR selectors `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
+* AMR selectors `ionophores()`, `peptides()`, `phosphonics()` and `spiropyrimidinetriones()`
-* Antimicrobials in the `antimicrobials` data set: ceftibuten/avibactam (`CTA`), kasugamycin (`KAS`), ostreogrycin (`OST`), thiostrepton (`THS`), xeruborbactam (`XER`), zorbamycin (`ZOR`)
 * Support for Wildtype (WT) / Non-wildtype (NWT) in `as.sir()`, all plotting functions, and all susceptibility/resistance functions.
   - `as.sir()` gained an argument `as_wt_nwt`, which defaults to `TRUE` only when `breakpoint_type = "ECOFF"` (#254)
   - This transforms the output from S/R to WT/NWT
   - Functions such as `susceptibility()` count WT as S and NWT as R
 * `interpretive_rules()`, which allows future implementation of CLSI interpretive rules (#235)
-  - `eucast_rules()` has become a wrapper around that function.
+  - `eucast_rules()` has become a wrapper around that function
+* `eucast_rules()` / `interpretive_rules()` gained argument `add_if_missing` (default: `TRUE`). When set to `FALSE`, rules are only applied to cells that already contain an SIR value; `NA` cells are left untouched. This is useful with `overwrite = TRUE` to update reported results without imputing values for drugs that were not tested (#259)
+* Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
 
 ### Fixes
+* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
+* Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved
+* Fixed a bug in `as.ab()` where certain AB codes containing "PH" or "TH" (such as `ETH`, `MTH`, `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when combined in a vector with any untranslatable value (#245)
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
 * Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `I`,  and `R` would not be considered (#244)
 * Fixed some foreign translations of antimicrobial drugs
 * Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
 * Fixed a bug to disregard `NI` for susceptibility proportion functions
 * Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256)
+* Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
+* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
 * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
+* Added to the `antimicrobials` data set: cefepime/taniborbactam (`FTA`), ceftibuten/avibactam (`CTA`), clorobiocin (`CLB`), kasugamycin (`KAS`), ostreogrycin (`OST`), taniborbactam (`TAN`), thiostrepton (`THS`), xeruborbactam (`XER`), and zorbamycin (`ZOR`)
 * `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
 * `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
 * `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)
-* Added taniborbactam (`TAN`) and cefepime/taniborbactam (`FTA`) to the `antimicrobials` data set
 * Added explaining message to `as.sir()` when interpreting numeric values (e.g., 1 for S, 2 for I, 3 for R) (#244)
 * Updated handling of capped MIC values (`<`, `<=`, `>`, `>=`) in `as.sir()` in the argument `capped_mic_handling`: (#243)
   * Introduced four clearly defined options: `"none"`, `"conservative"` (default), `"standard"`, and `"lenient"`

R/aa_helper_functions.R

@@ -387,6 +387,10 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
   if (isTRUE(error_on_fail)) {
     stop_ifnot_installed(pkg)
   }
+  if (pkg == "rstudioapi" && tryCatch(!rstudioapi::isAvailable(), error = function(e) TRUE)) {
+    # only allow rstudioapi to be imported if RStudio is available
+    return(NULL)
+  }
   tryCatch(
     # don't use get() to avoid fetching non-API functions
     getExportedValue(name = name, ns = asNamespace(pkg)),
@@ -1220,10 +1224,14 @@ try_colour <- function(..., before, after, collapse = " ") {
   }
 }
 is_dark <- function() {
-  AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
+  AMR_env$current_theme <- NULL
+  current_theme_fn <- import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)
+  if (!is.null(current_theme_fn)) {
+    AMR_env$current_theme <- current_theme_fn()$editor
+  }
   if (!identical(AMR_env$current_theme, AMR_env$former_theme) || is.null(AMR_env$is_dark_theme)) {
     AMR_env$former_theme <- AMR_env$current_theme
-    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) TRUE)
+    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(current_theme_fn()$dark), error = function(e) TRUE)
   }
   isTRUE(AMR_env$is_dark_theme)
 }

R/ab.R

@@ -119,7 +119,14 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x[x %like_case% "^PENICILLIN" & x %unlike_case% "[ /+-]"] <- "benzylpenicillin"
   x_bak_clean <- x
   if (already_regex == FALSE) {
+    x_bak_clean_before_gen <- x_bak_clean
     x_bak_clean <- generalise_antibiotic_name(x_bak_clean)
+    # generalise_antibiotic_name() rewrites "PH"->"F" and "TH"->"T", which
+    # mangles short valid AB codes (e.g. "ETH"->"ET", "PHN"->"FN", "STH"->"ST")
+    # making them unrecognisable in the lookup. Restore any values that were
+    # already valid AB codes before generalisation (#245).
+    is_valid_ab_code <- x_bak_clean_before_gen %in% AMR_env$AB_lookup$ab
+    x_bak_clean[is_valid_ab_code] <- x_bak_clean_before_gen[is_valid_ab_code]
   }
 
   x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)
@@ -507,6 +514,14 @@ ab_reset_session <- function() {
   }
 }
 
+#' @rdname as.ab
+#' @details `NA_ab_` is a missing value of the new `ab` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
+#' @format NULL
+#' @export
+NA_ab_ <- set_clean_class(NA_character_,
+  new_class = c("ab", "character")
+)
+
 # this prevents the requirement for putting the dependency in Imports:
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::pillar_shaft, ab)
 pillar_shaft.ab <- function(x, ...) {

R/ab_property.R

@@ -65,6 +65,7 @@
 #' ab_synonyms("AMX")
 #' ab_tradenames("AMX")
 #' ab_group("AMX")
+#' ab_group("AMX", all_groups = TRUE) # most specific to most general
 #' ab_atc_group1("AMX")
 #' ab_atc_group2("AMX")
 #' ab_url("AMX")
@@ -163,7 +164,7 @@ ab_tradenames <- function(x, ...) {
 }
 
 #' @rdname ab_property
-#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most distinctive group name.
+#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most specific group name.
 #' @export
 ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
   meet_criteria(x, allow_NA = TRUE)
@@ -172,6 +173,9 @@ ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
 
   grps <- ab_validate(x = x, property = "group", ...)
   for (i in seq_along(grps)) {
+    if (is.null(grps[[i]]) || all(is.na(grps[[i]]))) {
+      grps[[i]] <- NA_character_
+    }
     if (all_groups == FALSE) {
       # take the first match based on ABX_PRIORITY_LIST
       grps[[i]] <- grps[[i]][1]

R/amr_selectors.R

@@ -352,6 +352,14 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
   amr_select_exec("glycopeptides", only_sir_columns = only_sir_columns, return_all = return_all)
 }
 
+#' @rdname antimicrobial_selectors
+#' @export
+ionophores <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
+  meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
+  meet_criteria(return_all, allow_class = "logical", has_length = 1)
+  amr_select_exec("ionophores", only_sir_columns = only_sir_columns, return_all = return_all)
+}
+
 #' @rdname antimicrobial_selectors
 #' @export
 isoxazolylpenicillins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {

R/interpretive_rules.R

@@ -79,6 +79,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be included that were transformed to class [sir][as.sir()] on beforehand. Defaults to `FALSE` if no columns of `x` have a class [sir][as.sir()].
 #' @param custom_rules Custom rules to apply, created with [custom_eucast_rules()].
 #' @param overwrite A [logical] indicating whether to overwrite existing SIR values (default: `FALSE`). When `FALSE`, only non-SIR values are modified (i.e., any value that is not already S, I or R). To ensure compliance with EUCAST guidelines, **this should remain** `FALSE`, as EUCAST notes often state that an organism "should be tested for susceptibility to individual agents or be reported resistant".
+#' @param add_if_missing A [logical] indicating whether rules should also be applied to missing (`NA`) values (default: `TRUE`). When `FALSE`, rules are only applied to cells that already contain an SIR value; cells with `NA` are left untouched. This is particularly useful when using `overwrite = TRUE` with custom rules and you want to update reported results without imputing values for untested drugs.
 #' @inheritParams first_isolate
 #' @details
 #' **Note:** This function does not translate MIC values to SIR values. Use [as.sir()] for that. \cr
@@ -175,6 +176,7 @@ interpretive_rules <- function(x,
                                only_sir_columns = any(is.sir(x)),
                                custom_rules = NULL,
                                overwrite = FALSE,
+                               add_if_missing = TRUE,
                                ...) {
   meet_criteria(x, allow_class = "data.frame")
   meet_criteria(col_mo, allow_class = "character", has_length = 1, is_in = colnames(x), allow_NULL = TRUE)
@@ -189,6 +191,7 @@ interpretive_rules <- function(x,
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
   meet_criteria(overwrite, allow_class = "logical", has_length = 1)
+  meet_criteria(add_if_missing, allow_class = "logical", has_length = 1)
 
   stop_if(
     guideline == "CLSI",
@@ -538,7 +541,8 @@ interpretive_rules <- function(x,
           warned = warned,
           info = info,
           verbose = verbose,
-          overwrite = overwrite
+          overwrite = overwrite,
+          add_if_missing = add_if_missing
         )
         n_added <- n_added + run_changes$added
         n_changed <- n_changed + run_changes$changed
@@ -580,7 +584,8 @@ interpretive_rules <- function(x,
           warned = warned,
           info = info,
           verbose = verbose,
-          overwrite = overwrite
+          overwrite = overwrite,
+          add_if_missing = add_if_missing
         )
         n_added <- n_added + run_changes$added
         n_changed <- n_changed + run_changes$changed
@@ -877,7 +882,8 @@ interpretive_rules <- function(x,
       warned = warned,
       info = info,
       verbose = verbose,
-      overwrite = overwrite
+      overwrite = overwrite,
+      add_if_missing = add_if_missing
     )
     n_added <- n_added + run_changes$added
     n_changed <- n_changed + run_changes$changed
@@ -947,7 +953,8 @@ interpretive_rules <- function(x,
         warned = warned,
         info = info,
         verbose = verbose,
-        overwrite = overwrite
+        overwrite = overwrite,
+        add_if_missing = add_if_missing
       )
       n_added <- n_added + run_changes$added
       n_changed <- n_changed + run_changes$changed
@@ -1139,7 +1146,8 @@ edit_sir <- function(x,
                      warned,
                      info,
                      verbose,
-                     overwrite) {
+                     overwrite,
+                     add_if_missing) {
   cols <- unique(cols[!is.na(cols) & !is.null(cols)])
 
   # for Verbose Mode, keep track of all changes and return them
@@ -1172,13 +1180,15 @@ edit_sir <- function(x,
     if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
       warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
     }
+    # determine which cells to modify based on overwrite and add_if_missing
+    apply_mask <- if (isTRUE(overwrite)) {
+      if (isFALSE(add_if_missing)) !isNA else rep(TRUE, length(isNA))
+    } else {
+      if (isFALSE(add_if_missing)) isSIR else non_SIR
+    }
     tryCatch(
       # insert into original table
-      if (isTRUE(overwrite)) {
+      new_edits[rows, cols][apply_mask] <- to,
-        new_edits[rows, cols] <- to
-      } else {
-        new_edits[rows, cols][non_SIR] <- to
-      },
       warning = function(w) {
         if (w$message %like% "invalid factor level") {
           xyz <- vapply(FUN.VALUE = logical(1), cols, function(col) {
@@ -1188,11 +1198,7 @@ edit_sir <- function(x,
             )
             TRUE
           })
-          if (isTRUE(overwrite)) {
+          suppressWarnings(new_edits[rows, cols][apply_mask] <<- to)
-            suppressWarnings(new_edits[rows, cols] <<- to)
-          } else {
-            suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
-          }
           warning_(
             "in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
             ifelse(length(cols) == 1, "", "s"),

R/mdro.R

@@ -31,7 +31,7 @@
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
 #' @param x A [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank for automatic determination.
-#' @param guideline A specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
+#' @param guideline A specific guideline to follow, see sections *Supported International / National Guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
 #' @param esbl [logical] values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins).
 #' @param carbapenemase [logical] values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins).
 #' @param mecA [logical] values, or a column name containing logical values, indicating the presence of a *mecA* gene (or production of its proteins).
@@ -42,6 +42,7 @@
 #' @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 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.
+#' @param infer_from_combinations A [logical] to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does **not** imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to `TRUE`.
 #' @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*.
 #'
@@ -143,6 +144,7 @@ mdro <- function(x = NULL,
                  combine_SI = TRUE,
                  verbose = FALSE,
                  only_sir_columns = any(is.sir(x)),
+                 infer_from_combinations = TRUE,
                  ...) {
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
@@ -165,7 +167,7 @@ mdro <- function(x = NULL,
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-
+  meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
 
   if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
     stop_("There were no SIR columns found in the data set, despite `only_sir_columns` being `TRUE`. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
@@ -480,6 +482,52 @@ mdro <- function(x = NULL,
   }
   cols_ab <- cols_ab[!duplicated(cols_ab)]
 
+  # Infer resistance for missing base drugs ----
+  if (isTRUE(infer_from_combinations)) {
+    .combos_in_data <- AB_BETALACTAMS_WITH_INHIBITOR[AB_BETALACTAMS_WITH_INHIBITOR %in% names(cols_ab)]
+    if (length(.combos_in_data) > 0) {
+      .base_drugs <- suppressMessages(
+        as.ab(gsub("/.*", "", ab_name(as.character(.combos_in_data), language = NULL)))
+      )
+      .unique_bases <- unique(.base_drugs[!is.na(.base_drugs)])
+      for (.base in .unique_bases) {
+        .base_code <- as.character(.base)
+        if (!.base_code %in% names(cols_ab)) {
+          # Base drug column absent; find all available combo columns for this base drug
+          .combos <- .combos_in_data[!is.na(.base_drugs) & as.character(.base_drugs) == .base_code]
+          .combo_cols <- unname(cols_ab[as.character(.combos)])
+          .combo_cols <- .combo_cols[!is.na(.combo_cols)]
+          if (length(.combo_cols) > 0) {
+            # Vectorised: if ANY combination is R, infer base drug as R; otherwise NA
+            .sir_chars <- as.data.frame(
+              lapply(x[, .combo_cols, drop = FALSE], function(col) as.character(as.sir(col))),
+              stringsAsFactors = FALSE
+            )
+            .new_col <- paste0(.base_code, ".inferred_sir_proxy_from#", paste0(.combos, collapse = "/"), "#")
+            x[[.new_col]] <- ifelse(rowSums(.sir_chars == "R", na.rm = TRUE) > 0L, "R", NA_character_)
+            cols_ab <- c(cols_ab, stats::setNames(.new_col, .base_code))
+            if (isTRUE(info.bak)) {
+              message_(
+                "Inferring resistance for ",
+                ab_name(.base_code, language = NULL, tolower = TRUE),
+                " (", font_bold(.base_code, collapse = NULL), ", ", font_italic("missing"), ") from ",
+                vector_or(
+                  quotes = FALSE,
+                  last_sep = " and/or ",
+                  paste0(
+                    ab_name(.combos, language = NULL, tolower = TRUE),
+                    " (", font_bold(.combos, collapse = NULL), ", ", font_italic("available"), ")"
+                  )
+                )
+              )
+            }
+          }
+        }
+      }
+      cols_ab <- cols_ab[!duplicated(names(cols_ab))]
+    }
+  }
+
   # nolint start
   AMC <- cols_ab["AMC"]
   AMK <- cols_ab["AMK"]
@@ -674,6 +722,16 @@ mdro <- function(x = NULL,
     x
   }
 
+  ab_without_inhibitor <- function(ab_codes) {
+    # Get the base drug AB code from a drug+inhibitor combination.
+    # e.g., AMC (amoxicillin/clavulanic acid)  -> AMX (amoxicillin)
+    #        TZP (piperacillin/tazobactam)      -> PIP (piperacillin)
+    #        SAM (ampicillin/sulbactam)          -> AMP (ampicillin)
+    combo_names <- ab_name(ab_codes, language = NULL)
+    base_names <- gsub("/.*", "", combo_names)
+    suppressMessages(as.ab(base_names))
+  }
+
   # antimicrobial classes
   # nolint start
   aminoglycosides <- c(TOB, GEN)
@@ -1883,7 +1941,8 @@ mdro <- function(x = NULL,
     # format data set
     colnames(x)[colnames(x) == col_mo] <- "microorganism"
     x$microorganism <- mo_name(x$microorganism, language = NULL)
-    x$guideline <- paste0(guideline$author, " - ", guideline$name, ", ", guideline$version, ")")
+    x$guideline <- paste0(guideline$author, " - ", guideline$name, ifelse(is.na(guideline$version), "", paste0(" (", guideline$version, ")")))
+    x$all_nonsusceptible_columns <- gsub(".inferred_sir_proxy_from#(.*?)#", " (inferred from \\1)", x$all_nonsusceptible_columns, perl = TRUE)
     x[, c(
       "row_number",
       "microorganism",

R/mic.R

@@ -217,8 +217,9 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
     warning_("Some MICs were combined values, only the first values are kept")
     x[x %like% "[0-9]/.*[0-9]"] <- gsub("/.*", "", x[x %like% "[0-9]/.*[0-9]"])
   }
+  x <- trimws2(gsub("[^e\\P{L}]", "", x, perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
   # remove other invalid characters
-  x <- gsub("[^a-zA-Z0-9.><= -]+", "", x, perl = TRUE)
+  x <- gsub("[^0-9e.><= -]+", "", x, perl = TRUE)
   # transform => to >= and =< to <=
   x <- gsub("=<", "<=", x, fixed = TRUE)
   x <- gsub("=>", ">=", x, fixed = TRUE)

R/mo.R

@@ -38,13 +38,15 @@
 #'
 #' This excludes enterococci at default (who are in group D), use `Lancefield = "all"` to also categorise all enterococci as group D.
 #' @param minimum_matching_score A numeric value to set as the lower limit for the [MO matching score][mo_matching_score()]. When left blank, this will be determined automatically based on the character length of `x`, its [taxonomic kingdom][microorganisms] and [human pathogenicity][mo_matching_score()].
-#' @param keep_synonyms A [logical] to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`, which will return a note if old taxonomic names were processed. The default can be set with the package option [`AMR_keep_synonyms`][AMR-options], i.e. `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`.
+#' @param keep_synonyms A [logical] to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of *S. pyogenes*. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
+#'
+#' The default is `FALSE`, which will return a note if outdated taxonomic names were processed. The default can be set with the package option [`AMR_keep_synonyms`][AMR-options], i.e. `options(AMR_keep_synonyms = TRUE)` or `options(AMR_keep_synonyms = FALSE)`.
 #' @param reference_df A [data.frame] to be used for extra reference when translating `x` to a valid [`mo`]. See [set_mo_source()] and [get_mo_source()] to automate the usage of your own codes (e.g. used in your analysis or organisation).
 #' @param ignore_pattern A Perl-compatible [regular expression][base::regex] (case-insensitive) of which all matches in `x` must return `NA`. This can be convenient to exclude known non-relevant input and can also be set with the package option [`AMR_ignore_pattern`][AMR-options], e.g. `options(AMR_ignore_pattern = "(not reported|contaminated flora)")`.
 #' @param cleaning_regex A Perl-compatible [regular expression][base::regex] (case-insensitive) to clean the input of `x`. Every matched part in `x` will be removed. At default, this is the outcome of [mo_cleaning_regex()], which removes texts between brackets and texts such as "species" and "serovar". The default can be set with the package option [`AMR_cleaning_regex`][AMR-options].
 #' @param only_fungi A [logical] to indicate if only fungi must be found, making sure that e.g. misspellings always return records from the kingdom of Fungi. This can be set globally for [all microorganism functions][mo_property()] with the package option [`AMR_only_fungi`][AMR-options], i.e. `options(AMR_only_fungi = TRUE)`.
 #' @param language Language to translate text like "no growth", which defaults to the system language (see [get_AMR_locale()]).
-#' @param info A [logical] to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with old taxonomic names. The default is `TRUE` only in interactive mode.
+#' @param info A [logical] to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with outdated taxonomic names. The default is `TRUE` only in interactive mode.
 #' @param ... Other arguments passed on to functions.
 #' @rdname as.mo
 #' @aliases mo
@@ -82,7 +84,7 @@
 #' There are three helper functions that can be run after using the [as.mo()] function:
 #' - Use [mo_uncertainties()] to get a [data.frame] that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see *Matching Score for Microorganisms* below).
 #' - Use [mo_failures()] to get a [character] [vector] with all values that could not be coerced to a valid value.
-#' - Use [mo_renamed()] to get a [data.frame] with all values that could be coerced based on old, previously accepted taxonomic names.
+#' - Use [mo_renamed()] to get a [data.frame] with all values that could be coerced based on outdated, previously accepted taxonomic names.
 #'
 #' ### For Mycologists
 #'
@@ -476,7 +478,7 @@ as.mo <- function(x,
     }
   } else if (is.null(getOption("AMR_keep_synonyms")) && length(AMR_env$mo_renamed$old) > 0 && message_not_thrown_before("as.mo", "keep_synonyms_warning", entire_session = TRUE)) {
     # keep synonyms is TRUE, so check if any do have synonyms
-    warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " old taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
+    warning_("Function `as.mo()` returned ", nr2char(length(unique(AMR_env$mo_renamed$old))), " outdated taxonomic name", ifelse(length(unique(AMR_env$mo_renamed$old)) > 1, "s", ""), ". Use `as.mo(..., keep_synonyms = FALSE)` to clean the input to currently accepted taxonomic names, or set the R option `AMR_keep_synonyms` to `FALSE`. This warning will be shown once per session.", call = FALSE)
   }
 
   # Apply Becker ----
@@ -623,6 +625,14 @@ mo_cleaning_regex <- function() {
   )
 }
 
+#' @rdname as.mo
+#' @details `NA_mo_` is a missing value of the new `mo` class, analogous to e.g. base \R's [`NA_character_`][base::NA].
+#' @format NULL
+#' @export
+NA_mo_ <- set_clean_class(NA_character_,
+  new_class = c("mo", "character")
+)
+
 # UNDOCUMENTED METHODS ----------------------------------------------------
 
 # this prevents the requirement for putting the dependency in Imports:

R/sir.R

@@ -568,6 +568,7 @@ as.sir.default <- function(x,
     x[x %like% "dose"] <- "SDD"
     mtch <- grepl(paste0("(", S, "|", I, "|", R, "|", NI, "|", SDD, "|", WT, "|", NWT, "|", NS, "|[A-Z]+)"), x, perl = TRUE)
     x[!mtch] <- ""
+    x[mtch & x %unlike% "^[0-9+]$"] <- trimws2(gsub("[^\\p{L}]", "", x[mtch & x %unlike% "^[0-9+]$"], perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
     # apply regexes set by user
     x[x %like% S] <- "S"
     x[x %like% I] <- "I"

data-raw/_pre_commit_checks.R

@@ -369,6 +369,9 @@ pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
   filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
   pull(ab)
 pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
+pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>%
+  filter(name %like% "novobiocin|clorobiocin") %>%
+  pull(ab)
 pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
   filter(group %like% "antifungal") %>%
   pull(ab)
@@ -486,6 +489,18 @@ pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
 # this will be used for documentation:
 pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
 
+# Check that all AB_* groups with >= 4 members have a corresponding function
+for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) {
+  if (length(pre_commit_lst[[grp]]) >= 4) {
+    fn_name <- tolower(gsub("^AB_", "", grp))
+    if (!fn_name %in% ls(envir = asNamespace("AMR"))) {
+      stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]),
+           " members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.",
+           call. = FALSE)
+    }
+  }
+}
+
 # Update the antimicrobials$group column
 usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
 prettify_group_name <- function(name) {
@@ -557,6 +572,7 @@ pre_commit_lst$ABX_PRIORITY_LIST <- c("Aminopenicillins",
                                       "Beta-lactams",
                                       "Beta-lactamase inhibitors",
                                       "Pleuromutilins",
+                                      "Aminocoumarins",
                                       "Other")
 if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
   stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))

data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R

@@ -972,6 +972,17 @@ antimicrobials <- antimicrobials |>
       select(1:4),
   )
 
+antimicrobials <- antimicrobials |>
+  mutate(ab = as.character(ab)) |>
+  bind_rows(
+    antimicrobials |>
+      filter(ab == "NOV") |>
+      mutate(ab = "CLB",
+             cid = 54706138,
+             name = "Clorobiocin") |>
+      select(1:4),
+  )
+
 # update ATC codes from WHOCC website -------------------------------------
 
 library(rvest)
@@ -1171,6 +1182,11 @@ for (i in 1:nrow(antimicrobials)) {
     antimicrobials[i, "loinc"][[1]] <- ifelse(length(loinc) == 0, list(NA_character_), list(loinc))
   }
 }
+antimicrobials$group <- unname(antimicrobials$group)
+antimicrobials$atc <- unname(antimicrobials$atc)
+antimicrobials$abbreviations <- unname(antimicrobials$abbreviations)
+antimicrobials$synonyms <- unname(antimicrobials$synonyms)
+antimicrobials$loinc <- unname(antimicrobials$loinc)
 
 
 usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")

data-raw/ab.md5

@@ -1 +1 @@
-cf6618d042ec462d9eef1f422e2a5bfb
+11aade8a39bfdff02d01fb52b04eacdc

data-raw/datasets/antimicrobials.txt

@@ -142,7 +142,7 @@
 "CHL"	5959	"Chloramphenicol"	"Phenicols"	"D06AX02,D10AF03,G01AA05,J01BA01,QD06AX02,QD10AF03,QG01AA05,QJ01BA01,QJ51BA01,QS01AA01,QS02AA01,QS03AA08,S01AA01,S02AA01,S03AA08"	"Amphenicols"	"Amphenicols"	"c,chl,chlo,chlora,cl"	"alficetyn,ambofen,amphicol,amseclor,anacetin,aquamycetin,austracil,austracol,biocetin,biophenicol,catilan,chemicetin,chemicetina,chlomin,chlomycol,chloramex,chloramfenikol,chloramficin,chloramfilin,chloramphenicole,chloramphenicolum,chloramsaar,chlorasol,chlorbiotic,chloricol,chlornitromycin,chloroamphenicol,chlorocaps,chlorocid,chlorocide,chlorocin,chlorocol,chlorofair,chloromax,chloromycetin,chloromycetny,chloromyxin,chloronitrin,chloroptic,chlorovules,cidocetine,ciplamycetin,cloramfen,cloramfenicol,cloramfenicolo,cloramficin,cloramicol,cloramidina,cloranfenicol,cloroamfenicolo,clorocyn,cloromisan,clorosintex,comycetin,cylphenicol,desphen,detreomycin,detreomycine,dextramycin,dextromycetin,doctamicina,econochlor,embacetin,emetren,enteromycetin,erbaplast,ertilen,farmicetina,globenicol,glorous,gloveticol,halcetin,halomycetin,hortfenicol,intramycetin,isicetin,ismicetina,isophenicol,juvamycetin,kamaver,kemicetina,kemicetine,kloramfenikol,klorita,laevomycetinum,leukamycin,leukomyan,leukomycin,levocin,levomicetina,levomitsetin,levomycetin,levoplast,levosin,levovetin,loromisan,loromisin,mastiphen,maybridge,mediamycetine,medichol,micloretin,micochlorine,micoclorina,microcetina,mychel,mycinol,myclocin,mycochlorin,novochlorocap,novomycetin,novophenicol,ocuphenicol,oftalent,oleomycetin,opclor,opelor,ophthochlor,ophthocort,ophtochlor,optomycin,otachron,otophen,pantovernil,paraxin,pentamycetin,petnamycetin,quemicetina,rivomycin,romphenil,ronphenil,septicol,sificetina,sintomicetin,sintomicetina,soluthor,stanomycetin,synthomycetin,synthomycetine,synthomycine,syntomycin,tevcocin,tevcosin,tifomycin,tifomycine,tiromycetin,treomicetina,tyfomycine,unimycetin,veticol,viceton"	3	"g"	3	"g"	"15101-9,16603-3,16604-1,172-7,173-5,174-3,175-0,18903-5,25247-8,29214-4,29346-4,29347-2,3455-3,7001-1"
 "CTE"	54675777	"Chlortetracycline"	"Tetracyclines"	"A01AB21,D06AA02,J01AA03,QA01AB21,QD06AA02,QG51AA08,QJ01AA03,QJ51AA03,QS01AA02,S01AA02"	"Tetracyclines"	"Tetracyclines"	"chltet"	"acronize,alexomycin,aueromycin,aureocarmyl,aureociclina,aureocina,aureocycline,aureomycin,aureomykoin,aurofac,auxeomycin,biomitsin,biomycin,chlormax,chlorotetracycline,chlortetracyclinum,chrysomykine,clorocipan,clortetraciclina,clortetrin,declomycin,declostatin,deganol,demeclor,demeplus,demetraciclina,demetraclin,detracin,detravis,diuciclin,duomycin,elkamicina,flamycin,isphamycin,ledermicina,ledermycin,ledermycine,mexocine,novotriclina,pennchlor,perciclina,periciclina,sumaclina,uromycin,veraciclina"	1	"g"			"176-8,177-6,178-4,179-2,18904-3,55655-5,87600-3"
 "CIC"	19003	"Ciclacillin"	"Penicillins,Beta-lactams"	"NA"			"cyclac"	"bastcillin,calthor,ciclacilina,ciclacilline,ciclacillinum,ciclacillum,citosarin,cyclacillin,cyclapen,noblicil,orfilina,peamezin,syngacillin,ultracillin,vastcillin,vipicil,wyvital"					"NA"
-"CIX"	47472	"Ciclopirox"	"Antifungals"	"D01AE14,G01AX12,QD01AE14,QG01AX12"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"NA"					"NA"
+"CIX"		"Ciclopirox"	"Antifungals"	"D01AE14,G01AX12,QD01AE14,QG01AX12"	"Antifungals for topical use"	"Other antifungals for topical use"	"cipx"	"NA"					"NA"
 "CIN"	2762	"Cinoxacin"	"Quinolones"	"J01MB06,QJ01MB06"	"Quinolone antibacterials"	"Other quinolones"	"cino,cinoxa,cnox"	"cinobac,cinobactin,cinoxacine,cinoxacino,cinoxacinum,clinoxacin,noxigram,uronorm"	1	"g"			"180-0,181-8,182-6,183-4,18905-0,55656-3"
 "CIP"	2764	"Ciprofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA02,QJ01MA02,QS01AE03,QS02AA15,QS03AA07,S01AE03,S02AA15,S03AA07"	"Quinolone antibacterials"	"Fluoroquinolones"	"ci,cip,cipr,ciprof,cp"	"alcipro,bacquinor,baflox,belmacina,bernoflox,catex,cenin,ceprimax,cetraxal,ciflan,ciflosin,cifloxin,cilab,cilox,ciloxan,cipad,ciplus,ciprecu,ciprenit,ciprine,ciprinol,cipro,ciprobay,ciprocinal,ciprocinol,ciprodar,ciproflox,ciprofloxacina,ciprofloxacine,ciprofloxacino,ciprofloxacinum,ciprofur,ciprogis,ciproktan,ciprolin,ciprolon,cipromycin,cipronex,ciprooxacin,cipropol,ciproquinol,ciprowin,ciproxan,ciproxin,ciproxina,ciproxine,ciriax,citeral,citopcin,cixan,corsacin,cunesin,cycin,cyprobay,cyproxan,disfabac,felixene,fimoflox,flociprin,floxacipron,flunas,globuce,inkamil,ipiflox,italnik,keefloxin,linhaliq,loxacid,loxan,lypro,megaflox,microgan,nixin,novidat,novoquin,ofitin,oftacilox,ophaflox,otiprio,phaproxin,piprol,plenolyt,probiox,proflaxin,proksi,proquin,proxacin,quinoflox,quinolid,quintor,quipro,rancif,renator,roflazin,roxytal,sepcen,septicide,septocipro,siprogut,sophixin,spitacin,strox,suiflox,superocin,supraflox,uritent,utiminx,velmonit,zumaflox"	1	"g"	0.8	"g"	"101500-7,14031-9,14032-7,14058-2,14059-0,184-2,185-9,186-7,187-5,18906-8,20377-8,23621-6,25180-1,25181-9,25188-4,25189-2,25248-6,34636-1,3484-3,42644-5,55194-5,7002-9"
 "CIM"		"Ciprofloxacin/metronidazole"	"Fluoroquinolones,Quinolones"	"J01RA10,QJ01RA10"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
@@ -157,6 +157,7 @@
 "CLF1"	2799	"Clofoctol"	"Other"	"J01XX03,QJ01XX03"	"Other antibacterials"	"Other antibacterials"	"NA"	"clofoctolo,clofoctolum,gramplus,octofene,phenol"					"NA"
 "CLM"	71807	"Clometocillin"	"Penicillins,Beta-lactams"	"J01CE07,QJ01CE07"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"chlomethocillin,clometacillin,clomethacillin,clomethocillin,clometocilina,clometocilline,clometocillinsalt,clometocillinum,penicilline,rixapen"	1	"g"			"NA"
 "CLM1"	54680675	"Clomocycline"	"Tetracyclines"	"J01AA11,QJ01AA11"	"Tetracyclines"	"Tetracyclines"	"NA"	"clomociclina,clomocyclinum,megaclor"	1	"g"			"NA"
+"CLB"	54706138	"Clorobiocin"	"Aminocoumarins"	"NA"			"NA"	"chlorobiocin"					"NA"
 "CTR"	2812	"Clotrimazole"	"Antifungals"	"A01AB18,D01AC01,G01AF02,QA01AB18,QD01AC01,QG01AF02,QJ02AB90"			"clot"	"alevazol,bisphenyl,canesten,canestene,canestine,canifug,chlotrimazole,clomatin,clotrimaderm,clotrimazol,clotrimazolum,coltrimazole,cutistad,diphenylmethane,empecid,esparol,femmesil,footlogix,fortinia,gynix,imidazole,jidesheng,klotrimazole,lakesia,lombazol,lombazole,lombazolum,lotrimax,lotrimin,monobaycuten,mycelax,mycelex,mycofug,mycosporin,mykosporin,nalbix,otomax,pedesil,pedisafe,ringworm,stiemazol,tibatin,trimysten,trivagizole"					"10653-4,10654-2,18909-2,54177-1,55663-9"
 "CLO"	6098	"Cloxacillin"	"Isoxazolylpenicillins,Penicillins,Beta-lactams"	"J01CF02,QJ01CF02,QJ51CF02,QS01AA90"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase resistant penicillins"	"clox,cloxac"	"ankerbin,austrastaph,biocloxin,brispen,chloroxacillin,ciclex,clocil,clossacillina,cloxacilina,cloxacillinanhydrous,cloxacilline,cloxacillinsalt,cloxacillinum,cloxapen,constaphyl,dariclox,dichlorstapenor,diclocil,dicloxacillinhydrate,diflor,digloxilline,dynapen,ekvacillin,gelstaph,novapen,noxaben,orbenin,pathocil,stampen,staphybiotic,syntarpen,syntarpensalt,tegopen"	2	"g"	2	"g"	"16628-0,18910-0,196-6,197-4,198-2,199-0,25250-2,55664-7"
 "COL"	5311054	"Colistin"	"Polymyxins"	"A07AA10,J01XB01,QA07AA10,QJ01XB01,QJ51XB01"	"Other antibacterials"	"Polymyxins"	"cl,coli,colist,cs,cst,ct"	"colimycin,colisticin,colisticina,colistina,colistine,colistinum,colobreathe,colomycin,kangdisu,kolimitsin,kolimycin,promixin,sogecoli,totazina"	9	"MU"	9	"MU"	"16645-4,18912-6,204-8,205-5,206-3,207-1,29493-4,33333-6"
@@ -293,7 +294,7 @@
 "NAL-S"		"Nalidixic acid screening test"	"Quinolones"	"NA"			"nal screen"	"NA"					"NA"
 "NAR"	65452	"Narasin"	"Ionophores"	"QP51BB04"			"narasi"	"monteban,narasine,narasino,narasinum,skycis"					"87570-8"
 "NEM"	11993740	"Nemonoxacin"	"Fluoroquinolones,Quinolones"	"J01MB08,QJ01MB08"	"Quinolone antibacterials"	"Other quinolones"	"NA"	"NA"					"NA"
-"NEO"	8378	"Neomycin"	"Aminoglycosides"	"A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom,neomyc"	"NA"	5	"g"	1	"g"	"10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
+"NEO"		"Neomycin"	"Aminoglycosides"	"A01AB08,A07AA01,B05CA09,D06AX04,J01GB05,QA01AB08,QA07AA01,QB05CA09,QD06AX04,QJ01GB05,QR02AB01,QS01AA03,QS02AA07,QS03AA01,R02AB01,S01AA03,S02AA07,S03AA01"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neom,neomyc"	"NA"	5	"g"	1	"g"	"10995-9,18953-0,25262-7,354-1,355-8,356-6,357-4,41705-5"
 "NET"	441306	"Netilmicin"	"Aminoglycosides"	"J01GB07,QJ01GB07,QS01AA23,S01AA23"	"Aminoglycoside antibacterials"	"Other aminoglycosides"	"neti,netilm"	"netillin,netilmicina,netilmicine,netilmicinum,netilyn,netira,netromicine,netromycin,nettacin,ntromicine,ntromycin,vectacin,zetamicin"	0.35	"g"	0.35	"g"	"18954-8,25263-5,358-2,359-0,360-8,361-6,3848-9,3849-7,3850-5,47385-0,59565-2,59566-0,59567-8,7035-9"
 "NIC"	9507	"Nicarbazin"	"Other"	"NA"			"NA"	"nicarb,nicarbasin,nicarbazine,nicarmix,nicoxin,nicrazin,nicrazine,nirazin"					"NA"
 "NIF"	71946	"Nifuroquine"	"Fluoroquinolones,Quinolones"	"NA"			"NA"	"abimasten,nifuroquina,nifuroquinum,quinaldofur"					"NA"
@@ -307,7 +308,7 @@
 "NME"		"Norfloxacin/metronidazole"	"Fluoroquinolones,Quinolones"	"J01RA14,QJ01RA14"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NTI"		"Norfloxacin/tinidazole"	"Fluoroquinolones,Quinolones"	"J01RA13,QJ01RA13"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
 "NVA"	10419027	"Norvancomycin"	"Glycopeptides,Peptides"	"NA"			"NA"	"NA"					"NA"
-"NOV"	54675769	"Novobiocin"	"Other"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
+"NOV"	54675769	"Novobiocin"	"Aminocoumarins"	"QJ01XX95"			"novo,novobi"	"albadry,albamix,albamycin,biotexin,cardelmycin,cardelmycinsalt,cathocin,cathomycin,inabiocin,novobiocina,novobiocine,novobiocinsalt,novobiocinum,robiocina,sirbiocina,spheromycin,stilbiocina,streptonivicin,streptonivicinsalt,vulcamicina,vulcamycin,vulkamycin"					"17378-1,18957-1,370-7,371-5,372-3,373-1,41706-3"
 "NYS"	6433272	"Nystatin"	"Ionophores,Antifungals"	"A07AA02,D01AA01,G01AA01,QA07AA02,QD01AA01,QG01AA01"			"nyst,nystan"	"biofanal,diastatin,herniocid,moronal,myconystatin,mycostatin,mykostatyna,nilstat,nistatin,nistatina,nyotran,nystan,nystatyna,nystavescent,nystex"	1.5	"MU"			"10697-1,10698-9,18958-9,35824-2,55689-4"
 "OFX"	4583	"Ofloxacin"	"Fluoroquinolones,Quinolones"	"J01MA01,QJ01MA01,QS01AE01,QS02AA16,S01AE01,S02AA16"	"Quinolone antibacterials"	"Fluoroquinolones"	"of,ofl,oflo,ofloxa,ofx"	"exocin,exocine,flobacin,floxil,floxin,monoflocet,oflocet,ofloxacina,ofloxacine,ofloxacino,ofloxacinum,ofloxaxin,oxaldin,tarivid,visiren,zanocin"	0.4	"g"	0.4	"g"	"18959-7,20384-4,23948-3,25264-3,374-9,375-6,376-4,377-2,3877-8,41408-6,41409-4,41410-2,42653-6,7038-3,72168-8"
 "OOR"		"Ofloxacin/ornidazole"	"Fluoroquinolones,Quinolones"	"J01RA09,QJ01RA09"	"Combinations of antibacterials"	"Combinations of antibacterials"	"NA"	"NA"					"NA"
@@ -325,14 +326,14 @@
 "OXO"	4628	"Oxolinic acid"	"Quinolones"	"J01MB05,QJ01MB05"	"Quinolone antibacterials"	"Other quinolones"	"oxoaci"	"aqualinic,cistopax,dioxacin,emyrenil,gramurin,inoxyl,nidantin,oksaren,orthurine,ossian,oxoboi,oxolinic,pietil,prodoxal,prodoxol,starner,tiurasin,ultibid,urinox,uritrate,urotrate,uroxol,utibid"	1	"g"			"NA"
 "OXY"	54675779	"Oxytetracycline"	"Tetracyclines"	"A01AB25,D06AA03,G01AA07,J01AA06,QA01AB25,QD06AA03,QG01AA07,QG51AA01,QJ01AA06,QJ51AA06,QS01AA04,S01AA04"	"Tetracyclines"	"Tetracyclines"	"oxytet"	"achromycin,actisite,adamycin,artomycin,berkmycen,biostat,bristacycline,cancycline,cyclopar,dabicycline,diacycine,dumocyclin,embryostat,fanterrin,galsenomycin,geomycin,geotilin,hostacycline,hydroxytetracyclinum,lenocycline,macocyn,medamycin,mephacyclin,nitox,oksisyklin,ossitetraciclina,oxitetraciclina,oxitetracyclin,oxitetracycline,oxitetracyclinum,oxymycin,oxypam,oxyterracin,oxyterracine,oxyterracyne,oxytetracid,oxytetracyclin,oxytetracyclinum,paltet,partrex,pennox,piracaps,proteroxyna,qidtet,quadracycline,quatrex,remicyclin,retet,ricycline,riomitsin,ryomycin,solkaciclina,stevacin,stilciclina,subamycin,sumycin,supramycin,sustamycin,tarocyn,tarosin,tefilin,teline,telotrex,teravit,terrafungine,terramitsin,terramycine,tetrabakat,tetrabid,tetrablet,tetracaps,tetracompren,tetrakap,tetralution,tetramavan,tetramed,tetran,tetrosol,topicycline,triphacyclin,unicin,ursocyclin,ursocycline,vetquamycin"	1	"g"	1	"g"	"17396-3,18962-1,25266-8,386-3,387-1,388-9,389-7,55699-3,87595-5"
 "OZN"		"Ozenoxacin"	"Quinolones"	"D06AX14,QD06AX14"			"NA"	"NA"					"NA"
-"PAS"	4649	"P-aminosalicylic acid"	"Antimycobacterials"	"NA"			"pasraa"	"NA"					"NA"
+"PAS"		"P-aminosalicylic acid"	"Antimycobacterials"	"NA"			"pasraa"	"NA"					"NA"
 "PAN"	72015	"Panipenem"	"Carbapenems,Beta-lactams"	"NA"			"NA"	"carbenin,panipenemum,penipanem"					"100056-1,53823-1"
 "PAR"	165580	"Paromomycin"	"Other"	"A07AA06,QA07AA06,QJ01GB92"			"NA"	"aminosidin,amminosidin,crestomycin,estomycin,gabbromycin,gabromycin,humatin,humycin,hydroxymycin,monomycin,paramomycin,paromomicina,paromomycine,paromomycinum,paucimycin,paucimycinum"	3	"g"			"51719-3,53824-9,55700-9,55701-7,55702-5"
 "PAZ"	65957	"Pazufloxacin"	"Fluoroquinolones,Quinolones"	"J01MA18,QJ01MA18"	"Quinolone antibacterials"	"Fluoroquinolones"	"NA"	"pazufloxacine,pazufloxacino,pazufloxacinum"			1	"g"	"NA"
 "PEF"	51081	"Pefloxacin"	"Fluoroquinolones,Quinolones"	"J01MA03,QJ01MA03"	"Quinolone antibacterials"	"Fluoroquinolones"	"pefl,perflo"	"labocton,pefbid,pefloxacine,pefloxacinium,pefloxacino,pefloxacinum,pefocin,pefran,pelox"	0.8	"g"	0.8	"g"	"18963-9,35828-3,390-5,3906-5,7040-9"
 "PEF-S"		"Pefloxacin screening test"	"Fluoroquinolones,Quinolones"	"NA"			"pef screen"	"NA"					"NA"
 "PNM"	10250769	"Penamecillin"	"Penicillins,Beta-lactams"	"J01CE06,QJ01CE06"	"Beta-lactam antibacterials, penicillins"	"Beta-lactamase sensitive penicillins"	"NA"	"havapen,hydroxymethyl,penamecilina,penamecillina,penamecilline,penamecillinum"	1.05	"g"			"NA"
-"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
+"PNO"		"Penicillin/novobiocin"	"Penicillins,Beta-lactams,Aminocoumarins"	"NA"			"pennov"	"NA"					"35872-1,35873-9,35874-7"
 "PSU"		"Penicillin/sulbactam"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"NA"			"NA"	"NA"					"NA"
 "PNM1"	54686187	"Penimepicycline"	"Tetracyclines"	"J01AA10,QJ01AA10"	"Tetracyclines"	"Tetracyclines"	"NA"	"criseocil,duamine,geotricyn,hydrocycline,penetracyne,penimepiciclina,penimepicyclinum"					"NA"
 "PIM"	65453	"Pentisomicin"	"Aminoglycosides"	"NA"			"NA"	"mutamicin,mutamycin,pentisomicina,pentisomicine,pentisomicinum"					"NA"
@@ -423,7 +424,7 @@
 "SZO"	187764	"Sulfamazone"	"Trimethoprims,Sulfonamides"	"J01ED09"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"sulfamazona,sulfamazonum,sulfenazone"	1.5	"g"			"NA"
 "SLF3"	5325	"Sulfamerazine"	"Trimethoprims,Sulfonamides"	"D06BA06,J01ED07,QD06BA06,QJ01EQ17"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"sulmet"	"cremomerazine,kelamerazine,mebacid,mesulfa,methylpyrimal,methylsulfazin,methylsulfazine,metilsulfadiazin,metilsulfazin,percoccide,pyralcid,romezin,septacil,septosyl,solfamerazina,solumedin,solumedine,sulfameradine,sulfamerazin,sulfamerazina,sulfamerazinum,sulfamethyldiazine,sulphamerazine,sumedine"	3	"g"			"NA"
 "SLT3"		"Sulfamerazine/trimethoprim"	"Trimethoprims,Sulfonamides"	"J01EE07,QJ01EW18"	"Sulfonamides and trimethoprim"	"Combinations of sulfonamides and trimethoprim, incl. derivatives"	"NA"	"NA"					"NA"
-"SUM"	5327	"Sulfamethazine"	"Sulfonamides"	"NA"			"NA"	"NA"					"87592-2"
+"SUM"		"Sulfamethazine"	"Sulfonamides"	"NA"			"NA"	"NA"					"87592-2"
 "SLF4"	5328	"Sulfamethizole"	"Trimethoprims,Sulfonamides"	"B05CA04,D06BA04,J01EB02,QB05CA04,QD06BA04,QJ01EQ02,QS01AB01,S01AB01"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sfmz"	"aethazolum,ayerlucil,berlophen,gliprotiazol,globucid,globucin,globuzid,glyprothiazol,glyprothiazole,glyprothiazolum,glyprothizolum,lucosil,microsul,proklar,renasul,rufol,salimol,sethadil,solfametizolo,solfetidolo,sulfaethidiole,sulfaethidol,sulfaethidole,sulfaethidolum,sulfaetidol,sulfamethizol,sulfamethizolum,sulfametizol,sulfapyelon,sulfstat,sulfurine,sulphaethidole,sulphamethizole,tardipyrine,tetracid,thidicur,thiosulfil,ultrasul,urocydal,urodiaton,urolucosil,urosulfin"	4	"g"			"60175-7,60176-5,60177-3"
 "SMX"	5329	"Sulfamethoxazole"	"Trimethoprims,Sulfonamides"	"J01EC01,QJ01EQ11"	"Sulfonamides and trimethoprim"	"Intermediate-acting sulfonamides"	"sfmx,sulf,sulfam"	"septran,septrin,simsinomin,sinomin,solfametossazolo,sulfamethalazole,sulfamethoxazolum,sulfamethoxizole,sulfamethylisoxazole,sulfametoxazol,sulfiodizole,sulfisomezole,sulphisomezole,urobak"	2	"g"			"10342-4,11577-4,18985-2,25271-8,39772-9,467-1,468-9,469-7,470-5,59971-2,59972-0,60333-2,72674-5,80549-9,80974-9"
 "SLF5"	5330	"Sulfamethoxypyridazine"	"Trimethoprims,Sulfonamides"	"J01ED05,QJ01EQ15"	"Sulfonamides and trimethoprim"	"Long-acting sulfonamides"	"NA"	"altezol,cysul,davosin,depovernil,durox,kineks,kinex,kynex,lederkyn,lentac,lisulfen,longin,medicel,midicel,midikel,myasul,opinsul,paramid,petrisul,piridolo,quinoseptyl,retamid,retasulfin,retasulphine,slosul,spofadazine,succinylsulfathi,sulfalex,sulfapiridazin,sulfapyridazine,sulfdurazin,sulfozona,sultirene,vinces"	0.5	"g"			"NA"
@@ -439,7 +440,7 @@
 "SNA"	60582	"Sulfasuccinamide"	"Sulfonamides"	"NA"			"NA"	"sulfasuccinamid,sulfasuccinamida,sulfasuccinamidum"					"NA"
 "SUT"	5340	"Sulfathiazole"	"Trimethoprims,Sulfonamides"	"D06BA02,J01EB07,QD06BA02,QJ01EQ07"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"sulthi"	"azoquimiol,azoseptale,cerazol,cerazole,chemosept,cibazol,duatok,dulana,eleudron,enterobiocine,estafilol,formosulfathiazole,neostrepsan,norsulfasol,norsulfazol,norsulfazole,norsulfazolum,planomide,poliseptil,sanotiazol,septozol,solfatiazolo,soluthiazomide,streptosilthiazole,sulfamul,sulfaplex,sulfathiazol,sulfathiazolesalt,sulfathiazolum,sulfatiazol,sulfavitina,sulfocerol,sulphathiazole,sulzol,thiacoccine,thiasulfol,thiazamide,thiozamide,wintrazole"					"87591-4,87796-9,87797-7"
 "SLF13"	3000579	"Sulfathiourea"	"Trimethoprims,Sulfonamides"	"J01EB08"	"Sulfonamides and trimethoprim"	"Short-acting sulfonamides"	"NA"	"badional,baldinol,fontamide,salvoseptyl,solfatiourea,solufontamide,sulfanilthiourea,sulfathiocarbamid,sulfathiocarbamide,sulfathiocarbamidum,sulfathioureasalt,sulfathiouree,sulfatiourea,sulphathiourea"	6	"g"			"NA"
-"SOX"	5344	"Sulfisoxazole"	"Sulfonamides"	"NA"			"sulfiz"	"NA"					"11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
+"SOX"		"Sulfisoxazole"	"Sulfonamides"	"NA"			"sulfiz"	"NA"					"11578-2,18986-0,25226-2,471-3,472-1,473-9,474-7,9701-4"
 "SSS"	86225	"Sulfonamide"	"Sulfonamides"	"NA"			"sfna,sulami"	"NA"					"17674-3,17675-0,18987-8,35842-4,4040-2,4041-0,4042-8,475-4,476-2,477-0,478-8,75650-2"
 "SLP"	9950244	"Sulopenem"	"Other"	"NA"			"sulope"	"orlynvah"					"55289-3,55290-1,55291-9"
 "SLT6"	444022	"Sultamicillin"	"Penicillins,Beta-lactams,Beta-lactamase inhibitors"	"J01CR04,QJ01CR04"	"Beta-lactam antibacterials, penicillins"	"Combinations of penicillins, incl. beta-lactamase inhibitors"	"sultos"	"combisid,sultamicilina,sultamicilline,sultamicillinum,unacid"	1.5	"g"			"NA"
@@ -465,7 +466,7 @@
 "TET"	65450	"Tetroxoprim"	"Other"	"NA"			"NA"	"primsol,tetroxoprima,tetroxoprime,tetroxoprimum,trimpex,trimplex"					"NA"
 "THA"	9568512	"Thiacetazone"	"Oxazolidinones"	"NA"			"NA"	"acetanilide,aktivan,ambathizon,amitiozon,antib,benthiozone,benzothiozane,benzothiozon,berkazon,citazone,conteben,diasan,domakol,ilbion,livazone,mivizon,myvizone,neotibil,neustab,novakol,panrone,parazone,seroden,siocarbazone,tebalon,tebecure,tebemar,tebethion,tebethione,tebezon,thiacetone,thiacetozone,thibon,thibone,thioacetazon,thioacetazonum,thioazetazone,thiocarbazil,thiomicid,thionicid,thioparamizon,thioparamizone,thiosemicarbarzone,thiosemicarbazone,thiotebesin,thiotebezin,thiotebicina,thizone,tiacetazon,tibicur,tibion,tibione,tibizan,tibon,tibone,tioacetazon,tioacetazona,tioatsetazon,tiobicina,tiocarone,tiosecolo,tubercazon,tubigal,tubin"					"32384-0,54184-7,54204-3"
 "THI"	27200	"Thiamphenicol"	"Phenicols"	"J01BA02,QJ01BA02,QJ51BA02"	"Amphenicols"	"Amphenicols"	"thiaph"	"armai,dextrosulfenidol,dextrosulphenidol,igralin,racefenicol,racefenicolo,racefenicolum,raceophenidol,thiamphenicolum,thiocymetin,thiophenicol,tiamfenicol,tiamfenicolo,urfamycine"	1.5	"g"	1.5	"g"	"41723-8,41724-6,41725-3,54169-8"
-"TAT"	9568512	"Thioacetazone"	"Antimycobacterials"	"J04AK07,QJ04AK07"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
+"TAT"		"Thioacetazone"	"Antimycobacterials"	"J04AK07,QJ04AK07"	"Drugs for treatment of tuberculosis"	"Other drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
 "THI1"		"Thioacetazone/isoniazid"	"Antimycobacterials"	"J04AM04,QJ04AM04"	"Drugs for treatment of tuberculosis"	"Combinations of drugs for treatment of tuberculosis"	"NA"	"NA"					"NA"
 "THS"	16129666	"Thiostrepton"	"Peptides"	"NA"			"NA"	"alaninamide,bryamycin,gargon,pharmakon,prestwick,sporangiomycin,thiactin,tiostrepton"					"NA"
 "TIA"	656958	"Tiamulin"	"Pleuromutilins"	"QJ01XQ01"			"tiamul"	"denagard,thiamutilin,tiamulina,tiamuline,tiamulinum"					"35846-5,35847-3,35848-1,87589-8"
@@ -496,7 +497,7 @@
 "VAN"	14969	"Vancomycin"	"Glycopeptides,Peptides"	"A07AA09,J01XA01,QA07AA09,QJ01XA01,QS01AA28,S01AA28"	"Other antibacterials"	"Glycopeptide antibacterials"	"va,van,vanc,vancom"	"vancocin,vancoled,vancomicina,vancomycine,vancomycinum"	2	"g"	2	"g"	"13586-3,13587-1,19000-9,20578-1,23615-8,25228-8,31012-8,39092-2,39796-8,39797-6,4089-9,4090-7,4091-5,4092-3,50938-0,523-1,524-9,525-6,526-4,59381-4,7059-9,92241-9,97657-1"
 "VAM"		"Vancomycin-macromethod"	"Glycopeptides,Peptides"	"NA"			"NA"	"NA"					"NA"
 "VIO"	135398671	"Viomycin"	"Antimycobacterials"	"NA"			"NA"	"florimycin,floromycin,vioactane,viocin,viomicin,viomicina,viomycine,viomycinum"					"19001-7,23616-6,527-2,528-0,529-8,530-6"
-"VIR"	11979535	"Virginiamycine"	"Streptogramins"	"NA"			"NA"	"NA"					"NA"
+"VIR"		"Virginiamycine"	"Streptogramins"	"NA"			"NA"	"NA"					"NA"
 "VOR"	71616	"Voriconazole"	"Antifungals"	"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"
 "XER"	140830474	"Xeruborbactam"	"Beta-lactamase inhibitors"	"NA"			"NA"	"benzo,borate"					"NA"
 "XBR"	72144	"Xibornol"	"Other"	"J01XX02,QJ01XX02"	"Other antibacterials"	"Other antibacterials"	"NA"	"bactacine,bracen,nanbacine,xibornolo,xibornolum"					"NA"

man/ab_property.Rd

@@ -59,7 +59,7 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
 
 \item{...}{In case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: columns to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}.}
 
-\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most distinctive group name.}
+\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most specific group name.}
 
 \item{only_first}{A \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group).}
 
@@ -116,6 +116,7 @@ ab_cid("AMX")
 ab_synonyms("AMX")
 ab_tradenames("AMX")
 ab_group("AMX")
+ab_group("AMX", all_groups = TRUE) # most specific to most general
 ab_atc_group1("AMX")
 ab_atc_group2("AMX")
 ab_url("AMX")

man/antimicrobial_selectors.Rd

@@ -17,6 +17,7 @@
 \alias{cephalosporins_5th}
 \alias{fluoroquinolones}
 \alias{glycopeptides}
+\alias{ionophores}
 \alias{isoxazolylpenicillins}
 \alias{lincosamides}
 \alias{lipoglycopeptides}
@@ -81,6 +82,8 @@ fluoroquinolones(only_sir_columns = FALSE, only_treatable = TRUE,
 
 glycopeptides(only_sir_columns = FALSE, return_all = TRUE, ...)
 
+ionophores(only_sir_columns = FALSE, return_all = TRUE, ...)
+
 isoxazolylpenicillins(only_sir_columns = FALSE, only_treatable = TRUE,
   return_all = TRUE, ...)
 
@@ -202,6 +205,7 @@ The \code{\link[=not_intrinsic_resistant]{not_intrinsic_resistant()}} function c
 \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), and ceftolozane/tazobactam (CZT)
 \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin (BES), ciprofloxacin (CIP), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levofloxacin/ornidazole (LEO), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (NOR), norfloxacin screening test (NOR-S), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin (OFX), ofloxacin/ornidazole (OOR), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pefloxacin screening test (PEF-S), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), and trovafloxacin (TVA)
 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin (AVO), bleomycin (BLM), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM), and zorbamycin (ZOR)
+\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid (LAS), monensin sodium (MON), narasin (NAR), nystatin (NYS), and salinomycin (SAL)
 \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin (CLO), dicloxacillin (DIC), flucloxacillin (FLC), meticillin (MET), oxacillin (OXA), and oxacillin screening test (OXA-S)
 \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin (CLI), clindamycin inducible screening test (CLI-S), lincomycin (LIN), and pirlimycin (PRL)
 \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin (DAL), oritavancin (ORI), and telavancin (TLV)

man/antimicrobials.Rd

@@ -5,9 +5,9 @@
 \alias{antimicrobials}
 \alias{antibiotics}
 \alias{antivirals}
-\title{Data Sets with 624 Antimicrobial Drugs}
+\title{Data Sets with 625 Antimicrobial Drugs}
 \format{
-\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 504 observations and 14 variables:}{
+\subsection{For the \link{antimicrobials} data set: a \link[tibble:tibble]{tibble} with 505 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 504 rows and 14 columns.
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 505 rows and 14 columns.
 
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
 }

man/as.ab.Rd

@@ -1,10 +1,12 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ab.R
+\docType{data}
 \name{as.ab}
 \alias{as.ab}
 \alias{ab}
 \alias{is.ab}
 \alias{ab_reset_session}
+\alias{NA_ab_}
 \title{Transform Input to an Antibiotic ID}
 \usage{
 as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
@@ -13,6 +15,8 @@ as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
 is.ab(x)
 
 ab_reset_session()
+
+NA_ab_
 }
 \arguments{
 \item{x}{A \link{character} vector to determine to antibiotic ID.}
@@ -47,6 +51,8 @@ Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on th
 Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
 
 You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab()}} and all \code{\link[=ab_property]{ab_*}} functions, see \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
+
+\code{NA_ab_} is a missing value of the new \code{ab} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
 }
 \section{Source}{
 
@@ -111,3 +117,4 @@ if (require("dplyr")) {
 \item \code{\link[=ab_from_text]{ab_from_text()}} for a function to retrieve antimicrobial drugs from clinical text (from health care records)
 }
 }
+\keyword{datasets}

man/as.mo.Rd

@@ -1,5 +1,6 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/mo.R
+\docType{data}
 \name{as.mo}
 \alias{as.mo}
 \alias{mo}
@@ -9,6 +10,7 @@
 \alias{mo_failures}
 \alias{mo_reset_session}
 \alias{mo_cleaning_regex}
+\alias{NA_mo_}
 \title{Transform Arbitrary Input to Valid Microbial Taxonomy}
 \usage{
 as.mo(x, Becker = FALSE, Lancefield = FALSE,
@@ -31,6 +33,8 @@ mo_failures()
 mo_reset_session()
 
 mo_cleaning_regex()
+
+NA_mo_
 }
 \arguments{
 \item{x}{A \link{character} vector or a \link{data.frame} with one or two columns.}
@@ -45,7 +49,9 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
 
 \item{minimum_matching_score}{A numeric value to set as the lower limit for the \link[=mo_matching_score]{MO matching score}. When left blank, this will be determined automatically based on the character length of \code{x}, its \link[=microorganisms]{taxonomic kingdom} and \link[=mo_matching_score]{human pathogenicity}.}
 
-\item{keep_synonyms}{A \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
+\item{keep_synonyms}{A \link{logical} to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of \emph{S. pyogenes}. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
+
+The default is \code{FALSE}, which will return a note if outdated taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
 
 \item{reference_df}{A \link{data.frame} to be used for extra reference when translating \code{x} to a valid \code{\link{mo}}. See \code{\link[=set_mo_source]{set_mo_source()}} and \code{\link[=get_mo_source]{get_mo_source()}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
 
@@ -57,7 +63,7 @@ This excludes enterococci at default (who are in group D), use \code{Lancefield
 
 \item{language}{Language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}
 
-\item{info}{A \link{logical} to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with old taxonomic names. The default is \code{TRUE} only in interactive mode.}
+\item{info}{A \link{logical} to indicate that info must be printed, e.g. a progress bar when more than 25 items are to be coerced, or a list with outdated taxonomic names. The default is \code{TRUE} only in interactive mode.}
 
 \item{...}{Other arguments passed on to functions.}
 }
@@ -100,7 +106,7 @@ There are three helper functions that can be run after using the \code{\link[=as
 \itemize{
 \item Use \code{\link[=mo_uncertainties]{mo_uncertainties()}} to get a \link{data.frame} that prints in a pretty format with all taxonomic names that were guessed. The output contains the matching score for all matches (see \emph{Matching Score for Microorganisms} below).
 \item Use \code{\link[=mo_failures]{mo_failures()}} to get a \link{character} \link{vector} with all values that could not be coerced to a valid value.
-\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \link{data.frame} with all values that could be coerced based on old, previously accepted taxonomic names.
+\item Use \code{\link[=mo_renamed]{mo_renamed()}} to get a \link{data.frame} with all values that could be coerced based on outdated, previously accepted taxonomic names.
 }
 }
 
@@ -151,6 +157,8 @@ This is based on:
 \item Lancefield RC (1933). \strong{A serological differentiation of human and other groups of hemolytic streptococci.} \emph{J Exp Med.} 57(4): 571-95; \doi{10.1084/jem.57.4.571}
 }
 }
+
+\code{NA_mo_} is a missing value of the new \code{mo} class, analogous to e.g. base \R's \code{\link[base:NA]{NA_character_}}.
 }
 \section{Source}{
 
@@ -260,3 +268,4 @@ mo_is_intrinsic_resistant("ESCCOL", ab = "vanco")
 
 The \code{\link[=mo_property]{mo_*}} functions (such as \code{\link[=mo_genus]{mo_genus()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}) to get properties based on the returned code.
 }
+\keyword{datasets}

man/custom_eucast_rules.Rd

@@ -98,8 +98,9 @@ x
 #>      amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
 }\if{html}{\out{</div>}}
 
-These 42 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
+These 43 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
 \itemize{
+\item aminocoumarins\cr(clorobiocin, novobiocin, and penicillin/novobiocin)
 \item aminoglycosides\cr(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, kasugamycin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)
 \item aminopenicillins\cr(amoxicillin, amoxicillin/clavulanic acid, 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)

man/custom_mdro_guideline.Rd

@@ -94,7 +94,7 @@ You can define antimicrobial groups instead of single antimicrobials for the rul
 )
 }\if{html}{\out{</div>}}
 
-All 42 antimicrobial selectors are supported for use in the rules:
+All 43 antimicrobial selectors are supported for use in the rules:
 \itemize{
 \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, kasugamycin, 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, amoxicillin/clavulanic acid, and ampicillin
@@ -111,6 +111,7 @@ All 42 antimicrobial selectors are supported for use in the rules:
 \item \code{\link[=cephalosporins_5th]{cephalosporins_5th()}} can select: \cr ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, and ceftolozane/tazobactam
 \item \code{\link[=fluoroquinolones]{fluoroquinolones()}} can select: \cr besifloxacin, ciprofloxacin, ciprofloxacin/metronidazole, ciprofloxacin/ornidazole, ciprofloxacin/tinidazole, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levofloxacin/ornidazole, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, norfloxacin screening test, norfloxacin/metronidazole, norfloxacin/tinidazole, ofloxacin, ofloxacin/ornidazole, orbifloxacin, pazufloxacin, pefloxacin, pefloxacin screening test, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, and trovafloxacin
 \item \code{\link[=glycopeptides]{glycopeptides()}} can select: \cr avoparcin, bleomycin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod, and zorbamycin
+\item \code{\link[=ionophores]{ionophores()}} can select: \cr lasalocid, monensin sodium, narasin, nystatin, and salinomycin
 \item \code{\link[=isoxazolylpenicillins]{isoxazolylpenicillins()}} can select: \cr cloxacillin, dicloxacillin, flucloxacillin, meticillin, oxacillin, and oxacillin screening test
 \item \code{\link[=lincosamides]{lincosamides()}} can select: \cr clindamycin, clindamycin inducible screening test, lincomycin, and pirlimycin
 \item \code{\link[=lipoglycopeptides]{lipoglycopeptides()}} can select: \cr dalbavancin, oritavancin, and telavancin

man/mdro.Rd

@@ -18,7 +18,8 @@
 mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
   carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
   info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
-  verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
+  verbose = FALSE, only_sir_columns = any(is.sir(x)),
+  infer_from_combinations = TRUE, ...)
 
 brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
 
@@ -35,7 +36,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 \arguments{
 \item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
 
-\item{guideline}{A specific guideline to follow, see sections \emph{Supported international / national guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
+\item{guideline}{A specific guideline to follow, see sections \emph{Supported International / National Guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
 
 \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
@@ -61,6 +62,8 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 
 \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}.}
 
+\item{infer_from_combinations}{A \link{logical} to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does \strong{not} imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to \code{TRUE}.}
+
 \item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}
 }
 \value{

man/mo_property.Rd

@@ -155,7 +155,9 @@ mo_property(x, property = "fullname", language = get_AMR_locale(),
 
 \item{language}{Language to translate text like "no growth", which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}
 
-\item{keep_synonyms}{A \link{logical} to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}, which will return a note if old taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
+\item{keep_synonyms}{A \link{logical} to indicate if outdated, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. Do note that the term "synonym" is in this case jargon from the field of microbial taxonomy - it is not in place to denote that e.g. "Streptococcus Group A" is a synonym of \emph{S. pyogenes}. Though this is practically the case, taxonomically it is not as "Streptococcus Group A" is not even a valid taxonomic name.
+
+The default is \code{FALSE}, which will return a note if outdated taxonomic names were processed. The default can be set with the package option \code{\link[=AMR-options]{AMR_keep_synonyms}}, i.e. \code{options(AMR_keep_synonyms = TRUE)} or \code{options(AMR_keep_synonyms = FALSE)}.}
 
 \item{...}{Other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'.}
 

tests/testthat/test-data.R

@@ -35,7 +35,10 @@ test_that("test-data.R", {
   expect_identical(class(microorganisms$mo), c("mo", "character"))
   expect_identical(nrow(antimicrobials), length(unique(AMR::antimicrobials$ab)))
   expect_identical(class(AMR::antimicrobials$ab), c("ab", "character"))
-
+  expect_identical(
+    nrow(antimicrobials[!is.na(antimicrobials$cid), ]),
+    length(unique(AMR::antimicrobials$cid[!is.na(antimicrobials$cid)]))
+  )
 
   # check cross table reference
   expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))

tests/testthat/test-mdro.R

@@ -296,4 +296,55 @@ test_that("test-mdro.R", {
     expect_output(x <- mdro(example_isolates %>% group_by(ward), info = TRUE, pct_required_classes = 0))
     expect_output(x <- mdro(example_isolates %>% group_by(ward), guideline = custom, info = TRUE))
   }
+
+  # drug+inhibitor inference for missing base drug columns (issue #209) -------
+  # Resistance in drug+inhibitor implies resistance in the base drug.
+  # MRGN guideline is used because it explicitly requires PIP=R (not PIP OR TZP)
+  # for Pseudomonas aeruginosa 4MRGN, making the proxy effect directly testable.
+  pseud_no_pip <- data.frame(
+    mo = as.mo("Pseudomonas aeruginosa"),
+    TZP = as.sir("R"), # piperacillin/tazobactam; no PIP column
+    CAZ = as.sir("R"),
+    IPM = as.sir("R"),
+    MEM = as.sir("R"),
+    CIP = as.sir("R"),
+    stringsAsFactors = FALSE
+  )
+  # Inference message goes to message() / stderr, not stdout
+  # -> must use expect_message(), NOT expect_output()
+  expect_message(
+    suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = TRUE)),
+    "Inferring resistance"
+  )
+  inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE))
+  not_inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE, infer_from_combinations = FALSE))
+  expect_equal(as.character(inferred), "4MRGN")
+  expect_equal(as.character(not_inferred), "Negative")
+
+  # Susceptibility in combo does NOT propagate: proxy = NA, not S
+  # -> 4MRGN criteria no longer met -> lower level than when TZP=R
+  pseud_tzp_s <- pseud_no_pip
+  pseud_tzp_s$TZP <- as.sir("S")
+  result_tzp_s <- suppressMessages(suppressWarnings(
+    mdro(pseud_tzp_s, guideline = "mrgn", info = FALSE)
+  ))
+  expect_true(as.integer(result_tzp_s) < as.integer(inferred))
+
+  # Multiple combos for the same base drug: AMX can come from AMC (amoxi/clavulanic acid) and AXS (amoxi/sulbactam)
+  ente_no_amx <- data.frame(
+    mo = as.mo("Enterococcus faecium"),
+    AMC = as.sir("R"), # amoxicillin/clavulanic acid
+    AXS = as.sir("R"), # amoxicillin/sulbactam
+    VAN = as.sir("R"),
+    TEC = as.sir("R"),
+    LNZ = as.sir("R"),
+    DAP = as.sir("R"),
+    stringsAsFactors = FALSE
+  )
+  # Should have multiple columns in the verbose explanation
+  out <- mdro(ente_no_amx, guideline = "EUCAST 3.3", info = FALSE, verbose = TRUE)
+  expect_identical(
+    out$all_nonsusceptible_columns,
+    "AMC, AMX (inferred from AMC/AXS), AXS, DAP, LNZ, TEC, VAN"
+  )
 })

tests/testthat/test-zzz.R

@@ -178,9 +178,15 @@ test_that("test-zzz.R", {
       also_load = FALSE,
       min_version = if (pkg == "dplyr") "1.0.0" else NULL
     )) {
+      if (pkg == "rstudioapi") {
+        expect_true(is.function(tryCatch(get(fn, envir = asNamespace(pkg)), error = function(e) NULL)),
+          info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
+        )
+      } else {
         expect_true(!is.null(AMR:::import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
           info = paste0("Function does not exist (anymore): function `", pkg, "::", fn, "()`")
         )
+      }
     } else if (pkg != "rstudioapi") {
       warning("Package '", pkg, "' not available")
     }