From 4b171745debcfb9fc79230982e6188d3933eaeab Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Thu, 15 May 2025 10:39:48 +0200
Subject: [PATCH] (v2.1.1.9276) mdro() fix

---
 DESCRIPTION                    |  4 ++--
 NEWS.md                        |  3 ++-
 R/aa_helper_functions.R        | 37 ++----------------------------
 R/amr_selectors.R              |  2 +-
 R/eucast_rules.R               | 10 ++++----
 R/guess_ab_col.R               |  9 ++++++--
 R/key_antimicrobials.R         |  6 ++---
 R/mdro.R                       | 42 ++++++++++++++++------------------
 man/antimicrobial_selectors.Rd |  2 +-
 man/eucast_rules.Rd            | 10 ++++----
 man/guess_ab_col.Rd            |  2 +-
 man/key_antimicrobials.Rd      |  6 ++---
 man/mdro.Rd                    | 21 ++++++++---------
 tests/testthat/test-mdro.R     |  4 ++++
 14 files changed, 64 insertions(+), 94 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 1c29de0fa..1a3daa0e4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9275
-Date: 2025-05-13
+Version: 2.1.1.9276
+Date: 2025-05-15
 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
diff --git a/NEWS.md b/NEWS.md
index 45050954f..28539fc53 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9275
+# AMR 2.1.1.9276
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)*
 
@@ -136,6 +136,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * Updated all antimicrobial DDDs from WHOCC
 * Fix for using a manual value for `mo_transform` in `antibiogram()`
 * Fixed a bug for when `antibiogram()` returns an empty data set
+* Argument `only_sir_columns` now defaults to `TRUE` if any column of a data set contains a class 'sir' (functions `eucast_rules()`, `key_antimicrobials()`, `mdro()`, etc.)
 * Added Sensititre codes for animals, antimicrobials and microorganisms
 * Fix for mapping 'high level' antimicrobials in `as.ab()` (amphotericin B-high, gentamicin-high, kanamycin-high, streptomycin-high, tobramycin-high)
 * Improved overall algorithm of `as.ab()` for better performance and accuracy, including the new function `as_reset_session()` to remove earlier coercions.
diff --git a/R/aa_helper_functions.R b/R/aa_helper_functions.R
index 9b6f305e1..fced88cdd 100644
--- a/R/aa_helper_functions.R
+++ b/R/aa_helper_functions.R
@@ -711,40 +711,6 @@ format_included_data_number <- function(data) {
   paste0(ifelse(rounder == 0, "", "~"), format(round(n, rounder), decimal.mark = ".", big.mark = " "))
 }
 
-# for eucast_rules() and mdro(), creates markdown output with URLs and names
-create_eucast_ab_documentation <- function() {
-  x <- trimws(unique(toupper(unlist(strsplit(EUCAST_RULES_DF$then_change_these_antibiotics, ",", fixed = TRUE)))))
-  ab <- character()
-  for (val in x) {
-    if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
-      # antimicrobial group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
-      val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
-    } else if (val %in% AMR_env$AB_lookup$ab) {
-      # separate drugs, such as `AMX`
-      val <- as.ab(val)
-    } else {
-      val <- as.sir(NA)
-    }
-    ab <- c(ab, val)
-  }
-  ab <- unique(ab)
-  atcs <- ab_atc(ab, only_first = TRUE)
-  # only keep ABx with an ATC code:
-  ab <- ab[!is.na(atcs)]
-  atcs <- atcs[!is.na(atcs)]
-
-  # sort all vectors on name:
-  ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
-  ab <- ab[order(ab_names)]
-  atcs <- atcs[order(ab_names)]
-  ab_names <- ab_names[order(ab_names)]
-  # create the text:
-  atc_txt <- paste0("[", atcs, "](", ab_url(ab), ")")
-  out <- paste0(ab_names, " (`", ab, "`, ", atc_txt, ")", collapse = ", ")
-  substr(out, 1, 1) <- toupper(substr(out, 1, 1))
-  out
-}
-
 vector_or <- function(v, quotes = TRUE, reverse = FALSE, sort = TRUE, initial_captital = FALSE, last_sep = " or ") {
   # makes unique and sorts, and this also removed NAs
   v <- unique(v)
@@ -983,7 +949,8 @@ ascertain_sir_classes <- function(x, obj_name) {
     warning_(
       "the data provided in argument `", obj_name,
       "` should contain at least one column of class 'sir'. Eligible SIR column were now guessed. ",
-      "See `?as.sir`."
+      "See `?as.sir`.",
+      immediate = TRUE
     )
     sirs_eligible <- is_sir_eligible(x)
     for (col in colnames(x)[sirs_eligible]) {
diff --git a/R/amr_selectors.R b/R/amr_selectors.R
index a1757accd..6260d60b2 100755
--- a/R/amr_selectors.R
+++ b/R/amr_selectors.R
@@ -40,7 +40,7 @@
 #' ```
 #' @param amr_class An antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antimicrobials] data set will be searched (case-insensitive) for this value.
 #' @param filter An [expression] to be evaluated in the [antimicrobials] data set, such as `name %like% "trim"`.
-#' @param only_sir_columns A [logical] to indicate whether only columns of class `sir` must be selected (default is `FALSE`), see [as.sir()].
+#' @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`.
 #' @param only_treatable A [logical] to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`).
 #' @param return_all A [logical] to indicate whether all matched columns must be returned (default is `TRUE`). With `FALSE`, only the first of each unique antimicrobial will be returned, e.g. if both columns `"genta"` and `"gentamicin"` exist in the data, only the first hit for gentamicin will be returned.
 #' @param ... Ignored, only in place to allow future extensions.
diff --git a/R/eucast_rules.R b/R/eucast_rules.R
index 948adea4a..9aaff0809 100755
--- a/R/eucast_rules.R
+++ b/R/eucast_rules.R
@@ -70,7 +70,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #' @param ... Column name of an antimicrobial, see section *Antimicrobials* below.
 #' @param ab Any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()].
 #' @param administration Route of administration, either `r vector_or(dosage$administration)`.
-#' @param only_sir_columns A [logical] to indicate whether only antimicrobial columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
+#' @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".
 #' @inheritParams first_isolate
@@ -102,11 +102,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
 #'
 #' Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include `"other"` to the `rules` argument, or use `eucast_rules(..., rules = "all")`. You can also set the package option [`AMR_eucastrules`][AMR-options], i.e. run `options(AMR_eucastrules = "all")`.
 #' @section Antimicrobials:
-#' To define antimicrobials column names, leave as it is to determine it automatically with [guess_ab_col()] or input a text (case-insensitive), or use `NULL` to skip a column (e.g. `TIC = NULL` to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
+#' To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use [guess_ab_col()] to find them.
 #'
-#' The following antimicrobials are eligible for the functions [eucast_rules()] and [mdro()]. These are shown below in the format 'name (`antimicrobial ID`, [ATC code](https://atcddd.fhi.no/atc/structure_and_principles/))', sorted alphabetically:
-#'
-#' `r create_eucast_ab_documentation()`
+#' To manually specify a column, provide its name (case-insensitive) as an argument, e.g. `AMX = "amoxicillin"`. To skip a specific antimicrobial, set it to `NULL`, e.g. `TIC = NULL` to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.
 #' @aliases EUCAST
 #' @rdname eucast_rules
 #' @export
@@ -171,7 +169,7 @@ eucast_rules <- function(x,
                          version_expected_phenotypes = 1.2,
                          version_expertrules = 3.3,
                          ampc_cephalosporin_resistance = NA,
-                         only_sir_columns = FALSE,
+                         only_sir_columns = any(is.sir(x)),
                          custom_rules = NULL,
                          overwrite = FALSE,
                          ...) {
diff --git a/R/guess_ab_col.R b/R/guess_ab_col.R
index 983fc678a..1645d3ffa 100755
--- a/R/guess_ab_col.R
+++ b/R/guess_ab_col.R
@@ -33,7 +33,7 @@
 #' @param x A [data.frame].
 #' @param search_string A text to search `x` for, will be checked with [as.ab()] if this value is not a column in `x`.
 #' @param verbose A [logical] to indicate whether additional info should be printed.
-#' @param only_sir_columns A [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
+#' @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()].
 #' @details You can look for an antibiotic (trade) name or abbreviation and it will search `x` and the [antimicrobials] data set for any column containing a name or code of that antibiotic.
 #' @return A column name of `x`, or `NULL` when no result is found.
 #' @export
@@ -211,7 +211,7 @@ get_column_abx <- function(x,
     newnames <- suppressWarnings(as.ab(names(dots), info = FALSE))
     if (anyNA(newnames)) {
       if (isTRUE(info)) {
-        message_(" WARNING", add_fn = list(font_yellow, font_bold), as_note = FALSE)
+        message_(paste0(font_yellow(font_bold(" WARNING: ")), "some columns returned `NA` for `as.ab()`"), as_note = FALSE)
       }
       warning_("Invalid antibiotic reference(s): ", vector_and(names(dots)[is.na(newnames)], quotes = FALSE),
         call = FALSE,
@@ -254,7 +254,10 @@ get_column_abx <- function(x,
     out <- out[order(names(out), out)]
   }
 
+  dups <- FALSE
+
   if (return_all == FALSE) {
+    dups <- names(out)[names(out) %in% names(out)[duplicated(names(out))]]
     # only keep the first hits, no duplicates
     duplicates <- c(out[duplicated(names(out))], out[duplicated(unname(out))])
     if (length(duplicates) > 0) {
@@ -264,6 +267,8 @@ get_column_abx <- function(x,
     if (isTRUE(info)) {
       if (all_okay == TRUE) {
         message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
+      } else if (!isFALSE(dups)) {
+        message_(paste0(font_yellow(font_bold(" WARNING: ")), "some results from `as.ab()` are duplicated: ", vector_and(dups, quotes = "`")), as_note = FALSE)
       } else {
         message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
       }
diff --git a/R/key_antimicrobials.R b/R/key_antimicrobials.R
index 0e3af1f4f..b8165e7b8 100755
--- a/R/key_antimicrobials.R
+++ b/R/key_antimicrobials.R
@@ -37,7 +37,7 @@
 #' @param gram_negative Names of antibiotic drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs.
 #' @param gram_positive Names of antibiotic drugs for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs.
 #' @param antifungal Names of antifungal drugs for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antifungal drugs.
-#' @param only_sir_columns A [logical] to indicate whether only columns must be included that were transformed to class `sir` (see [as.sir()]) on beforehand (default is `FALSE`).
+#' @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 ... Ignored, only in place to allow future extensions.
 #' @details
 #' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
@@ -134,7 +134,7 @@ key_antimicrobials <- function(x = NULL,
                                  "anidulafungin", "caspofungin", "fluconazole",
                                  "miconazole", "nystatin", "voriconazole"
                                ),
-                               only_sir_columns = FALSE,
+                               only_sir_columns = any(is.sir(x)),
                                ...) {
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
@@ -246,7 +246,7 @@ key_antimicrobials <- function(x = NULL,
 #' @rdname key_antimicrobials
 #' @export
 all_antimicrobials <- function(x = NULL,
-                               only_sir_columns = FALSE,
+                               only_sir_columns = any(is.sir(x)),
                                ...) {
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
diff --git a/R/mdro.R b/R/mdro.R
index 51f2a35b4..34b5d3a96 100755
--- a/R/mdro.R
+++ b/R/mdro.R
@@ -195,13 +195,14 @@ mdro <- function(x = NULL,
                  pct_required_classes = 0.5,
                  combine_SI = TRUE,
                  verbose = FALSE,
-                 only_sir_columns = FALSE,
+                 only_sir_columns = any(is.sir(x)),
                  ...) {
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
     # is also a fix for using a grouped df as input (i.e., a dot as first argument)
     x <- tryCatch(get_current_data(arg_name = "x", call = -2), error = function(e) x)
   }
+
   meet_criteria(x, allow_class = "data.frame") # also checks dimensions to be >0
   meet_criteria(guideline, allow_class = c("list", "character"), allow_NULL = TRUE)
   if (!is.list(guideline)) meet_criteria(guideline, allow_class = "character", has_length = 1, allow_NULL = TRUE)
@@ -218,7 +219,8 @@ mdro <- function(x = NULL,
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
 
-  if (!any(is_sir_eligible(x))) {
+
+  if (!isTRUE(only_sir_columns) && (!any(is.sir(x)) || !any(is_sir_eligible(x)))) {
     stop_("There were no possible SIR columns found in the data set. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
   }
 
@@ -600,6 +602,7 @@ mdro <- function(x = NULL,
   CTX <- cols_ab["CTX"]
   CTZ <- cols_ab["CTZ"]
   CXM <- cols_ab["CXM"]
+  CZA <- cols_ab["CZA"]
   CZD <- cols_ab["CZD"]
   CZO <- cols_ab["CZO"]
   CZX <- cols_ab["CZX"]
@@ -697,7 +700,6 @@ mdro <- function(x = NULL,
   abx_tb <- abx_tb[!is.na(abx_tb)]
   stop_if(guideline$code == "tb" & length(abx_tb) == 0, "no antimycobacterials found in data set")
   # nolint end
-
   if (isTRUE(combine_SI)) {
     search_result <- "R"
   } else {
@@ -1618,28 +1620,24 @@ mdro <- function(x = NULL,
     )
 
     # Pseudomonas aeruginosa
-    if (ab_missing(PIP) && !ab_missing(TZP)) {
-      # take pip/tazo if just pip is not available - many labs only test for pip/tazo because of availability on a Vitek card
-      PIP <- TZP
-    }
     x$psae <- 0
-    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R" | col_values(x, AMK) == "R"), 1, 0)
-    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R" | col_values(x, MEM) == "R"), 1, 0)
-    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R"), 1, 0)
-    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R"), 1, 0)
-    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R"), 1, 0)
+    x$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$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R") | NA_as_FALSE(col_values(x, TZP) == "R"), 1, 0)
+    x$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$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R") | NA_as_FALSE(col_values(x, NOR) == "R") | NA_as_FALSE(col_values(x, LVX) == "R"), 1, 0)
     trans_tbl(
-      3,
+      1,
       rows = which(x$genus == "Pseudomonas" & x$species == "aeruginosa"),
-      cols = c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
+      cols = "any",
       any_all = "all", # this will set all negatives to "guideline criteria not met" instead of "not covered by guideline"
-      reason = "P. aeruginosa: at least 3 classes contain R"
+      reason = "guideline criteria not met"
     )
     trans_tbl(
       3,
       rows = which(x$genus == "Pseudomonas" & x$species == "aeruginosa" & x$psae >= 3),
-      cols = c(CAZ, CIP, GEN, IPM, MEM, TOB, PIP),
-      any_all = "any", # this is the actual one, changing the ones with x$psae >= 3
+      cols = "any",
+      any_all = "any", # this is the actual one, overwriting the ones with x$psae >= 3
       reason = "P. aeruginosa: at least 3 classes contain R"
     )
 
@@ -2147,7 +2145,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
 
 #' @rdname mdro
 #' @export
-brmo <- function(x = NULL, only_sir_columns = FALSE, ...) {
+brmo <- function(x = NULL, only_sir_columns = any(is.sir(x)), ...) {
   meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   stop_if(
@@ -2160,7 +2158,7 @@ brmo <- function(x = NULL, only_sir_columns = FALSE, ...) {
 
 #' @rdname mdro
 #' @export
-mrgn <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
+mrgn <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
   meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   stop_if(
@@ -2172,7 +2170,7 @@ mrgn <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
 
 #' @rdname mdro
 #' @export
-mdr_tb <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
+mdr_tb <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
   meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   stop_if(
@@ -2184,7 +2182,7 @@ mdr_tb <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
 
 #' @rdname mdro
 #' @export
-mdr_cmi2012 <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
+mdr_cmi2012 <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
   meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   stop_if(
@@ -2196,7 +2194,7 @@ mdr_cmi2012 <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...
 
 #' @rdname mdro
 #' @export
-eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...) {
+eucast_exceptional_phenotypes <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...) {
   meet_criteria(x, allow_class = "data.frame", allow_NULL = TRUE)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
   stop_if(
diff --git a/man/antimicrobial_selectors.Rd b/man/antimicrobial_selectors.Rd
index f032b0640..b0dd11aa0 100644
--- a/man/antimicrobial_selectors.Rd
+++ b/man/antimicrobial_selectors.Rd
@@ -131,7 +131,7 @@ not_intrinsic_resistant(only_sir_columns = FALSE, col_mo = NULL,
   version_expected_phenotypes = 1.2, ...)
 }
 \arguments{
-\item{only_sir_columns}{A \link{logical} to indicate whether only columns of class \code{sir} must be selected (default is \code{FALSE}), see \code{\link[=as.sir]{as.sir()}}.}
+\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}.}
 
 \item{only_treatable}{A \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (default is \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE}).}
 
diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd
index 36364d1a0..61c13e2e3 100644
--- a/man/eucast_rules.Rd
+++ b/man/eucast_rules.Rd
@@ -23,7 +23,7 @@ eucast_rules(x, col_mo = NULL, info = interactive(),
   rules = getOption("AMR_eucastrules", default = c("breakpoints",
   "expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
   version_expected_phenotypes = 1.2, version_expertrules = 3.3,
-  ampc_cephalosporin_resistance = NA, only_sir_columns = FALSE,
+  ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
   custom_rules = NULL, overwrite = FALSE, ...)
 
 eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
@@ -47,7 +47,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 
 \item{ampc_cephalosporin_resistance}{(only applies when \code{rules} contains \code{"expert"} or \code{"all"}) a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these versions of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia}, and \emph{Serratia}.}
 
-\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
+\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{custom_rules}{Custom rules to apply, created with \code{\link[=custom_eucast_rules]{custom_eucast_rules()}}.}
 
@@ -98,11 +98,9 @@ Since these rules are not officially approved by EUCAST, they are not applied at
 }
 \section{Antimicrobials}{
 
-To define antimicrobials column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
+To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use \code{\link[=guess_ab_col]{guess_ab_col()}} to find them.
 
-The following antimicrobials are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
-
-Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), amoxicillin/sulbactam (\code{AXS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), aztreonam/avibactam (\code{AZA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), aztreonam/nacubactam (\code{ANC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&showdescription=no}{QS01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), bleomycin (\code{BLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no}{L01DC01}), brodimoprim (\code{BDP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&showdescription=no}{J01EA02}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/clavulanic acid (\code{CPC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/enmetazobactam (\code{FPE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/nacubactam (\code{FNC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/tazobactam (\code{FPT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/zidebactam (\code{FPZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefiderocol (\code{FDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI04&showdescription=no}{J01DI04}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD51&showdescription=no}{J01DD51}), cefotaxime/sulbactam (\code{CTS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD51&showdescription=no}{J01DD51}), cefotetan (\code{CTT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC07&showdescription=no}{J01DC07}), cefovecin (\code{FOV}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01DD91&showdescription=no}{QJ01DD91}), cefoxitin (\code{FOX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC01&showdescription=no}{J01DC01}), cefozopran (\code{ZOP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE03&showdescription=no}{J01DE03}), cefpiramide (\code{CPM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD13&showdescription=no}{J01DD13}), cefpodoxime/clavulanic acid (\code{CDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD64&showdescription=no}{J01DD64}), cefprozil (\code{CPR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC10&showdescription=no}{J01DC10}), cefquinome (\code{CEQ}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA07&showdescription=no}{QG51AA07}), cefroxadine (\code{CRD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB11&showdescription=no}{J01DB11}), cefsulodin (\code{CFS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD03&showdescription=no}{J01DD03}), ceftazidime (\code{CAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD02&showdescription=no}{J01DD02}), ceftazidime/avibactam (\code{CZA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD52&showdescription=no}{J01DD52}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD52&showdescription=no}{J01DD52}), cefteram (\code{CEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD18&showdescription=no}{J01DD18}), ceftezole (\code{CTL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB12&showdescription=no}{J01DB12}), ceftibuten (\code{CTB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD14&showdescription=no}{J01DD14}), ceftiofur (\code{TIO}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01DD90&showdescription=no}{QJ01DD90}), ceftizoxime (\code{CZX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD07&showdescription=no}{J01DD07}), ceftobiprole medocaril (\code{CFM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI01&showdescription=no}{J01DI01}), ceftolozane/tazobactam (\code{CZT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI54&showdescription=no}{J01DI54}), ceftriaxone (\code{CRO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD04&showdescription=no}{J01DD04}), ceftriaxone/beta-lactamase inhibitor (\code{CEB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD63&showdescription=no}{J01DD63}), cefuroxime (\code{CXM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC02&showdescription=no}{J01DC02}), chloramphenicol (\code{CHL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01BA01&showdescription=no}{J01BA01}), chlortetracycline (\code{CTE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA03&showdescription=no}{J01AA03}), ciprofloxacin (\code{CIP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA02&showdescription=no}{J01MA02}), ciprofloxacin/metronidazole (\code{CIM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA10&showdescription=no}{J01RA10}), ciprofloxacin/ornidazole (\code{CIO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA12&showdescription=no}{J01RA12}), ciprofloxacin/tinidazole (\code{CIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA11&showdescription=no}{J01RA11}), clarithromycin (\code{CLR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA09&showdescription=no}{J01FA09}), clindamycin (\code{CLI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FF01&showdescription=no}{J01FF01}), clometocillin (\code{CLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE07&showdescription=no}{J01CE07}), clomocycline (\code{CLM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA11&showdescription=no}{J01AA11}), cloxacillin (\code{CLO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF02&showdescription=no}{J01CF02}), colistin (\code{COL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XB01&showdescription=no}{J01XB01}), cycloserine (\code{CYC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J04AB01&showdescription=no}{J04AB01}), dalbavancin (\code{DAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA04&showdescription=no}{J01XA04}), danofloxacin (\code{DAN}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA92&showdescription=no}{QJ01MA92}), daptomycin (\code{DAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX09&showdescription=no}{J01XX09}), delafloxacin (\code{DFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA23&showdescription=no}{J01MA23}), demeclocycline (\code{DEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA01&showdescription=no}{J01AA01}), dibekacin (\code{DKB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB09&showdescription=no}{J01GB09}), dicloxacillin (\code{DIC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF01&showdescription=no}{J01CF01}), difloxacin (\code{DIF}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA94&showdescription=no}{QJ01MA94}), dirithromycin (\code{DIR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA13&showdescription=no}{J01FA13}), doripenem (\code{DOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH04&showdescription=no}{J01DH04}), doxycycline (\code{DOX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA02&showdescription=no}{J01AA02}), enoxacin (\code{ENX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA04&showdescription=no}{J01MA04}), enrofloxacin (\code{ENR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA90&showdescription=no}{QJ01MA90}), epicillin (\code{EPC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA07&showdescription=no}{J01CA07}), eravacycline (\code{ERV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA13&showdescription=no}{J01AA13}), ertapenem (\code{ETP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH03&showdescription=no}{J01DH03}), erythromycin (\code{ERY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA01&showdescription=no}{J01FA01}), fleroxacin (\code{FLE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA08&showdescription=no}{J01MA08}), flucloxacillin (\code{FLC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF05&showdescription=no}{J01CF05}), flurithromycin (\code{FLR1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA14&showdescription=no}{J01FA14}), fosfomycin (\code{FOS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX01&showdescription=no}{J01XX01}), framycetin (\code{FRM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=D09AA01&showdescription=no}{D09AA01}), fusidic acid (\code{FUS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XC01&showdescription=no}{J01XC01}), gamithromycin (\code{GAM}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA95&showdescription=no}{QJ01FA95}), garenoxacin (\code{GRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA19&showdescription=no}{J01MA19}), gatifloxacin (\code{GAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA16&showdescription=no}{J01MA16}), gemifloxacin (\code{GEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA15&showdescription=no}{J01MA15}), gentamicin (\code{GEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB03&showdescription=no}{J01GB03}), grepafloxacin (\code{GRX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA11&showdescription=no}{J01MA11}), hetacillin (\code{HET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA18&showdescription=no}{J01CA18}), imipenem (\code{IPM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH51&showdescription=no}{J01DH51}), imipenem/relebactam (\code{IMR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH56&showdescription=no}{J01DH56}), isepamicin (\code{ISE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB11&showdescription=no}{J01GB11}), josamycin (\code{JOS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA07&showdescription=no}{J01FA07}), kanamycin (\code{KAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB04&showdescription=no}{J01GB04}), kitasamycin (\code{KIT}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA93&showdescription=no}{QJ01FA93}), lascufloxacin (\code{LSC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA25&showdescription=no}{J01MA25}), latamoxef (\code{LTM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD06&showdescription=no}{J01DD06}), levofloxacin (\code{LVX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA12&showdescription=no}{J01MA12}), levofloxacin/ornidazole (\code{LEO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA05&showdescription=no}{J01RA05}), levonadifloxacin (\code{LND}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA24&showdescription=no}{J01MA24}), lincomycin (\code{LIN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FF02&showdescription=no}{J01FF02}), linezolid (\code{LNZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX08&showdescription=no}{J01XX08}), lomefloxacin (\code{LOM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA07&showdescription=no}{J01MA07}), loracarbef (\code{LOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC08&showdescription=no}{J01DC08}), lymecycline (\code{LYM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA04&showdescription=no}{J01AA04}), marbofloxacin (\code{MAR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA93&showdescription=no}{QJ01MA93}), mecillinam (\code{MEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA11&showdescription=no}{J01CA11}), meropenem (\code{MEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH02&showdescription=no}{J01DH02}), meropenem/vaborbactam (\code{MEV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH52&showdescription=no}{J01DH52}), metacycline (\code{MTC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA05&showdescription=no}{J01AA05}), metampicillin (\code{MTM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA14&showdescription=no}{J01CA14}), meticillin (\code{MET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF03&showdescription=no}{J01CF03}), mezlocillin (\code{MEZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA10&showdescription=no}{J01CA10}), micronomicin (\code{MCR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AA22&showdescription=no}{QS01AA22}), midecamycin (\code{MID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA03&showdescription=no}{J01FA03}), minocycline (\code{MNO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA08&showdescription=no}{J01AA08}), miocamycin (\code{MCM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA11&showdescription=no}{J01FA11}), moxifloxacin (\code{MFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA14&showdescription=no}{J01MA14}), nadifloxacin (\code{NAD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=D10AF05&showdescription=no}{D10AF05}), nafcillin (\code{NAF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF06&showdescription=no}{J01CF06}), nalidixic acid (\code{NAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MB02&showdescription=no}{J01MB02}), nemonoxacin (\code{NEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MB08&showdescription=no}{J01MB08}), neomycin (\code{NEO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB05&showdescription=no}{J01GB05}), netilmicin (\code{NET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB07&showdescription=no}{J01GB07}), nitrofurantoin (\code{NIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XE01&showdescription=no}{J01XE01}), nitroxoline (\code{NTR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX07&showdescription=no}{J01XX07}), norfloxacin (\code{NOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA06&showdescription=no}{J01MA06}), norfloxacin/metronidazole (\code{NME}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA14&showdescription=no}{J01RA14}), norfloxacin/tinidazole (\code{NTI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA13&showdescription=no}{J01RA13}), novobiocin (\code{NOV}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01XX95&showdescription=no}{QJ01XX95}), ofloxacin (\code{OFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA01&showdescription=no}{J01MA01}), ofloxacin/ornidazole (\code{OOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA09&showdescription=no}{J01RA09}), oleandomycin (\code{OLE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA05&showdescription=no}{J01FA05}), omadacycline (\code{OMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA15&showdescription=no}{J01AA15}), orbifloxacin (\code{ORB}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA95&showdescription=no}{QJ01MA95}), oritavancin (\code{ORI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA05&showdescription=no}{J01XA05}), oxacillin (\code{OXA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF04&showdescription=no}{J01CF04}), oxytetracycline (\code{OXY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA06&showdescription=no}{J01AA06}), pazufloxacin (\code{PAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA18&showdescription=no}{J01MA18}), pefloxacin (\code{PEF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA03&showdescription=no}{J01MA03}), penamecillin (\code{PNM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE06&showdescription=no}{J01CE06}), penimepicycline (\code{PNM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA10&showdescription=no}{J01AA10}), pheneticillin (\code{PHE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE05&showdescription=no}{J01CE05}), phenoxymethylpenicillin (\code{PHN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE02&showdescription=no}{J01CE02}), piperacillin (\code{PIP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA12&showdescription=no}{J01CA12}), piperacillin/sulbactam (\code{PIS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR05&showdescription=no}{J01CR05}), piperacillin/tazobactam (\code{TZP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR05&showdescription=no}{J01CR05}), pirlimycin (\code{PRL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ51FF90&showdescription=no}{QJ51FF90}), pivampicillin (\code{PVM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA02&showdescription=no}{J01CA02}), pivmecillinam (\code{PME}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA08&showdescription=no}{J01CA08}), plazomicin (\code{PLZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB14&showdescription=no}{J01GB14}), polymyxin B (\code{PLB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XB02&showdescription=no}{J01XB02}), pradofloxacin (\code{PRA}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA97&showdescription=no}{QJ01MA97}), pristinamycin (\code{PRI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FG01&showdescription=no}{J01FG01}), procaine benzylpenicillin (\code{PRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE09&showdescription=no}{J01CE09}), propicillin (\code{PRP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE03&showdescription=no}{J01CE03}), prulifloxacin (\code{PRU}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA17&showdescription=no}{J01MA17}), quinupristin/dalfopristin (\code{QDA}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FG02&showdescription=no}{QJ01FG02}), ribostamycin (\code{RST}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB10&showdescription=no}{J01GB10}), rifampicin (\code{RIF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J04AB02&showdescription=no}{J04AB02}), rokitamycin (\code{ROK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA12&showdescription=no}{J01FA12}), rolitetracycline (\code{RLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA09&showdescription=no}{J01AA09}), roxithromycin (\code{RXT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA06&showdescription=no}{J01FA06}), rufloxacin (\code{RFL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA10&showdescription=no}{J01MA10}), sarafloxacin (\code{SAR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA98&showdescription=no}{QJ01MA98}), sarecycline (\code{SRC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA14&showdescription=no}{J01AA14}), sisomicin (\code{SIS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB08&showdescription=no}{J01GB08}), sitafloxacin (\code{SIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA21&showdescription=no}{J01MA21}), solithromycin (\code{SOL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA16&showdescription=no}{J01FA16}), sparfloxacin (\code{SPX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA09&showdescription=no}{J01MA09}), spiramycin (\code{SPI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA02&showdescription=no}{J01FA02}), streptoduocin (\code{STR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GA02&showdescription=no}{J01GA02}), streptomycin (\code{STR1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GA01&showdescription=no}{J01GA01}), sulbenicillin (\code{SBC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA16&showdescription=no}{J01CA16}), sulfadiazine (\code{SDI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC02&showdescription=no}{J01EC02}), sulfadiazine/tetroxoprim (\code{SLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE06&showdescription=no}{J01EE06}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE02&showdescription=no}{J01EE02}), sulfadimethoxine (\code{SUD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED01&showdescription=no}{J01ED01}), sulfadimidine (\code{SDM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB03&showdescription=no}{J01EB03}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE05&showdescription=no}{J01EE05}), sulfafurazole (\code{SLF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB05&showdescription=no}{J01EB05}), sulfaisodimidine (\code{SLF1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB01&showdescription=no}{J01EB01}), sulfalene (\code{SLF2}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED02&showdescription=no}{J01ED02}), sulfamazone (\code{SZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED09&showdescription=no}{J01ED09}), sulfamerazine (\code{SLF3}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED07&showdescription=no}{J01ED07}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE07&showdescription=no}{J01EE07}), sulfamethizole (\code{SLF4}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB02&showdescription=no}{J01EB02}), sulfamethoxazole (\code{SMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC01&showdescription=no}{J01EC01}), sulfamethoxypyridazine (\code{SLF5}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED05&showdescription=no}{J01ED05}), sulfametomidine (\code{SLF6}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED03&showdescription=no}{J01ED03}), sulfametoxydiazine (\code{SLF7}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED04&showdescription=no}{J01ED04}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE03&showdescription=no}{J01EE03}), sulfamoxole (\code{SLF8}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC03&showdescription=no}{J01EC03}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE04&showdescription=no}{J01EE04}), sulfanilamide (\code{SLF9}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB06&showdescription=no}{J01EB06}), sulfaperin (\code{SLF10}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED06&showdescription=no}{J01ED06}), sulfaphenazole (\code{SLF11}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED08&showdescription=no}{J01ED08}), sulfapyridine (\code{SLF12}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB04&showdescription=no}{J01EB04}), sulfathiazole (\code{SUT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB07&showdescription=no}{J01EB07}), sulfathiourea (\code{SLF13}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB08&showdescription=no}{J01EB08}), sultamicillin (\code{SLT6}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR04&showdescription=no}{J01CR04}), talampicillin (\code{TAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA15&showdescription=no}{J01CA15}), tedizolid (\code{TZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX11&showdescription=no}{J01XX11}), teicoplanin (\code{TEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA02&showdescription=no}{J01XA02}), telavancin (\code{TLV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA03&showdescription=no}{J01XA03}), telithromycin (\code{TLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA15&showdescription=no}{J01FA15}), temafloxacin (\code{TMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA05&showdescription=no}{J01MA05}), temocillin (\code{TEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA17&showdescription=no}{J01CA17}), tetracycline (\code{TCY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA07&showdescription=no}{J01AA07}), ticarcillin (\code{TIC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA13&showdescription=no}{J01CA13}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR03&showdescription=no}{J01CR03}), tigecycline (\code{TGC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA12&showdescription=no}{J01AA12}), tilbroquinol (\code{TBQ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=P01AA05&showdescription=no}{P01AA05}), tildipirosin (\code{TIP}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA96&showdescription=no}{QJ01FA96}), tilmicosin (\code{TIL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA91&showdescription=no}{QJ01FA91}), tobramycin (\code{TOB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB01&showdescription=no}{J01GB01}), tosufloxacin (\code{TFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA22&showdescription=no}{J01MA22}), trimethoprim (\code{TMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA01&showdescription=no}{J01EA01}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE01&showdescription=no}{J01EE01}), troleandomycin (\code{TRL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA08&showdescription=no}{J01FA08}), trovafloxacin (\code{TVA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA13&showdescription=no}{J01MA13}), tulathromycin (\code{TUL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA94&showdescription=no}{QJ01FA94}), tylosin (\code{TYL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA90&showdescription=no}{QJ01FA90}), tylvalosin (\code{TYL1}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA92&showdescription=no}{QJ01FA92}), vancomycin (\code{VAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA01&showdescription=no}{J01XA01})
+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.
 }
 
 \section{Download Our Reference Data}{
diff --git a/man/guess_ab_col.Rd b/man/guess_ab_col.Rd
index 1ae56226a..efa87e87e 100644
--- a/man/guess_ab_col.Rd
+++ b/man/guess_ab_col.Rd
@@ -14,7 +14,7 @@ guess_ab_col(x = NULL, search_string = NULL, verbose = FALSE,
 
 \item{verbose}{A \link{logical} to indicate whether additional info should be printed.}
 
-\item{only_sir_columns}{A \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
+\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}.}
 }
 \value{
 A column name of \code{x}, or \code{NULL} when no result is found.
diff --git a/man/key_antimicrobials.Rd b/man/key_antimicrobials.Rd
index 3dbf860a5..abbd08213 100644
--- a/man/key_antimicrobials.Rd
+++ b/man/key_antimicrobials.Rd
@@ -13,9 +13,9 @@ key_antimicrobials(x = NULL, col_mo = NULL, universal = c("ampicillin",
   "ceftazidime", "meropenem"), gram_positive = c("vancomycin", "teicoplanin",
   "tetracycline", "erythromycin", "oxacillin", "rifampin"),
   antifungal = c("anidulafungin", "caspofungin", "fluconazole", "miconazole",
-  "nystatin", "voriconazole"), only_sir_columns = FALSE, ...)
+  "nystatin", "voriconazole"), only_sir_columns = any(is.sir(x)), ...)
 
-all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)
+all_antimicrobials(x = NULL, only_sir_columns = any(is.sir(x)), ...)
 
 antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
   ignore_I = TRUE, points_threshold = 2, ...)
@@ -33,7 +33,7 @@ antimicrobials_equal(y, z, type = c("points", "keyantimicrobials"),
 
 \item{antifungal}{Names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs.}
 
-\item{only_sir_columns}{A \link{logical} to indicate whether only columns must be included that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
+\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{...}{Ignored, only in place to allow future extensions.}
 
diff --git a/man/mdro.Rd b/man/mdro.Rd
index f6d1783e7..d0f31b13f 100644
--- a/man/mdro.Rd
+++ b/man/mdro.Rd
@@ -22,19 +22,20 @@ See the supported guidelines above for the \link{list} of publications used for
 mdro(x = NULL, guideline = "CMI2012", 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 = FALSE, ...)
+  verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
 
 custom_mdro_guideline(..., as_factor = TRUE)
 
-brmo(x = NULL, only_sir_columns = FALSE, ...)
+brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
 
-mrgn(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
+mrgn(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
 
-mdr_tb(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
+mdr_tb(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE, ...)
 
-mdr_cmi2012(x = NULL, only_sir_columns = FALSE, verbose = FALSE, ...)
+mdr_cmi2012(x = NULL, only_sir_columns = any(is.sir(x)), verbose = FALSE,
+  ...)
 
-eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE,
+eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
   verbose = FALSE, ...)
 }
 \arguments{
@@ -64,7 +65,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE,
 
 \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{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be detected that were transformed to class \code{sir} (see \code{\link[=as.sir]{as.sir()}}) on beforehand (default is \code{FALSE}).}
+\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{...}{In case of \code{\link[=custom_mdro_guideline]{custom_mdro_guideline()}}: a set of rules, see section \emph{Using Custom Guidelines} below. Otherwise: column name of an antibiotic, see section \emph{Antimicrobials} below.}
 
@@ -180,11 +181,9 @@ The rules set (the \code{custom} object in this case) could be exported to a sha
 
 \section{Antimicrobials}{
 
-To define antimicrobials column names, leave as it is to determine it automatically with \code{\link[=guess_ab_col]{guess_ab_col()}} or input a text (case-insensitive), or use \code{NULL} to skip a column (e.g. \code{TIC = NULL} to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.
+To let the function automatically detect antimicrobial column names, do not provide any named arguments. It will then use \code{\link[=guess_ab_col]{guess_ab_col()}} to find them.
 
-The following antimicrobials are eligible for the functions \code{\link[=eucast_rules]{eucast_rules()}} and \code{\link[=mdro]{mdro()}}. These are shown below in the format 'name (\verb{antimicrobial ID}, \href{https://atcddd.fhi.no/atc/structure_and_principles/}{ATC code})', sorted alphabetically:
-
-Amikacin (\code{AMK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB06&showdescription=no}{J01GB06}), amoxicillin (\code{AMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA04&showdescription=no}{J01CA04}), amoxicillin/clavulanic acid (\code{AMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), amoxicillin/sulbactam (\code{AXS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR02&showdescription=no}{J01CR02}), ampicillin (\code{AMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA01&showdescription=no}{J01CA01}), ampicillin/sulbactam (\code{SAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR01&showdescription=no}{J01CR01}), apramycin (\code{APR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QA07AA92&showdescription=no}{QA07AA92}), arbekacin (\code{ARB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB12&showdescription=no}{J01GB12}), aspoxicillin (\code{APX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA19&showdescription=no}{J01CA19}), azidocillin (\code{AZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE04&showdescription=no}{J01CE04}), azithromycin (\code{AZM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA10&showdescription=no}{J01FA10}), azlocillin (\code{AZL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA09&showdescription=no}{J01CA09}), aztreonam (\code{ATM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF01&showdescription=no}{J01DF01}), aztreonam/avibactam (\code{AZA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), aztreonam/nacubactam (\code{ANC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF51&showdescription=no}{J01DF51}), bacampicillin (\code{BAM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA06&showdescription=no}{J01CA06}), bekanamycin (\code{BEK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB13&showdescription=no}{J01GB13}), benzathine benzylpenicillin (\code{BNB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE08&showdescription=no}{J01CE08}), benzathine phenoxymethylpenicillin (\code{BNP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE10&showdescription=no}{J01CE10}), benzylpenicillin (\code{PEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE01&showdescription=no}{J01CE01}), besifloxacin (\code{BES}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AE08&showdescription=no}{QS01AE08}), biapenem (\code{BIA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH05&showdescription=no}{J01DH05}), bleomycin (\code{BLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=L01DC01&showdescription=no}{L01DC01}), brodimoprim (\code{BDP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA02&showdescription=no}{J01EA02}), carbenicillin (\code{CRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA03&showdescription=no}{J01CA03}), carindacillin (\code{CRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA05&showdescription=no}{J01CA05}), carumonam (\code{CAR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DF02&showdescription=no}{J01DF02}), cefacetrile (\code{CAC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB10&showdescription=no}{J01DB10}), cefaclor (\code{CEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC04&showdescription=no}{J01DC04}), cefadroxil (\code{CFR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB05&showdescription=no}{J01DB05}), cefalexin (\code{LEX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB01&showdescription=no}{J01DB01}), cefaloridine (\code{RID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB02&showdescription=no}{J01DB02}), cefalotin (\code{CEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB03&showdescription=no}{J01DB03}), cefamandole (\code{MAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC03&showdescription=no}{J01DC03}), cefapirin (\code{HAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB08&showdescription=no}{J01DB08}), cefatrizine (\code{CTZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB07&showdescription=no}{J01DB07}), cefazedone (\code{CZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB06&showdescription=no}{J01DB06}), cefazolin (\code{CZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB04&showdescription=no}{J01DB04}), cefcapene (\code{CCP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD17&showdescription=no}{J01DD17}), cefdinir (\code{CDR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD15&showdescription=no}{J01DD15}), cefditoren (\code{DIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD16&showdescription=no}{J01DD16}), cefepime (\code{FEP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE01&showdescription=no}{J01DE01}), cefepime/amikacin (\code{CFA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/clavulanic acid (\code{CPC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/enmetazobactam (\code{FPE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/nacubactam (\code{FNC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/tazobactam (\code{FPT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefepime/zidebactam (\code{FPZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE51&showdescription=no}{J01DE51}), cefetamet (\code{CAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD10&showdescription=no}{J01DD10}), cefiderocol (\code{FDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI04&showdescription=no}{J01DI04}), cefixime (\code{CFM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD08&showdescription=no}{J01DD08}), cefmenoxime (\code{CMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD05&showdescription=no}{J01DD05}), cefmetazole (\code{CMZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC09&showdescription=no}{J01DC09}), cefodizime (\code{DIZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD09&showdescription=no}{J01DD09}), cefonicid (\code{CID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC06&showdescription=no}{J01DC06}), cefoperazone (\code{CFP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD12&showdescription=no}{J01DD12}), cefoperazone/sulbactam (\code{CSL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD62&showdescription=no}{J01DD62}), ceforanide (\code{CND}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC11&showdescription=no}{J01DC11}), cefotaxime (\code{CTX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD01&showdescription=no}{J01DD01}), cefotaxime/clavulanic acid (\code{CTC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD51&showdescription=no}{J01DD51}), cefotaxime/sulbactam (\code{CTS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD51&showdescription=no}{J01DD51}), cefotetan (\code{CTT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC05&showdescription=no}{J01DC05}), cefotiam (\code{CTF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC07&showdescription=no}{J01DC07}), cefovecin (\code{FOV}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01DD91&showdescription=no}{QJ01DD91}), cefoxitin (\code{FOX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC01&showdescription=no}{J01DC01}), cefozopran (\code{ZOP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE03&showdescription=no}{J01DE03}), cefpiramide (\code{CPM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD11&showdescription=no}{J01DD11}), cefpirome (\code{CPO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DE02&showdescription=no}{J01DE02}), cefpodoxime (\code{CPD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD13&showdescription=no}{J01DD13}), cefpodoxime/clavulanic acid (\code{CDC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD64&showdescription=no}{J01DD64}), cefprozil (\code{CPR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC10&showdescription=no}{J01DC10}), cefquinome (\code{CEQ}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA07&showdescription=no}{QG51AA07}), cefroxadine (\code{CRD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB11&showdescription=no}{J01DB11}), cefsulodin (\code{CFS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD03&showdescription=no}{J01DD03}), ceftazidime (\code{CAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD02&showdescription=no}{J01DD02}), ceftazidime/avibactam (\code{CZA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD52&showdescription=no}{J01DD52}), ceftazidime/clavulanic acid (\code{CCV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD52&showdescription=no}{J01DD52}), cefteram (\code{CEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD18&showdescription=no}{J01DD18}), ceftezole (\code{CTL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DB12&showdescription=no}{J01DB12}), ceftibuten (\code{CTB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD14&showdescription=no}{J01DD14}), ceftiofur (\code{TIO}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01DD90&showdescription=no}{QJ01DD90}), ceftizoxime (\code{CZX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD07&showdescription=no}{J01DD07}), ceftobiprole medocaril (\code{CFM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI01&showdescription=no}{J01DI01}), ceftolozane/tazobactam (\code{CZT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DI54&showdescription=no}{J01DI54}), ceftriaxone (\code{CRO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD04&showdescription=no}{J01DD04}), ceftriaxone/beta-lactamase inhibitor (\code{CEB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD63&showdescription=no}{J01DD63}), cefuroxime (\code{CXM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC02&showdescription=no}{J01DC02}), chloramphenicol (\code{CHL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01BA01&showdescription=no}{J01BA01}), chlortetracycline (\code{CTE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA03&showdescription=no}{J01AA03}), ciprofloxacin (\code{CIP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA02&showdescription=no}{J01MA02}), ciprofloxacin/metronidazole (\code{CIM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA10&showdescription=no}{J01RA10}), ciprofloxacin/ornidazole (\code{CIO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA12&showdescription=no}{J01RA12}), ciprofloxacin/tinidazole (\code{CIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA11&showdescription=no}{J01RA11}), clarithromycin (\code{CLR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA09&showdescription=no}{J01FA09}), clindamycin (\code{CLI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FF01&showdescription=no}{J01FF01}), clometocillin (\code{CLM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE07&showdescription=no}{J01CE07}), clomocycline (\code{CLM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA11&showdescription=no}{J01AA11}), cloxacillin (\code{CLO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF02&showdescription=no}{J01CF02}), colistin (\code{COL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XB01&showdescription=no}{J01XB01}), cycloserine (\code{CYC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J04AB01&showdescription=no}{J04AB01}), dalbavancin (\code{DAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA04&showdescription=no}{J01XA04}), danofloxacin (\code{DAN}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA92&showdescription=no}{QJ01MA92}), daptomycin (\code{DAP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX09&showdescription=no}{J01XX09}), delafloxacin (\code{DFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA23&showdescription=no}{J01MA23}), demeclocycline (\code{DEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA01&showdescription=no}{J01AA01}), dibekacin (\code{DKB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB09&showdescription=no}{J01GB09}), dicloxacillin (\code{DIC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF01&showdescription=no}{J01CF01}), difloxacin (\code{DIF}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA94&showdescription=no}{QJ01MA94}), dirithromycin (\code{DIR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA13&showdescription=no}{J01FA13}), doripenem (\code{DOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH04&showdescription=no}{J01DH04}), doxycycline (\code{DOX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA02&showdescription=no}{J01AA02}), enoxacin (\code{ENX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA04&showdescription=no}{J01MA04}), enrofloxacin (\code{ENR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA90&showdescription=no}{QJ01MA90}), epicillin (\code{EPC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA07&showdescription=no}{J01CA07}), eravacycline (\code{ERV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA13&showdescription=no}{J01AA13}), ertapenem (\code{ETP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH03&showdescription=no}{J01DH03}), erythromycin (\code{ERY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA01&showdescription=no}{J01FA01}), fleroxacin (\code{FLE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA08&showdescription=no}{J01MA08}), flucloxacillin (\code{FLC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF05&showdescription=no}{J01CF05}), flurithromycin (\code{FLR1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA14&showdescription=no}{J01FA14}), fosfomycin (\code{FOS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX01&showdescription=no}{J01XX01}), framycetin (\code{FRM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=D09AA01&showdescription=no}{D09AA01}), fusidic acid (\code{FUS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XC01&showdescription=no}{J01XC01}), gamithromycin (\code{GAM}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA95&showdescription=no}{QJ01FA95}), garenoxacin (\code{GRN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA19&showdescription=no}{J01MA19}), gatifloxacin (\code{GAT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA16&showdescription=no}{J01MA16}), gemifloxacin (\code{GEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA15&showdescription=no}{J01MA15}), gentamicin (\code{GEN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB03&showdescription=no}{J01GB03}), grepafloxacin (\code{GRX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA11&showdescription=no}{J01MA11}), hetacillin (\code{HET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA18&showdescription=no}{J01CA18}), imipenem (\code{IPM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH51&showdescription=no}{J01DH51}), imipenem/relebactam (\code{IMR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH56&showdescription=no}{J01DH56}), isepamicin (\code{ISE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB11&showdescription=no}{J01GB11}), josamycin (\code{JOS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA07&showdescription=no}{J01FA07}), kanamycin (\code{KAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB04&showdescription=no}{J01GB04}), kitasamycin (\code{KIT}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA93&showdescription=no}{QJ01FA93}), lascufloxacin (\code{LSC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA25&showdescription=no}{J01MA25}), latamoxef (\code{LTM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DD06&showdescription=no}{J01DD06}), levofloxacin (\code{LVX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA12&showdescription=no}{J01MA12}), levofloxacin/ornidazole (\code{LEO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA05&showdescription=no}{J01RA05}), levonadifloxacin (\code{LND}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA24&showdescription=no}{J01MA24}), lincomycin (\code{LIN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FF02&showdescription=no}{J01FF02}), linezolid (\code{LNZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX08&showdescription=no}{J01XX08}), lomefloxacin (\code{LOM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA07&showdescription=no}{J01MA07}), loracarbef (\code{LOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DC08&showdescription=no}{J01DC08}), lymecycline (\code{LYM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA04&showdescription=no}{J01AA04}), marbofloxacin (\code{MAR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA93&showdescription=no}{QJ01MA93}), mecillinam (\code{MEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA11&showdescription=no}{J01CA11}), meropenem (\code{MEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH02&showdescription=no}{J01DH02}), meropenem/vaborbactam (\code{MEV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01DH52&showdescription=no}{J01DH52}), metacycline (\code{MTC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA05&showdescription=no}{J01AA05}), metampicillin (\code{MTM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA14&showdescription=no}{J01CA14}), meticillin (\code{MET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF03&showdescription=no}{J01CF03}), mezlocillin (\code{MEZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA10&showdescription=no}{J01CA10}), micronomicin (\code{MCR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QS01AA22&showdescription=no}{QS01AA22}), midecamycin (\code{MID}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA03&showdescription=no}{J01FA03}), minocycline (\code{MNO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA08&showdescription=no}{J01AA08}), miocamycin (\code{MCM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA11&showdescription=no}{J01FA11}), moxifloxacin (\code{MFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA14&showdescription=no}{J01MA14}), nadifloxacin (\code{NAD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=D10AF05&showdescription=no}{D10AF05}), nafcillin (\code{NAF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF06&showdescription=no}{J01CF06}), nalidixic acid (\code{NAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MB02&showdescription=no}{J01MB02}), nemonoxacin (\code{NEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MB08&showdescription=no}{J01MB08}), neomycin (\code{NEO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB05&showdescription=no}{J01GB05}), netilmicin (\code{NET}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB07&showdescription=no}{J01GB07}), nitrofurantoin (\code{NIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XE01&showdescription=no}{J01XE01}), nitroxoline (\code{NTR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX07&showdescription=no}{J01XX07}), norfloxacin (\code{NOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA06&showdescription=no}{J01MA06}), norfloxacin/metronidazole (\code{NME}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA14&showdescription=no}{J01RA14}), norfloxacin/tinidazole (\code{NTI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA13&showdescription=no}{J01RA13}), novobiocin (\code{NOV}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01XX95&showdescription=no}{QJ01XX95}), ofloxacin (\code{OFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA01&showdescription=no}{J01MA01}), ofloxacin/ornidazole (\code{OOR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01RA09&showdescription=no}{J01RA09}), oleandomycin (\code{OLE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA05&showdescription=no}{J01FA05}), omadacycline (\code{OMC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA15&showdescription=no}{J01AA15}), orbifloxacin (\code{ORB}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA95&showdescription=no}{QJ01MA95}), oritavancin (\code{ORI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA05&showdescription=no}{J01XA05}), oxacillin (\code{OXA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CF04&showdescription=no}{J01CF04}), oxytetracycline (\code{OXY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA06&showdescription=no}{J01AA06}), pazufloxacin (\code{PAZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA18&showdescription=no}{J01MA18}), pefloxacin (\code{PEF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA03&showdescription=no}{J01MA03}), penamecillin (\code{PNM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE06&showdescription=no}{J01CE06}), penimepicycline (\code{PNM1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA10&showdescription=no}{J01AA10}), pheneticillin (\code{PHE}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE05&showdescription=no}{J01CE05}), phenoxymethylpenicillin (\code{PHN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE02&showdescription=no}{J01CE02}), piperacillin (\code{PIP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA12&showdescription=no}{J01CA12}), piperacillin/sulbactam (\code{PIS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR05&showdescription=no}{J01CR05}), piperacillin/tazobactam (\code{TZP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR05&showdescription=no}{J01CR05}), pirlimycin (\code{PRL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ51FF90&showdescription=no}{QJ51FF90}), pivampicillin (\code{PVM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA02&showdescription=no}{J01CA02}), pivmecillinam (\code{PME}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA08&showdescription=no}{J01CA08}), plazomicin (\code{PLZ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB14&showdescription=no}{J01GB14}), polymyxin B (\code{PLB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XB02&showdescription=no}{J01XB02}), pradofloxacin (\code{PRA}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA97&showdescription=no}{QJ01MA97}), pristinamycin (\code{PRI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FG01&showdescription=no}{J01FG01}), procaine benzylpenicillin (\code{PRB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE09&showdescription=no}{J01CE09}), propicillin (\code{PRP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CE03&showdescription=no}{J01CE03}), prulifloxacin (\code{PRU}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA17&showdescription=no}{J01MA17}), quinupristin/dalfopristin (\code{QDA}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FG02&showdescription=no}{QJ01FG02}), ribostamycin (\code{RST}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB10&showdescription=no}{J01GB10}), rifampicin (\code{RIF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J04AB02&showdescription=no}{J04AB02}), rokitamycin (\code{ROK}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA12&showdescription=no}{J01FA12}), rolitetracycline (\code{RLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA09&showdescription=no}{J01AA09}), roxithromycin (\code{RXT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA06&showdescription=no}{J01FA06}), rufloxacin (\code{RFL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA10&showdescription=no}{J01MA10}), sarafloxacin (\code{SAR}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01MA98&showdescription=no}{QJ01MA98}), sarecycline (\code{SRC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA14&showdescription=no}{J01AA14}), sisomicin (\code{SIS}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB08&showdescription=no}{J01GB08}), sitafloxacin (\code{SIT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA21&showdescription=no}{J01MA21}), solithromycin (\code{SOL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA16&showdescription=no}{J01FA16}), sparfloxacin (\code{SPX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA09&showdescription=no}{J01MA09}), spiramycin (\code{SPI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA02&showdescription=no}{J01FA02}), streptoduocin (\code{STR}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GA02&showdescription=no}{J01GA02}), streptomycin (\code{STR1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GA01&showdescription=no}{J01GA01}), sulbenicillin (\code{SBC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA16&showdescription=no}{J01CA16}), sulfadiazine (\code{SDI}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC02&showdescription=no}{J01EC02}), sulfadiazine/tetroxoprim (\code{SLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE06&showdescription=no}{J01EE06}), sulfadiazine/trimethoprim (\code{SLT1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE02&showdescription=no}{J01EE02}), sulfadimethoxine (\code{SUD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED01&showdescription=no}{J01ED01}), sulfadimidine (\code{SDM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB03&showdescription=no}{J01EB03}), sulfadimidine/trimethoprim (\code{SLT2}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE05&showdescription=no}{J01EE05}), sulfafurazole (\code{SLF}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB05&showdescription=no}{J01EB05}), sulfaisodimidine (\code{SLF1}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB01&showdescription=no}{J01EB01}), sulfalene (\code{SLF2}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED02&showdescription=no}{J01ED02}), sulfamazone (\code{SZO}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED09&showdescription=no}{J01ED09}), sulfamerazine (\code{SLF3}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED07&showdescription=no}{J01ED07}), sulfamerazine/trimethoprim (\code{SLT3}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE07&showdescription=no}{J01EE07}), sulfamethizole (\code{SLF4}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB02&showdescription=no}{J01EB02}), sulfamethoxazole (\code{SMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC01&showdescription=no}{J01EC01}), sulfamethoxypyridazine (\code{SLF5}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED05&showdescription=no}{J01ED05}), sulfametomidine (\code{SLF6}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED03&showdescription=no}{J01ED03}), sulfametoxydiazine (\code{SLF7}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED04&showdescription=no}{J01ED04}), sulfametrole/trimethoprim (\code{SLT4}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE03&showdescription=no}{J01EE03}), sulfamoxole (\code{SLF8}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EC03&showdescription=no}{J01EC03}), sulfamoxole/trimethoprim (\code{SLT5}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE04&showdescription=no}{J01EE04}), sulfanilamide (\code{SLF9}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB06&showdescription=no}{J01EB06}), sulfaperin (\code{SLF10}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED06&showdescription=no}{J01ED06}), sulfaphenazole (\code{SLF11}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01ED08&showdescription=no}{J01ED08}), sulfapyridine (\code{SLF12}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB04&showdescription=no}{J01EB04}), sulfathiazole (\code{SUT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB07&showdescription=no}{J01EB07}), sulfathiourea (\code{SLF13}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EB08&showdescription=no}{J01EB08}), sultamicillin (\code{SLT6}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR04&showdescription=no}{J01CR04}), talampicillin (\code{TAL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA15&showdescription=no}{J01CA15}), tedizolid (\code{TZD}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XX11&showdescription=no}{J01XX11}), teicoplanin (\code{TEC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA02&showdescription=no}{J01XA02}), telavancin (\code{TLV}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA03&showdescription=no}{J01XA03}), telithromycin (\code{TLT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA15&showdescription=no}{J01FA15}), temafloxacin (\code{TMX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA05&showdescription=no}{J01MA05}), temocillin (\code{TEM}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA17&showdescription=no}{J01CA17}), tetracycline (\code{TCY}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA07&showdescription=no}{J01AA07}), ticarcillin (\code{TIC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CA13&showdescription=no}{J01CA13}), ticarcillin/clavulanic acid (\code{TCC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01CR03&showdescription=no}{J01CR03}), tigecycline (\code{TGC}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01AA12&showdescription=no}{J01AA12}), tilbroquinol (\code{TBQ}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=P01AA05&showdescription=no}{P01AA05}), tildipirosin (\code{TIP}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA96&showdescription=no}{QJ01FA96}), tilmicosin (\code{TIL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA91&showdescription=no}{QJ01FA91}), tobramycin (\code{TOB}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01GB01&showdescription=no}{J01GB01}), tosufloxacin (\code{TFX}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA22&showdescription=no}{J01MA22}), trimethoprim (\code{TMP}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EA01&showdescription=no}{J01EA01}), trimethoprim/sulfamethoxazole (\code{SXT}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01EE01&showdescription=no}{J01EE01}), troleandomycin (\code{TRL}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01FA08&showdescription=no}{J01FA08}), trovafloxacin (\code{TVA}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01MA13&showdescription=no}{J01MA13}), tulathromycin (\code{TUL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA94&showdescription=no}{QJ01FA94}), tylosin (\code{TYL}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA90&showdescription=no}{QJ01FA90}), tylvalosin (\code{TYL1}, \href{https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01FA92&showdescription=no}{QJ01FA92}), vancomycin (\code{VAN}, \href{https://atcddd.fhi.no/atc_ddd_index//?code=J01XA01&showdescription=no}{J01XA01})
+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.
 }
 
 \section{Interpretation of SIR}{
diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R
index 751d8ac0b..ff6267064 100755
--- a/tests/testthat/test-mdro.R
+++ b/tests/testthat/test-mdro.R
@@ -286,6 +286,10 @@ test_that("test-mdro.R", {
     colnames(suppressWarnings(mdro(example_isolates[1:10, ], verbose = TRUE, info = FALSE))),
     c("row_number", "microorganism", "MDRO", "reason", "all_nonsusceptible_columns", "guideline")
   )
+  expect_equal(
+    colnames(suppressWarnings(mdro(example_isolates[1:10, ], verbose = TRUE, info = FALSE, guideline = custom_mdro_guideline(AMX == "R" ~ "Positive")))),
+    c("row_number", "microorganism", "MDRO", "reason", "all_nonsusceptible_columns", "guideline")
+  )
 
   # print groups
   if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {