(v2.1.1.9276) mdro() fix

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9275
+Version: 2.1.1.9276
-Date: 2025-05-13
+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

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.

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]) {

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.

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:
+#' 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.
-#'
-#' `r create_eucast_ab_documentation()`
 #' @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,
                          ...) {

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)
       }

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)

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$psae + ifelse(NA_as_FALSE(col_values(x, TOB) == "R") | NA_as_FALSE(col_values(x, AMK) == "R"), 1, 0)
-    x$psae <- x$psae + ifelse(NA_as_FALSE(col_values(x, IPM) == "R" | col_values(x, MEM) == "R"), 1, 0)
+    x$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$psae + ifelse(NA_as_FALSE(col_values(x, PIP) == "R"), 1, 0)
+    x$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$psae + ifelse(NA_as_FALSE(col_values(x, CAZ) == "R"), 1, 0)
+    x$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$psae + ifelse(NA_as_FALSE(col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R"), 1, 0)
+    x$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),
+      cols = "any",
-      any_all = "any", # this is the actual one, changing the ones with x$psae >= 3
+      any_all = "any", # this is the actual one, overwriting the ones with x$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(

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}).}
 

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.

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.}
 

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)) {