(v2.1.1.9288) mdro fix

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9287
+Version: 2.1.1.9288
 Date: 2025-06-01
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9287
+# AMR 2.1.1.9288
 
 *(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).)*
 

R/guess_ab_col.R

@@ -272,25 +272,24 @@ get_column_abx <- function(x,
       } else {
         message_(" WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
       }
+
       for (i in seq_len(length(out))) {
-        if (isTRUE(verbose) && !names(out[i]) %in% names(duplicates)) {
+        if (isTRUE(verbose) && !out[i] %in% duplicates) {
           message_(
             "Using column '", font_bold(out[i]), "' as input for ", names(out)[i],
             " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")."
           )
         }
-        if (names(out[i]) %in% names(duplicates)) {
+        if (out[i] %in% duplicates) {
-          already_set_as <- out[unname(out) == unname(out[i])][1L]
+          already_set_as <- out[which(out == out[i])[1L]]
-          if (names(out)[i] != names(already_set_as)) {
+          if (names(out)[i] != already_set_as) {
-            warning_(
+            message_(
               paste0(
                 "Column '", font_bold(out[i]), "' will not be used for ",
-                names(out)[i], " (", ab_name(names(out)[i], tolower = TRUE, language = NULL), ")",
+                names(out)[i], " (", suppressMessages(ab_name(names(out)[i], tolower = TRUE, language = NULL, fast_mode = TRUE)), ")",
-                ", as it is already set for ",
+                ", as this antimicrobial has already been set."
-                names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"
               ),
-              add_fn = font_red,
+              add_fn = font_red
-              immediate = verbose
             )
           }
         }

R/mdro.R

@@ -204,14 +204,14 @@ mdro <- function(x = NULL,
   }
   if (is.character(vanA)) {
     meet_criteria(vanA, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanA <- x[[vanA]]
+    vanA <- x[[VanA]]
     meet_criteria(vanA, allow_class = "logical", allow_NA = TRUE)
   } else if (length(vanA) == 1) {
     vanA <- rep(vanA, NROW(x))
   }
   if (is.character(vanB)) {
     meet_criteria(vanB, is_in = colnames(x), allow_NA = FALSE, has_length = 1)
-    vanB <- x[[vanB]]
+    vanB <- x[[VanB]]
     meet_criteria(vanB, allow_class = "logical", allow_NA = TRUE)
   } else if (length(vanB) == 1) {
     vanB <- rep(vanB, NROW(x))
@@ -1526,9 +1526,9 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      rows = which(x[[SXT]] == "R" &
+      rows = which(col_values(x, SXT) == "R" &
-        (x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
+        (col_values(x, GEN) == "R" | col_values(x, TOB) == "R" | col_values(x, AMK) == "R") &
-        (x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
+        (col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R") &
         (x$genus %in% c("Enterobacter", "Providencia") | paste(x$genus, x$species) %in% c("Citrobacter freundii", "Klebsiella aerogenes", "Hafnia alvei", "Morganella morganii"))),
       cols = c(SXT, aminoglycosides, fluoroquinolones),
       any_all = "any",
@@ -1536,9 +1536,9 @@ mdro <- function(x = NULL,
     )
     trans_tbl(
       3,
-      rows = which(x[[SXT]] == "R" &
+      rows = which(col_values(x, SXT) == "R" &
-        x[[GEN]] == "R" &
+        col_values(x, GEN) == "R" &
-        (x[[CIP]] == "R" | x[[NOR]] == "R" | x[[LVX]] == "R") &
+        (col_values(x, CIP) == "R" | col_values(x, NOR) == "R" | col_values(x, LVX) == "R") &
         paste(x$genus, x$species) == "Serratia marcescens"),
       cols = c(SXT, aminoglycosides_serratia_marcescens, fluoroquinolones),
       any_all = "any",
@@ -1548,8 +1548,8 @@ mdro <- function(x = NULL,
     # Acinetobacter baumannii-calcoaceticus complex
     trans_tbl(
       3,
-      rows = which((x[[GEN]] == "R" | x[[TOB]] == "R" | x[[AMK]] == "R") &
+      rows = which((col_values(x, GEN) == "R" | col_values(x, TOB) == "R" | col_values(x, AMK) == "R") &
-        (x[[CIP]] == "R" | x[[LVX]] == "R") &
+        (col_values(x, CIP) == "R" | col_values(x, LVX) == "R") &
         x[[col_mo]] %in% AMR::microorganisms.groups$mo[AMR::microorganisms.groups$mo_group_name == "Acinetobacter baumannii complex"]),
       cols = c(aminoglycosides, CIP, LVX),
       any_all = "any",

tests/testthat/test-data.R

@@ -71,6 +71,7 @@ test_that("test-data.R", {
   if (AMR:::pkg_is_available("tibble")) {
     # there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
     datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
+    datasets <- datasets[datasets != "antibiotics"]
     for (i in seq_len(length(datasets))) {
       dataset <- get(datasets[i], envir = asNamespace("AMR"))
       expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])