(v2.1.1.9290) typo

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9288
+Version: 2.1.1.9290
 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 2.1.1.9288
+# AMR 2.1.1.9290
 
 *(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/data.R

@@ -29,7 +29,10 @@
 
 #' Data Sets with `r format(nrow(antimicrobials) + nrow(antivirals), big.mark = " ")` Antimicrobial Drugs
 #'
+#' @description
 #' Two data sets containing all antimicrobials and antivirals. Use [as.ab()] or one of the [`ab_*`][ab_property()] functions to retrieve values from the [antimicrobials] data set. Three identifiers are included in this data set: an antimicrobial ID (`ab`, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (`atc`) as defined by the WHO, and a Compound ID (`cid`) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
+#'
+#' **The `antibiotics` data set has been renamed to `antimicrobials`. The old name will be removed in a future version.**
 #' @format
 #' ### For the [antimicrobials] data set: a [tibble][tibble::tibble] with `r nrow(antimicrobials)` observations and `r ncol(antimicrobials)` variables:
 #' - `ab`\cr antimicrobial ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. ***This is a unique identifier.***
@@ -88,6 +91,9 @@
 #' antivirals
 "antimicrobials"
 
+#' @rdname antimicrobials
+"antibiotics"
+
 #' @rdname antimicrobials
 "antivirals"
 

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))
@@ -1490,7 +1490,7 @@ mdro <- function(x = NULL,
     if (length(ESBLs) > 0) {
       trans_tbl(
         2, # positive, unconfirmed
-        rows = which(x$order == "Enterobacterales" & x[[ESBLs[1]]] == "R" & x[[ESBLs[2]]] == "R" & is.na(esbl)),
+        rows = which(x$order == "Enterobacterales" & col_values(x, ESBLs[1]) == "R" & col_values(x, ESBLs[2]) == "R" & is.na(esbl)),
         cols = c(AMX %or% AMP, cephalosporins_3rd),
         any_all = "all",
         reason = "Enterobacterales: potential ESBL"

man/antimicrobials.Rd

@@ -3,6 +3,7 @@
 \docType{data}
 \name{antimicrobials}
 \alias{antimicrobials}
+\alias{antibiotics}
 \alias{antivirals}
 \title{Data Sets with 617 Antimicrobial Drugs}
 \format{
@@ -49,6 +50,8 @@ LOINC:
 }
 }
 
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
+
 An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 120 rows and 11 columns.
 }
 \source{
@@ -61,10 +64,14 @@ An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) w
 \usage{
 antimicrobials
 
+antibiotics
+
 antivirals
 }
 \description{
 Two data sets containing all antimicrobials and antivirals. Use \code{\link[=as.ab]{as.ab()}} or one of the \code{\link[=ab_property]{ab_*}} functions to retrieve values from the \link{antimicrobials} data set. Three identifiers are included in this data set: an antimicrobial ID (\code{ab}, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (\code{atc}) as defined by the WHO, and a Compound ID (\code{cid}) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
+
+\strong{The \code{antibiotics} data set has been renamed to \code{antimicrobials}. The old name will be removed in a future version.}
 }
 \details{
 Properties that are based on an ATC code are only available when an ATC is available. These properties are: \code{atc_group1}, \code{atc_group2}, \code{oral_ddd}, \code{oral_units}, \code{iv_ddd} and \code{iv_units}. Do note that ATC codes are not unique. For example, J01CR02 is officially the ATC code for "amoxicillin and beta-lactamase inhibitor". Consequently, these two items from the \link{antimicrobials} data set both return \code{"J01CR02"}:

tests/testthat/test-mdro.R

@@ -48,7 +48,7 @@ test_that("test-mdro.R", {
   # example_isolates should have these finding using Dutch guidelines
   expect_equal(
     as.double(table(outcome)),
-    c(1977, 23, 0)
+    c(1977, 21, 2)
   )
 
   expect_equal(