(v2.1.1.9286) deprecate antibiotics better, add ATC for ceftaroline

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 2.1.1.9285
+Version: 2.1.1.9286
-Date: 2025-05-21
+Date: 2025-06-01
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NAMESPACE

@@ -1,12 +1,14 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method("!=",amr_selector)
+S3method("$",deprecated_amr_dataset)
 S3method("&",amr_selector)
 S3method("+",ab)
 S3method("+",amr_selector)
 S3method("==",amr_selector)
 S3method("[",ab)
 S3method("[",av)
+S3method("[",deprecated_amr_dataset)
 S3method("[",disk)
 S3method("[",mic)
 S3method("[",mo)
@@ -18,6 +20,7 @@ S3method("[<-",mo)
 S3method("[<-",sir)
 S3method("[[",ab)
 S3method("[[",av)
+S3method("[[",deprecated_amr_dataset)
 S3method("[[",disk)
 S3method("[[",mic)
 S3method("[[",mo)
@@ -40,6 +43,7 @@ S3method(any,amr_selector)
 S3method(any,amr_selector_any_all)
 S3method(as.data.frame,ab)
 S3method(as.data.frame,av)
+S3method(as.data.frame,deprecated_amr_dataset)
 S3method(as.data.frame,mic)
 S3method(as.data.frame,mo)
 S3method(as.double,mic)
@@ -93,6 +97,7 @@ S3method(print,av)
 S3method(print,bug_drug_combinations)
 S3method(print,custom_eucast_rules)
 S3method(print,custom_mdro_guideline)
+S3method(print,deprecated_amr_dataset)
 S3method(print,disk)
 S3method(print,mic)
 S3method(print,mo)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9285
+# AMR 2.1.1.9286
 
 *(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/zz_deprecated.R

@@ -36,9 +36,45 @@
 NULL
 
 #' @rdname AMR-deprecated
-#' @usage NULL
+#' @usage antibiotics
 #' @export
-"antibiotics"
+antibiotics <- local({
+  warned <- FALSE
+  value <- AMR::antimicrobials
+  structure(
+    value,
+    class = c("deprecated_amr_dataset", class(value))
+  )
+})
+.amr_deprecation_warn <- function() {
+  deprecation_warning(old = "antibiotics", new = "antimicrobials", is_dataset = TRUE)
+  invisible(NULL)
+}
+#' @export
+`[.deprecated_amr_dataset` <- function(x, ...) {
+  .amr_deprecation_warn()
+  NextMethod("[")
+}
+#' @export
+`[[.deprecated_amr_dataset` <- function(x, ...) {
+  .amr_deprecation_warn()
+  NextMethod("[[")
+}
+#' @export
+`$.deprecated_amr_dataset` <- function(x, name) {
+  .amr_deprecation_warn()
+  NextMethod("$")
+}
+#' @export
+print.deprecated_amr_dataset <- function(x, ...) {
+  .amr_deprecation_warn()
+  NextMethod("print")
+}
+#' @export
+as.data.frame.deprecated_amr_dataset <- function(x, ...) {
+  .amr_deprecation_warn()
+  NextMethod("as.data.frame")
+}
 
 # REMEMBER to search for `deprecation_warning` in the package code to find all instances.
 # currently deprecated arguments at least:

R/zzz.R

@@ -110,14 +110,6 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
     AB_LOOKUP <- create_AB_AV_lookup(AMR::antimicrobials)
   }
 
-  # deprecated antibiotics data set
-  makeActiveBinding("antibiotics", function() {
-    if (interactive()) {
-      deprecation_warning(old = "antibiotics", new = "antimicrobials", is_dataset = TRUE)
-    }
-    AMR::antimicrobials
-  }, env = asNamespace(pkgname))
-
   AMR_env$AB_lookup <- cbind(AMR::antimicrobials, AB_LOOKUP)
   AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
 }

data-raw/_reproduction_scripts/reproduction_of_antimicrobials.R

@@ -948,6 +948,8 @@ get_atc_code <- function(ab) {
   # exception for imipenem
   if (ab_name == "imipenem") ab_name <- "imipenem/cilastatin"
   if (ab_name == "imipenem/relebactam") ab_name <- "imipenem/cilastatin/relebactam"
+  if (ab_name == "ceftaroline") ab_name <- "ceftaroline fosamil"
+  ab_name.bak <- ab_name
   if (ab_name %like% "/") {
     ab_name <- strsplit(ab_name, "[/ ]")[[1]]
   }
@@ -971,28 +973,33 @@ get_atc_code <- function(ab) {
   } else if (ab_name_full %like% " and " && ab_name_bla %in% atc_tbl[[2]]) {
     out <- atc_tbl[[1]][which(atc_tbl[[2]] == ab_name_bla)]
   } else {
+    if (any(atc_tbl_human$X1 %like% ab_name.bak, na.rm = TRUE)) {
+      message("returning NA, but DO MIND: ", ab_name.bak, " resembles ATC name(s) ", toString(atc_tbl_human$X1), appendLF = FALSE)
+    }
     out <- NA_character_
   }
   unique(out)
 }
 
+# update all:
+to_update <- 1:nrow(antimicrobials)
+# or just the empty ones:
+to_update <- which(sapply(antimicrobials$atc, function(x) length(x[!is.na(x)])) == 0)
+
 updated_atc <- lapply(seq_len(length(to_update)),
                       function(x) NA_character_)
 
-to_update <- 1:nrow(antimicrobials)
-# or just the empty ones:
-to_update <- which(sapply(antimicrobials$atc, length) == 0)
 
-# this takes around 10 minutes (some are skipped and go faster)
+# this takes around 10 minutes for the whole table (some ABx are skipped and go faster)
 for (i in to_update) {
-  message(percentage(i / length(updated_atc), digits = 1),
+  message(percentage(which(to_update == i) / length(updated_atc), digits = 1),
     " - Downloading ", antimicrobials$name[i],
     appendLF = FALSE
   )
   atcs <- get_atc_code(antimicrobials$name[i])
   if (length(atcs[!is.na(atcs)]) > 0) {
     updated_atc[[i]] <- atcs
-    message(" (", length(atcs[!is.na(atcs)]), " results: ", toString(atcs[!is.na(atcs)]), ")")
+    message(font_blue(paste0(" (", length(atcs[!is.na(atcs)]), " results: ", toString(atcs[!is.na(atcs)]), ")")))
     # let the WHO server rest for a second - they might have a limitation on the queries per second
     Sys.sleep(1)
   } else {
@@ -1001,7 +1008,8 @@ for (i in to_update) {
 }
 
 updated_atc <- lapply(updated_atc, function(x) sort(x[!is.na(x)]))
-antimicrobials$atc <- updated_atc
+antimicrobials$atc[to_update] <- updated_atc[to_update]
+
 # DO NOT FORGET TO UPDATE R/aa_globals.R!
 
 

data-raw/ab.md5

@@ -1 +1 @@
-959459b92fe6ff57c02bab08381a73a8
+228840b3941753c4adee2b781d901590

data-raw/datasets/antimicrobials.txt

@@ -114,7 +114,7 @@
 "CRD"	5284529	"Cefroxadine"	"Cephalosporins (1st gen.)"	"J01DB11,QJ01DB11"	"Other beta-lactam antibacterials"	"First-generation cephalosporins"	"ceftix"	"cefroxadin,cefroxadino,cefroxadinum,oraspor"	2.1	"g"			"NA"
 "CFS"	656575	"Cefsulodin"	"Cephalosporins (3rd gen.)"	"J01DD03,QJ01DD03"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"cefsul,cfsl,cfsu"	"cefomonil,cefonomil,cefsulodine,cefsulodinhydrate,cefsulodino,cefsulodinum,pseudocef,pseudomonil,pyocefal,sulcephalosporin,takesulin,tilmapor,ulfaret"			4	"g"	"127-1,128-9,129-7,130-5,131-3,18892-0,25242-9,55647-2"
 "CSU"	68718	"Cefsumide"	"Cephalosporins (unclassified gen.)"	"NA"			"NA"	"cefsulmid,cefsumido,cefsumidum"					"NA"
-"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"NA"			"ceftar,cfro"	"ceftaroine,teflaro,zinforo"					"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
+"CPT"	56841980	"Ceftaroline"	"Cephalosporins (5th gen.)"	"J01DI02,QJ01DI02"			"ceftar,cfro"	"ceftaroine,teflaro,zinforo"					"73604-1,73605-8,73626-4,73627-2,73649-6,73650-4,74170-2"
 "CPA"		"Ceftaroline/avibactam"	"Cephalosporins (5th gen.)"	"NA"			"NA"	"NA"					"73604-1,73626-4,73649-6"
 "CAZ"	5481173	"Ceftazidime"	"Cephalosporins (3rd gen.)"	"J01DD02,QJ01DD02"	"Other beta-lactam antibacterials"	"Third-generation cephalosporins"	"caz,cefta,ceftaz,cfta,cftz,taz,tz,xtz"	"ceftazimide,ceptaz,fortam,fortaz,fortum,glazidim,kefazim,modacin,pentacef,tazicef,tizime"			4	"g"	"101481-0,101482-8,101483-6,132-1,133-9,134-7,135-4,18893-8,21151-6,3449-6,35774-9,35775-6,35776-4,42352-5,55648-0,55649-8,55650-6,55651-4,58705-5,6995-5,73603-3,73625-6,73648-8,80960-8,87734-0,90850-9"
 "CZA"	90643431	"Ceftazidime/avibactam"	"Cephalosporins (3rd gen.)"	"J01DD52,QJ01DD52"			"cfav"	"avycaz,zavicefta"			6	"g"	"101483-6,73603-3,73625-6,73648-8,87734-0"

man/AMR-deprecated.Rd

@@ -8,9 +8,11 @@
 \alias{ab_selector}
 \title{Deprecated Functions, Arguments, or Datasets}
 \format{
-An object of class \code{tbl_df} (inherits from \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
+An object of class \code{deprecated_amr_dataset} (inherits from \code{tbl_df}, \code{tbl}, \code{data.frame}) with 497 rows and 14 columns.
 }
 \usage{
+antibiotics
+
 ab_class(...)
 
 ab_selector(...)