NEWS.md

@@ -12,7 +12,6 @@ This version will eventually become v2.0! We're happy to reach a new major miles
 * The MO matching score algorithm (`mo_matching_score()`) now counts deletions and substitutions as 2 instead of 1, which impacts the outcome of `as.mo()` and any `mo_*()` function
 * **Argument `combine_IR` has been removed** from this package (affecting functions `count_df()`, `proportion_df()`, and `rsi_df()` and some plotting functions), since it was replaced with `combine_SI` three years ago
 * Interpretation **guidelines older than 10 years were removed**, the oldest now included guidelines of EUCAST and CLSI are from 2013
-* Using `units` in `ab_ddd(..., units = "...")` had been deprecated and is now not supported anymore. Use `ab_ddd_units()` instead.
 
 ### New
 * **EUCAST 2022 and CLSI 2022 guidelines** have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.

R/ab_property.R

@@ -241,7 +241,20 @@ ab_ddd <- function(x, administration = "oral", ...) {
   meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
 
   x <- as.ab(x, ...)
-  ddd_prop <- paste0(administration, "_ddd")
+  ddd_prop <- administration
+  # old behaviour
+  units <- list(...)$units
+  if (!is.null(units) && isTRUE(units)) {
+    if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
+      warning_(
+        "in `ab_ddd()`: using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead.",
+        "This warning will be shown once per session."
+      )
+    }
+    ddd_prop <- paste0(ddd_prop, "_units")
+  } else {
+    ddd_prop <- paste0(ddd_prop, "_ddd")
+  }
   out <- ab_validate(x = x, property = ddd_prop)
 
   if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
@@ -261,17 +274,16 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
   meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
 
   x <- as.ab(x, ...)
-  ddd_prop <- paste0(administration, "_units")
+  if (any(ab_name(x, language = NULL) %like% "/")) {
-  out <- ab_validate(x = x, property = ddd_prop)
-
-  if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in `ab_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in `ab_ddd_units()`: DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "www.whocc.no/ddd/list_of_ddds_combined_products/"
     )
   }
-  out
+
+  ddd_prop <- paste0(administration, "_units")
+  ab_validate(x = x, property = ddd_prop)
 }
 
 #' @rdname ab_property

R/av.R

@@ -506,7 +506,6 @@ is.av <- function(x) {
 # will be exported using s3_register() in R/zzz.R
 pillar_shaft.av <- function(x, ...) {
   out <- trimws(format(x))
-  out[!is.na(x)] <- gsub("+", font_subtle("+"), out[!is.na(x)], fixed = TRUE)
   out[is.na(x)] <- font_na(NA)
   create_pillar_column(out, align = "left", min_width = 4)
 }
@@ -557,7 +556,7 @@ as.data.frame.av <- function(x, ...) {
 "[<-.av" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av)
+  return_after_integrity_check(y, "antimicrobial code", AMR_env$AV_lookup$av)
 }
 #' @method [[<- av
 #' @export
@@ -565,7 +564,7 @@ as.data.frame.av <- function(x, ...) {
 "[[<-.av" <- function(i, j, ..., value) {
   y <- NextMethod()
   attributes(y) <- attributes(i)
-  return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av)
+  return_after_integrity_check(y, "antimicrobial code", AMR_env$AV_lookup$av)
 }
 #' @method c av
 #' @export
@@ -574,7 +573,7 @@ c.av <- function(...) {
   x <- list(...)[[1L]]
   y <- NextMethod()
   attributes(y) <- attributes(x)
-  return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av)
+  return_after_integrity_check(y, "antimicrobial code", AMR_env$AV_lookup$av)
 }
 
 #' @method unique av

R/av_property.R

@@ -130,11 +130,35 @@ av_group <- function(x, language = get_AMR_locale(), ...) {
 }
 
 #' @rdname av_property
+#' @aliases ATC
 #' @export
-av_atc <- function(x, ...) {
+av_atc <- function(x, only_first = FALSE, ...) {
   meet_criteria(x, allow_NA = TRUE)
-  # ATCs in the antivirals data set are not a list
+  meet_criteria(only_first, allow_class = "logical", has_length = 1)
-  av_validate(x = x, property = "atc", ...)
+  
+  atcs <- av_validate(x = x, property = "atc", ...)
+  
+  if (only_first == TRUE) {
+    atcs <- vapply(
+      FUN.VALUE = character(1),
+      # get only the first ATC code
+      atcs,
+      function(x) {
+        # try to get the J-group
+        if (any(x %like% "^J")) {
+          x[x %like% "^J"][1L]
+        } else {
+          as.character(x[1L])
+        }
+      }
+    )
+  } else if (length(atcs) == 1) {
+    atcs <- unname(unlist(atcs))
+  } else {
+    names(atcs) <- x
+  }
+  
+  atcs
 }
 
 #' @rdname av_property
@@ -157,7 +181,20 @@ av_ddd <- function(x, administration = "oral", ...) {
   meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
   
   x <- as.av(x, ...)
-  ddd_prop <- paste0(administration, "_ddd")
+  ddd_prop <- administration
+  # old behaviour
+  units <- list(...)$units
+  if (!is.null(units) && isTRUE(units)) {
+    if (message_not_thrown_before("av_ddd", entire_session = TRUE)) {
+      warning_(
+        "in `av_ddd()`: using `av_ddd(..., units = TRUE)` is deprecated, use `av_ddd_units()` to retrieve units instead.",
+        "This warning will be shown once per session."
+      )
+    }
+    ddd_prop <- paste0(ddd_prop, "_units")
+  } else {
+    ddd_prop <- paste0(ddd_prop, "_ddd")
+  }
   out <- av_validate(x = x, property = ddd_prop)
   
   if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
@@ -177,17 +214,16 @@ av_ddd_units <- function(x, administration = "oral", ...) {
   meet_criteria(administration, is_in = c("oral", "iv"), has_length = 1)
   
   x <- as.av(x, ...)
-  ddd_prop <- paste0(administration, "_units")
+  if (any(av_name(x, language = NULL) %like% "/")) {
-  out <- av_validate(x = x, property = ddd_prop)
-  
-  if (any(av_name(x, language = NULL) %like% "/" & is.na(out))) {
     warning_(
-      "in `av_ddd_units()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
+      "in `av_ddd_units()`: DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package.",
       "Please refer to the WHOCC website:\n",
       "www.whocc.no/ddd/list_of_ddds_combined_products/"
     )
   }
-  out
+  
+  ddd_prop <- paste0(administration, "_units")
+  av_validate(x = x, property = ddd_prop)
 }
 
 #' @rdname av_property

R/vctrs.R

@@ -70,20 +70,6 @@ vec_cast.ab.character <- function(x, to, ...) {
   return_after_integrity_check(x, "antimicrobial code", as.character(AMR_env$AB_lookup$ab))
 }
 
-# S3: av
-vec_ptype2.character.av <- function(x, y, ...) {
-  x
-}
-vec_ptype2.av.character <- function(x, y, ...) {
-  y
-}
-vec_cast.character.av <- function(x, to, ...) {
-  as.character(x)
-}
-vec_cast.av.character <- function(x, to, ...) {
-  return_after_integrity_check(x, "antiviral agent code", as.character(AMR_env$AV_lookup$av))
-}
-
 # S3: mo
 vec_ptype2.character.mo <- function(x, y, ...) {
   x

R/zzz.R

@@ -50,11 +50,6 @@ AMR_env$ab_previously_coerced <- data.frame(
   ab = character(0),
   stringsAsFactors = FALSE
 )
-AMR_env$av_previously_coerced <- data.frame(
-  x = character(0),
-  av = character(0),
-  stringsAsFactors = FALSE
-)
 AMR_env$rsi_interpretation_history <- data.frame(
   datetime = Sys.time()[0],
   index = integer(0),
@@ -92,13 +87,11 @@ if (utf8_supported && !is_latex) {
   # developers of the vctrs package:
   # https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
   s3_register("pillar::pillar_shaft", "ab")
-  s3_register("pillar::pillar_shaft", "av")
   s3_register("pillar::pillar_shaft", "mo")
   s3_register("pillar::pillar_shaft", "rsi")
   s3_register("pillar::pillar_shaft", "mic")
   s3_register("pillar::pillar_shaft", "disk")
   s3_register("tibble::type_sum", "ab")
-  s3_register("tibble::type_sum", "av")
   s3_register("tibble::type_sum", "mo")
   s3_register("tibble::type_sum", "rsi")
   s3_register("tibble::type_sum", "mic")
@@ -136,11 +129,6 @@ if (utf8_supported && !is_latex) {
   s3_register("vctrs::vec_ptype2", "ab.character")
   s3_register("vctrs::vec_cast", "character.ab")
   s3_register("vctrs::vec_cast", "ab.character")
-  # S3: av
-  s3_register("vctrs::vec_ptype2", "character.av")
-  s3_register("vctrs::vec_ptype2", "av.character")
-  s3_register("vctrs::vec_cast", "character.av")
-  s3_register("vctrs::vec_cast", "av.character")
   # S3: mo
   s3_register("vctrs::vec_ptype2", "character.mo")
   s3_register("vctrs::vec_ptype2", "mo.character")

man/av_property.Rd

@@ -8,6 +8,7 @@
 \alias{av_tradenames}
 \alias{av_group}
 \alias{av_atc}
+\alias{ATC}
 \alias{av_loinc}
 \alias{av_ddd}
 \alias{av_ddd_units}
@@ -25,7 +26,7 @@ av_tradenames(x, ...)
 
 av_group(x, language = get_AMR_locale(), ...)
 
-av_atc(x, ...)
+av_atc(x, only_first = FALSE, ...)
 
 av_loinc(x, ...)