Fixes #57

.github/prehooks/pre-commit

@@ -3,29 +3,28 @@
 echo "Running pre-commit hook..."
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-echo ">>  Updating R documentation..."
 if command -v Rscript > /dev/null; then
   if [ "$(Rscript -e 'cat(all(c('"'pkgload'"', '"'devtools'"', '"'dplyr'"', '"'styler'"') %in% rownames(installed.packages())))')" = "TRUE" ]; then
     Rscript -e "source('data-raw/_pre_commit_hook.R')"
     currentpkg=`Rscript -e "cat(pkgload::pkg_name())"`
-    echo ">>  Adding all files in folders 'data-raw', 'inst', 'man', and 'R' to this git commit"
+    echo "-> Adding all files in folders 'data-raw', 'inst', 'man', and 'R' to this git commit"
     git add data-raw/*
     git add inst/*
     git add man/*
     git add R/*
   else
-    echo ">>  R package 'pkgload', 'devtools', 'dplyr', or 'styler' not installed!"
+    echo "- R package 'pkgload', 'devtools', 'dplyr', or 'styler' not installed!"
     currentpkg="your"
   fi
 else
-  echo ">>  R is not available on your system!"
+  echo "- R is not available on your system!"
   currentpkg="your"
 fi
-echo ">>  "
+echo ""
 
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-echo ">>  Updating semantic versioning and date..."
+echo ">> Updating semantic versioning and date..."
 
 # get tags from remote, and remove tags not on remote:
 git fetch origin --prune --prune-tags --quiet

.github/workflows/check.yaml

@@ -130,7 +130,7 @@ jobs:
           _R_CHECK_LENGTH_1_CONDITION_: verbose
           _R_CHECK_LENGTH_1_LOGIC2_: verbose
           # no check for old R versions - these packages require higher R versions
-          _R_CHECK_RD_XREFS_: {{ matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' && matrix.config.r != '3.3' && matrix.config.r != '3.4' }}
+          _R_CHECK_RD_XREFS_: ${{ matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2' && matrix.config.r != '3.3' && matrix.config.r != '3.4' }}
           _R_CHECK_FORCE_SUGGESTS_: false
           R_CHECK_CONSTANTS: 5
           R_JIT_STRATEGY: 3

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.1.9042
+Version: 1.8.1.9043
 Date: 2022-08-28
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.8.1.9042
+# AMR 1.8.1.9043
 
 ### 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.
@@ -21,6 +21,7 @@
 * All data sets in this package are now exported as `tibble`, instead of base R `data.frame`s. Older R versions are still supported.
 * Automatic language determination will give a note once a session
 * For all interpretation guidelines using `as.rsi()` on amoxicillin, the rules for ampicillin will be used if amoxicillin rules are not available
+* Fix for using `ab_atc()` on non-existing ATC codes
 
 ### Other
 * New website to make use of the new Bootstrap 5 and pkgdown v2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions

R/ab.R

@@ -125,6 +125,7 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   x <- unique(x_bak_clean) # this means that every x is in fact generalise_antibiotic_name(x)
   x_new <- rep(NA_character_, length(x))
   x_unknown <- character(0)
+  x_unknown_ATCs <- character(0)
 
   note_if_more_than_one_found <- function(found, index, from_text) {
     if (initial_search == TRUE & isTRUE(length(from_text) > 1)) {
@@ -183,6 +184,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
       x_unknown <- c(x_unknown, x_bak[x[i] == x_bak_clean][1])
       next
     }
+    if (x[i] %like_case% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]") {
+      # seems an ATC code, but the available ones are in `already_known`, so:
+      x_unknown <- c(x_unknown, x[i])
+      x_unknown_ATCs <- c(x_unknown_ATCs, x[i])
+      x_new[i] <- NA_character_
+      next
+    }
 
     if (fast_mode == FALSE && flag_multiple_results == TRUE && x[i] %like% "[ ]") {
       from_text <- tryCatch(suppressWarnings(ab_from_text(x[i], initial_search = FALSE, translate_ab = FALSE)[[1]]),
@@ -474,16 +482,15 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
   }
 
   # take failed ATC codes apart from rest
-  x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
-  x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
-  if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
+  if (length(x_unknown_ATCs) > 0 && fast_mode == FALSE) {
     warning_(
       "in `as.ab()`: these ATC codes are not (yet) in the antibiotics data set: ",
       vector_and(x_unknown_ATCs), "."
     )
   }
+  x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
 
-  if (length(x_unknown) > 0 & fast_mode == FALSE) {
+  if (length(x_unknown) > 0 && fast_mode == FALSE) {
     warning_(
       "in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
       vector_and(x_unknown), "."

R/ab_property.R

@@ -457,7 +457,11 @@ ab_validate <- function(x, property, ...) {
 
     if (!all(x %in% AB_lookup[, property, drop = TRUE])) {
       x <- as.ab(x, ...)
-      x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
+      if (all(is.na(x)) && is.list(AB_lookup[, property, drop = TRUE])) {
+        x <- rep(NA_character_, length(x))
+      } else {
+        x <- AB_lookup[match(x, AB_lookup$ab), property, drop = TRUE]
+      }
     }
   }