fixes

R/interpretive_rules.R

@@ -200,6 +200,12 @@ interpretive_rules <- function(x,
 
   add_MO_lookup_to_AMR_env()
 
+  if (guideline %like% "EUCAST") {
+    guideline <- "EUCAST"
+  } else if (guideline %like% "CLSI") {
+    guideline <- "CLSI"
+  }
+
   if ("custom" %in% rules && is.null(custom_rules)) {
     warning_("in {.help [{.fun interpretive_rules}](AMR::interpretive_rules)}: no custom rules were set with the {.arg custom_rules} argument",
       immediate = TRUE
@@ -619,18 +625,9 @@ interpretive_rules <- function(x,
   } else if (!is.null(list(...)$eucast_rules_df)) {
     # deprecated parameter name kept for backward compatibility
     interpretive_rules_df_total <- list(...)$eucast_rules_df
-  } else if (exists("INTERPRETIVE_RULES_DF", envir = asNamespace("AMR"), inherits = FALSE)) {
+  } else {
     # internal data file, created in data-raw/_pre_commit_checks.R
     interpretive_rules_df_total <- INTERPRETIVE_RULES_DF
-  } else {
-    # transitional fallback: sysdata.rda predates the rename from EUCAST_RULES_DF
-    # re-run data-raw/_pre_commit_checks.R to regenerate sysdata.rda
-    interpretive_rules_df_total <- EUCAST_RULES_DF
-    interpretive_rules_df_total$rule.provider <- "EUCAST"
-    interpretive_rules_df_total <- interpretive_rules_df_total[
-      , c("rule.provider", setdiff(colnames(interpretive_rules_df_total), "rule.provider")),
-      drop = FALSE
-    ]
   }
 
   ## filter on guideline provider and user-set guideline versions ----

tests/testthat/test-_deprecated.R

@@ -32,4 +32,11 @@ test_that("test-_deprecated.R", {
 
   expect_warning(example_isolates[, ab_class("mycobact")])
   expect_warning(example_isolates[, ab_selector(name %like% "trim")])
+
+  # deprecated custom_interpretive_rules() still works and emits a warning
+  expect_warning(
+    x_old <- custom_eucast_rules(AMC == "R" ~ aminopenicillins == "R"),
+    regexp = "custom_eucast_rules"
+  )
+  expect_inherits(x_old, "custom_interpretive_rules")
 })

tests/testthat/test-data.R

@@ -53,12 +53,12 @@ test_that("test-data.R", {
   expect_false(anyNA(microorganisms.codes$mo))
   expect_true(all(dosage$ab %in% AMR::antimicrobials$ab))
   expect_true(all(dosage$name %in% AMR::antimicrobials$name))
-  eucast_abx <- AMR:::EUCAST_RULES_DF$and_these_antibiotics
+  interpretive_abx <- AMR:::INTERPRETIVE_RULES_DF$and_these_antibiotics
-  eucast_abx <- unique(unlist(strsplit(eucast_abx[!is.na(eucast_abx)], ", +")))
+  interpretive_abx <- unique(unlist(strsplit(interpretive_abx[!is.na(interpretive_abx)], ", +")))
-  expect_true(all(eucast_abx %in% AMR::antimicrobials$ab),
+  expect_true(all(interpretive_abx %in% AMR::antimicrobials$ab),
     info = paste0(
       "Missing in `antimicrobials` data set: ",
-      toString(eucast_abx[which(!eucast_abx %in% AMR::antimicrobials$ab)])
+      toString(interpretive_abx[which(!interpretive_abx %in% AMR::antimicrobials$ab)])
     )
   )
 

tests/testthat/test-interpretive_rules.R

@@ -242,13 +242,6 @@ test_that("test-interpretive_rules.R", {
     tolerance = 0.5
   )
 
-  # deprecated custom_interpretive_rules() still works and emits a warning
-  expect_warning(
-    x_old <- custom_interpretive_rules(AMC == "R" ~ aminopenicillins == "R"),
-    regexp = "custom_interpretive_rules"
-  )
-  expect_inherits(x_old, "custom_interpretive_rules")
-
   # clsi_rules() no longer errors (returns data unchanged until CLSI rows are added)
   expect_identical(
     suppressWarnings(clsi_rules(example_isolates, info = FALSE)),