Fix unit tests for custom reference_data (#239)

- Do not override my_bp$mo / my_bp$ab in tests: assigning plain character
  strips the <mo>/<ab> class, which check_reference_data() rejects. Use the
  mo/ab values already present in the source row instead.
- Use NA_character_ instead of NA for my_bp$host so the host column keeps
  its character class.
- Pass breakpoint_type = "animal" explicitly in the host-fallback test since
  the custom reference_data only contains animal-type breakpoints.

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

tests/testthat/test-sir.R

@@ -532,30 +532,32 @@ test_that("test-sir.R", {
 
 # issue #239 — custom reference_data support
 test_that("custom reference_data: non-EUCAST/CLSI guideline produces R", {
-  # use any MIC/human row as structural template, then override mo/ab/guideline/breakpoints
+  # Take the first MIC/human row (B_ACHRMB_XYLS / MEM) as a template.
+  # Only override guideline and breakpoints; keep mo/ab as <mo>/<ab> class objects.
   my_bp <- clinical_breakpoints[clinical_breakpoints$method == "MIC" &
     clinical_breakpoints$type == "human", ][1, ]
   my_bp$guideline    <- "MyLab 2025"
-  my_bp$mo           <- "B_ESCHR_COLI"
-  my_bp$ab           <- "AMC"
   my_bp$breakpoint_S <- 8
   my_bp$breakpoint_R <- 32
 
-  # guideline omitted: all rows in reference_data are used
+  mo_val <- as.character(my_bp$mo)  # "B_ACHRMB_XYLS"
+  ab_val <- as.character(my_bp$ab)  # "MEM"
+
+  # guideline omitted: all rows in reference_data are used; R via open interval (>)
   expect_equal(as.character(suppressMessages(
-    as.sir(as.mic(64), mo = "E. coli", ab = "AMC", reference_data = my_bp)
+    as.sir(as.mic(64), mo = mo_val, ab = ab_val, reference_data = my_bp)
   )), "R")
   expect_equal(as.character(suppressMessages(
-    as.sir(as.mic(16), mo = "E. coli", ab = "AMC", reference_data = my_bp)
+    as.sir(as.mic(16), mo = mo_val, ab = ab_val, reference_data = my_bp)
   )), "I")
   # at R breakpoint value must be I (open interval: > not >=)
   expect_equal(as.character(suppressMessages(
-    as.sir(as.mic(32), mo = "E. coli", ab = "AMC", reference_data = my_bp)
+    as.sir(as.mic(32), mo = mo_val, ab = ab_val, reference_data = my_bp)
   )), "I")
 
   # guideline explicitly set: same result when it matches the data
   expect_equal(as.character(suppressMessages(
-    as.sir(as.mic(64), mo = "E. coli", ab = "AMC",
+    as.sir(as.mic(64), mo = mo_val, ab = ab_val,
       guideline = "MyLab 2025", reference_data = my_bp)
   )), "R")
 })
@@ -564,16 +566,18 @@ test_that("custom reference_data: host = NA acts as host-agnostic fallback", {
   my_bp <- clinical_breakpoints[clinical_breakpoints$method == "MIC" &
     clinical_breakpoints$type == "human", ][1, ]
   my_bp$guideline    <- "MyLab 2025"
-  my_bp$mo           <- "B_ESCHR_COLI"
-  my_bp$ab           <- "AMC"
   my_bp$type         <- "animal"
-  my_bp$host         <- NA
+  my_bp$host         <- NA_character_  # must stay character class, not logical NA
   my_bp$breakpoint_S <- 8
   my_bp$breakpoint_R <- 32
 
+  mo_val <- as.character(my_bp$mo)
+  ab_val <- as.character(my_bp$ab)
+
   # NA host should match when no species-specific row exists; guideline omitted
   result <- suppressMessages(
-    as.sir(as.mic(64), mo = "E. coli", ab = "AMC", host = "dogs", reference_data = my_bp)
+    as.sir(as.mic(64), mo = mo_val, ab = ab_val,
+      host = "dogs", breakpoint_type = "animal", reference_data = my_bp)
   )
   expect_equal(as.character(result), "R")
 })