Fix custom reference_data support in as.sir() (fixes #239)

- custom guideline names now correctly classify values as R: CLSI convention
  (>= breakpoint_R for MIC, <= for disk) applies only when guideline contains
  "CLSI"; all other guidelines including custom ones use the EUCAST convention
  (> breakpoint_R for MIC, < for disk)
- guideline argument is now optional when reference_data is manually set: if
  omitted or if its value does not match any row in the custom data, all rows
  in reference_data are used; if set to a value present in the data, only
  matching rows are filtered — useful for multi-guideline custom tables
- host = NA in custom reference_data now acts as a host-agnostic fallback
  when no host-specific breakpoint row exists for the current animal species
- updated reference_data argument documentation to explain these conventions

https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U

tests/testthat/test-sir.R

@@ -529,3 +529,51 @@ test_that("test-sir.R", {
     expect_lte(n_mentions, 1L)
   }
 })
+
+# 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
+  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$breakpoint_R <- 32
+
+  # guideline omitted: all rows in reference_data are used
+  expect_equal(as.character(suppressMessages(
+    as.sir(as.mic(64), mo = "E. coli", ab = "AMC", reference_data = my_bp)
+  )), "R")
+  expect_equal(as.character(suppressMessages(
+    as.sir(as.mic(16), mo = "E. coli", ab = "AMC", reference_data = my_bp)
+  )), "I")
+  # at R breakpoint value must be I (open interval: > not >=)
+  expect_equal(as.character(suppressMessages(
+    as.sir(as.mic(32), mo = "E. coli", ab = "AMC", reference_data = my_bp)
+  )), "I")
+
+  # guideline explicitly set: same result when it matches the data
+  expect_equal(as.character(suppressMessages(
+    as.sir(as.mic(64), mo = "E. coli", ab = "AMC",
+      guideline = "MyLab 2025", reference_data = my_bp)
+  )), "R")
+})
+
+test_that("custom reference_data: host = NA acts as host-agnostic fallback", {
+  my_bp <- clinical_breakpoints[clinical_breakpoints$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$breakpoint_S <- 8
+  my_bp$breakpoint_R <- 32
+
+  # 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)
+  )
+  expect_equal(as.character(result), "R")
+})