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Author	SHA1	Message	Date
Claude	ba09fba08b	Add coerce_reference_data_columns() for lenient reference_data validation ... check_reference_data() now returns the (possibly coerced) reference_data and the call site captures the result so downstream code sees the fixed columns. A new coerce_reference_data_columns() helper is called before the strict class check inside check_reference_data(). It coerces columns to the expected types: - mo -> as.mo() if not already <mo> class - ab -> as.ab() if not already <ab> class - character columns -> as.character() (e.g. host = NA becomes NA_character_) - numeric columns -> as.double() - logical columns -> as.logical() This allows users to build a custom reference_data from a plain data.frame without having to pre-apply as.mo()/as.ab() or worry about NA column types. Updated the reference_data roxygen argument to document the auto-coercion and restored the tests to the simpler form that uses plain character assignments, relying on the new coercion instead of workarounds. https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U	2026-04-25 12:09:22 +00:00
Claude	7277534d40	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	2026-04-25 11:37:32 +00:00
Claude	c43339d6ed	Refactor R-classification logic using custom_breakpoints_set flag ... Introduce custom_breakpoints_set <- !identical(reference_data, AMR::clinical_breakpoints) at the top of as_sir_method() and replace all identical() calls inside that function with this variable. In the case_when_AMR interpretation blocks (MIC and disk), the R-classification now has three explicit arms: - !custom_breakpoints_set & EUCAST guideline -> open interval (> / <) - !custom_breakpoints_set & CLSI guideline -> closed interval (>= / <=) - custom_breakpoints_set -> open interval (> / <), always, regardless of the guideline name in the custom data (e.g. "CLSI_custom" must not accidentally trigger CLSI convention) https://claude.ai/code/session_01Q8KtFFGG9qrjAgLJBbxG2U	2026-04-25 08:50:33 +00:00
Claude	6ef7441d51	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	2026-04-25 08:20:40 +00:00