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
c43339d6ed