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mdro(): infer base drug resistance from drug+inhibitor combination columns (#209)
When a base beta-lactam column (e.g., piperacillin/PIP) is absent but a corresponding drug+inhibitor combination (e.g., piperacillin/tazobactam/TZP) is present and resistant, resistance in the base drug is now correctly inferred. This is clinically sound: resistance in a combination implies the inhibitor provided no benefit, so the base drug is also resistant. Susceptibility in a combination is NOT propagated to the base drug (the inhibitor may be responsible for susceptibility), so only R values are inferred; missing base drugs remain NA otherwise. Implementation details: - Uses AB_BETALACTAMS_WITH_INHIBITOR to identify all beta-lactam+inhibitor combinations present in the user's data - Derives base drug AB codes by stripping the "/inhibitor" part from names - Creates synthetic proxy columns (.sir_proxy_<AB>) in x, set to "R" when any matching combination is R, otherwise NA - Proxy columns are added to cols_ab before drug variable assignment, so all existing guideline logic benefits without any changes - Multiple combos for the same base drug are OR-ed (any R → R) - Adds internal ab_without_inhibitor() helper for the name->base mapping - Verbose mode reports which combinations are used for inference Bumps version: 3.0.1.9028 -> 3.0.1.9029 https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG
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Package: AMR
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Version: 3.0.1.9028
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Version: 3.0.1.9029
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Date: 2026-03-06
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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