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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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Claude
2026-03-06 19:16:21 +00:00
parent daab605ca4
commit 485ae25e09
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Package: AMR
Version: 3.0.1.9028
Version: 3.0.1.9029
Date: 2026-03-06
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)