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
* fix: restore valid AB codes mangled by generalise_antibiotic_name() (#245)
When as.ab() received a vector containing both valid AB codes (like ETH,
PHN, PHE, STH, THA, MTH, THI1) and an untranslatable value, the fast
path at line 100 was skipped. The slow path then applied
generalise_antibiotic_name(), which rewrites "TH"->"T" and "PH"->"F",
mangling these short AB codes (e.g. ETH->"ET", PHN->"FN") so they could
no longer be found in the lookup table.
Fix: save the pre-generalised values before applying
generalise_antibiotic_name(), then restore any elements that were already
valid AB codes in their original form.
https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9
* fix: use toupper() in AB code restoration to handle lowercase input (#245)
Ensures that lowercase user input (e.g. 'eth', 'phn') is matched
case-insensitively against the uppercase AB codes in $ab, and that
the restored value is stored in uppercase to match the lookup table.
https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9
* revert: remove unnecessary toupper() since x is already uppercased
https://claude.ai/code/session_01Sujw89qa48NoUmMPDBJLz9
* Revise versioning and date bump requirements for PRs
Updated versioning instructions for pull requests to include date bump.
---------
Co-authored-by: Claude <noreply@anthropic.com>
* add CLAUDE.md with project context for Claude Code
Provides development commands, architecture overview, file conventions,
custom S3 classes, data files, testing setup, and versioning guidelines
to help Claude Code assist effectively in this repository.
https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx
* add CLAUDE.md to .Rbuildignore
Excludes the Claude Code context file from the R package build tarball.
https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx
* document version-bump requirement for every PR in CLAUDE.md
Each PR must increment the .9zzz dev counter by 1 in both
DESCRIPTION (Version: field) and NEWS.md (top-level heading).
https://claude.ai/code/session_01L3fTxqsg3Gc6J1znpWN1Mx
---------
Co-authored-by: Claude <noreply@anthropic.com>
