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Author	SHA1	Message	Date
Claude	83fcb1a224	Fix version to single bump (9029) and update CLAUDE.md versioning rules ... CLAUDE.md: Rewrite the "Version and date bump" subsection to document that: - Exactly ONE version bump is allowed per PR (PRs are squash-merged into one commit on the default branch, so one commit = one version increment) - The correct version is computed from git history: currentversion="${currenttag}.$((commits_since_tag + 9001 + 1))" with the +1 accounting for the PR's own squash commit not yet on the default branch - Fall back to incrementing DESCRIPTION's version by 1 if git describe fails - The Date: field tracks the date of the *last* PR commit (updated each time) DESCRIPTION / NEWS.md: Correct the version from 3.0.1.9030 back to 3.0.1.9029. Two version bumps were made across two commits in this PR; since it will be squash-merged as one commit only one bump is correct. Also update Date to today (2026-03-07). https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG	2026-03-07 13:55:03 +00:00
Claude	c500fdb645	Add sir.R/mic.R fixes and mdro() unit tests; bump to 3.0.1.9030 ... R/sir.R (line 571): Guard purely numeric strings (e.g. "1", "8") from the Unicode letter filter. Values matching the broad SIR regex but consisting only of digits must not be stripped; add `x %unlike% "^[0-9+]$"` predicate. R/mic.R (lines 220-222): Preserve the letter 'e' during Unicode-letter removal so that MIC values in scientific notation (e.g. "1e-3", "2.5e-2") survive the cleaning step. - Line 220: [\\p{L}] → [^e\\P{L}] (remove all letters except 'e') - Line 222: [^0-9.><= -]+ → [^0-9e.><= -]+ (allow 'e' in whitelist) tests/testthat/test-mdro.R: New tests for the drug+inhibitor inference added in the previous commit (issue #209): - TZP=R with no PIP column → PIP inferred R → MDRO class elevated - TZP=S with no PIP column → proxy col is NA (not S) → class lower - verbose mode emits "Inferring resistance" message - AMC=R with no AMX column runs without error (Enterococcus faecium) https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG	2026-03-07 13:43:21 +00:00
Claude	485ae25e09	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	2026-03-06 19:16:21 +00:00