mdro(): infer base drug resistance from drug+inhibitor combination co… (#263)

* 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

* 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

* 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

* Fix stats::setNames, test accessor bug, and version script verification

R/mdro.R:
  Qualify setNames() as stats::setNames() in the drug+inhibitor inference
  block to satisfy R CMD CHECK's global-function checks.

tests/testthat/test-mdro.R:
  mdro() with verbose=FALSE returns an atomic ordered factor, not a
  data.frame. Fix three test errors introduced in the previous commit:
  - Line 320: result_no_pip$MDRO -> result_no_pip (factor, no $ accessor)
  - Line 328: result_tzp_s$MDRO / result_no_pip$MDRO -> direct factor refs
  - Line 347: expect_inherits(..., "data.frame") -> c("factor","ordered")
  Also fix the comment on line 347 to match the actual return type.

Version: confirmed at 3.0.1.9029 (no further bump; one bump already made
this PR). git describe failed (no tags in dev environment) — fallback
applies. The +1 in CLAUDE.md's formula is correct for tagged repos:
currentcommit + 9001 + 1 = 27 + 9001 + 1 = 9029 ✓

https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG

* Fix unit tests: use mrgn guideline and expect_message() for proxy tests

Three failures corrected:

1. Classification tests (lines 321, 329): The EUCAST guideline for
   P. aeruginosa already has OR logic (PIP OR TZP), so TZP=R alone
   satisfies it regardless of whether the PIP proxy exists. Switch to
   guideline="mrgn": the MRGN 4MRGN criterion for P. aeruginosa
   requires PIP=R explicitly (lines 1488-1496 of mdro.R), with no TZP
   fallback. Without the proxy: PIP missing -> not 4MRGN -> level 1.
   With the proxy (TZP=R infers PIP=R): 4MRGN reached -> level 3.
   The TZP=S case leaves proxy=NA, so PIP is still absent effectively
   -> level 1, which is < level 3 as expected.

2. Verbose/message test (line 335): message_() routes through message()
   to stderr, not cat() to stdout. expect_output() only captures stdout
   so it always saw nothing. Fix: use expect_message() instead, and
   remove the inner suppressMessages() that was swallowing the message
   before expect_message() could capture it.

Also trim two stale lines left over from the old expect_output block.

https://claude.ai/code/session_01Cp154UtssHg84bw38xiiTG

---------

Co-authored-by: Claude <noreply@anthropic.com>

tests/testthat/test-mdro.R

@@ -296,4 +296,50 @@ test_that("test-mdro.R", {
     expect_output(x <- mdro(example_isolates %>% group_by(ward), info = TRUE, pct_required_classes = 0))
     expect_output(x <- mdro(example_isolates %>% group_by(ward), guideline = custom, info = TRUE))
   }
+
+  # drug+inhibitor inference for missing base drug columns (issue #209) -------
+  # Resistance in drug+inhibitor implies resistance in the base drug.
+  # MRGN guideline is used because it explicitly requires PIP=R (not PIP OR TZP)
+  # for Pseudomonas aeruginosa 4MRGN, making the proxy effect directly testable.
+  pseud_no_pip <- data.frame(
+    mo  = as.mo("Pseudomonas aeruginosa"),
+    TZP = as.sir("R"), # piperacillin/tazobactam; no PIP column
+    CAZ = as.sir("R"),
+    IPM = as.sir("R"),
+    MEM = as.sir("R"),
+    CIP = as.sir("R"),
+    stringsAsFactors = FALSE
+  )
+  # Inference message goes to message() / stderr, not stdout
+  # -> must use expect_message(), NOT expect_output()
+  expect_message(
+    suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE, verbose = TRUE)),
+    "Inferring resistance"
+  )
+  # With TZP=R, PIP is inferred R -> 4MRGN criteria met -> level 3 (> 1)
+  result_no_pip <- suppressMessages(suppressWarnings(
+    mdro(pseud_no_pip, guideline = "mrgn", info = FALSE)
+  ))
+  expect_true(as.integer(result_no_pip) > 1L)
+  # Susceptibility in combo does NOT propagate: proxy = NA, not S
+  # -> 4MRGN criteria no longer met -> lower level than when TZP=R
+  pseud_tzp_s <- pseud_no_pip
+  pseud_tzp_s$TZP <- as.sir("S")
+  result_tzp_s <- suppressMessages(suppressWarnings(
+    mdro(pseud_tzp_s, guideline = "mrgn", info = FALSE)
+  ))
+  expect_true(as.integer(result_tzp_s) < as.integer(result_no_pip))
+
+  # Multiple combos for the same base drug: AMX can come from AMC (amoxicillin/clavulanic acid)
+  ente_no_amx <- data.frame(
+    mo  = as.mo("Enterococcus faecium"),
+    AMC = as.sir("R"), # amoxicillin/clavulanic acid; no AMX column
+    VAN = as.sir("R"),
+    TEC = as.sir("R"),
+    LNZ = as.sir("R"),
+    DAP = as.sir("R"),
+    stringsAsFactors = FALSE
+  )
+  # Should run without error and return an ordered factor; AMX inferred R from AMC
+  expect_inherits(suppressMessages(suppressWarnings(mdro(ente_no_amx, guideline = "EUCAST", info = FALSE))), c("factor", "ordered"))
 })