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>

R/mdro.R

@@ -480,6 +480,50 @@ mdro <- function(x = NULL,
   }
   cols_ab <- cols_ab[!duplicated(cols_ab)]
 
+  # Infer resistance for missing base drugs from available drug+inhibitor combination columns.
+  # Clinical principle: resistance in drug+inhibitor (e.g., piperacillin/tazobactam = R)
+  # always implies resistance in the base drug (e.g., piperacillin = R), because the
+  # enzyme inhibitor adds nothing when the organism is truly resistant to the base drug.
+  # NOTE: susceptibility in a combination does NOT imply susceptibility in the base drug
+  # (the inhibitor may be responsible), so synthetic proxy columns only propagate R, not S/I.
+  .combos_in_data <- AB_BETALACTAMS_WITH_INHIBITOR[AB_BETALACTAMS_WITH_INHIBITOR %in% names(cols_ab)]
+  if (length(.combos_in_data) > 0) {
+    .base_drugs <- suppressMessages(
+      as.ab(gsub("/.*", "", ab_name(as.character(.combos_in_data), language = NULL)))
+    )
+    .unique_bases <- unique(.base_drugs[!is.na(.base_drugs)])
+    for (.base in .unique_bases) {
+      .base_code <- as.character(.base)
+      if (!.base_code %in% names(cols_ab)) {
+        # Base drug column absent; find all available combo columns for this base drug
+        .combos <- .combos_in_data[!is.na(.base_drugs) & as.character(.base_drugs) == .base_code]
+        .combo_cols <- unname(cols_ab[as.character(.combos)])
+        .combo_cols <- .combo_cols[!is.na(.combo_cols)]
+        if (length(.combo_cols) > 0) {
+          # Vectorised: if ANY combination is R, infer base drug as R; otherwise NA
+          .sir_chars <- as.data.frame(
+            lapply(x[, .combo_cols, drop = FALSE], function(col) as.character(as.sir(col))),
+            stringsAsFactors = FALSE
+          )
+          .new_col <- paste0(".sir_proxy_", .base_code)
+          x[[.new_col]] <- ifelse(rowSums(.sir_chars == "R", na.rm = TRUE) > 0L, "R", NA_character_)
+          cols_ab <- c(cols_ab, stats::setNames(.new_col, .base_code))
+          if (isTRUE(verbose)) {
+            message_(
+              "Inferring resistance for ", ab_name(.base_code, language = NULL),
+              " from available drug+inhibitor combination(s): ",
+              paste(ab_name(as.character(.combos), language = NULL), collapse = ", "),
+              " (resistance in a combination always implies resistance in the base drug)",
+              add_fn = font_blue
+            )
+          }
+        }
+      }
+    }
+    cols_ab <- cols_ab[!duplicated(names(cols_ab))]
+  }
+  rm(list = intersect(ls(), c(".combos_in_data", ".base_drugs", ".unique_bases", ".base", ".base_code", ".combos", ".combo_cols", ".sir_chars", ".new_col")))
+
   # nolint start
   AMC <- cols_ab["AMC"]
   AMK <- cols_ab["AMK"]
@@ -674,6 +718,16 @@ mdro <- function(x = NULL,
     x
   }
 
+  ab_without_inhibitor <- function(ab_codes) {
+    # Get the base drug AB code from a drug+inhibitor combination.
+    # e.g., AMC (amoxicillin/clavulanic acid)  -> AMX (amoxicillin)
+    #        TZP (piperacillin/tazobactam)      -> PIP (piperacillin)
+    #        SAM (ampicillin/sulbactam)          -> AMP (ampicillin)
+    combo_names <- ab_name(ab_codes, language = NULL)
+    base_names <- gsub("/.*", "", combo_names)
+    suppressMessages(as.ab(base_names))
+  }
+
   # antimicrobial classes
   # nolint start
   aminoglycosides <- c(TOB, GEN)