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

CLAUDE.md

@@ -148,24 +148,34 @@ Version format: `major.minor.patch.dev` (e.g., `3.0.1.9021`)
 
 ### Version and date bump required for every PR
 
-Before opening a pull request, always increment the four-digit dev counter by 1 in **both** of these files:
+All PRs are **squash-merged**, so each PR lands as exactly **one commit** on the default branch. Version numbers are kept in sync with the cumulative commit count since the last released tag. Therefore **exactly one version bump is allowed per PR**, regardless of how many intermediate commits are made on the branch.
 
-1. **`DESCRIPTION`** — the `Version:` field:
+#### Computing the correct version number
-   ```
-   Version: 3.0.1.9021  →  Version: 3.0.1.9022
-   ```
 
-2. **`NEWS.md`** — the top-level heading:
+Run the following from the repo root to determine the version string to use:
-   ```
-   # AMR 3.0.1.9021  →  # AMR 3.0.1.9022
-   ```
 
-Read the current version from `DESCRIPTION`, add 1 to the last numeric component, and write the new version to both files in the same commit as the rest of the PR changes.
+```bash
+currenttag=$(git describe --tags --abbrev=0 | sed 's/v//')
+currenttagfull=$(git describe --tags --abbrev=0)
+defaultbranch=$(git branch | cut -c 3- | grep -E '^master$|^main$')
+currentcommit=$(git rev-list --count ${currenttagfull}..${defaultbranch})
+currentversion="${currenttag}.$((currentcommit + 9001 + 1))"
+echo "$currentversion"
+```
 
-Also bump the date to the current date in **`DESCRIPTION`**, where it's in the `Date:` field in ISO format:
+The `+ 1` accounts for the fact that this PR's squash commit is not yet on the default branch. Set **both** of these files to the resulting version string (and only once per PR, even across multiple commits):
+
+1. **`DESCRIPTION`** — the `Version:` field
+2. **`NEWS.md`** — the top-level heading `# AMR <version>`
+
+If `git describe` fails (e.g. no tags exist in the environment), fall back to reading the current version from `DESCRIPTION` and adding 1 to the last numeric component — but only if no bump has already been made in this PR.
+
+#### Date field
+
+The `Date:` field in `DESCRIPTION` must reflect the date of the **last commit to the PR** (not the first), in ISO format. Update it with every commit so it is always current:
 
 ```
-Date: 2025-12-31
+Date: 2026-03-07
 ```
 
 ## Internal State

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9028
+Version: 3.0.1.9029
-Date: 2026-03-06
+Date: 2026-03-07
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9028
+# AMR 3.0.1.9029
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -18,6 +18,9 @@
 * Two new `NA` objects, `NA_ab_` and `NA_mo_`, analogous to base R's `NA_character_` and `NA_integer_`, for use in pipelines that require typed missing values
 
 ### Fixes
+* `mdro()`: when a base beta-lactam drug column is missing but a corresponding drug+inhibitor combination is present in the data and resistant (e.g., piperacillin/tazobactam = R while piperacillin is absent), the base drug is now correctly inferred as resistant. This ensures MDRO classification is not missed due to test-ordering differences in the laboratory. The reverse direction is also valid: susceptibility in a combination does not imply susceptibility in the base drug (the inhibitor may be responsible), so only resistance is propagated. Closes #209
+* Fixed a bug in `as.sir()` where values that were purely numeric (e.g., `"1"`) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter
+* Fixed a bug in `as.mic()` where MIC values in scientific notation (e.g., `"1e-3"`) were incorrectly handled because the letter `e` was removed along with other Unicode letters; scientific notation `e` is now preserved
 * Fixed a bug in `as.ab()` where certain AB codes containing "PH" or "TH" (such as `ETH`, `MTH`, `PHE`, `PHN`, `STH`, `THA`, `THI1`) would incorrectly return `NA` when combined in a vector with any untranslatable value (#245)
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
 * Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `I`,  and `R` would not be considered (#244)

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)

R/mic.R

@@ -217,9 +217,9 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all", round_to_next_log2
     warning_("Some MICs were combined values, only the first values are kept")
     x[x %like% "[0-9]/.*[0-9]"] <- gsub("/.*", "", x[x %like% "[0-9]/.*[0-9]"])
   }
-  x <- trimws2(gsub("[\\p{L}]", "", x, perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
+  x <- trimws2(gsub("[^e\\P{L}]", "", x, perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
   # remove other invalid characters
-  x <- gsub("[^0-9.><= -]+", "", x, perl = TRUE)
+  x <- gsub("[^0-9e.><= -]+", "", x, perl = TRUE)
   # transform => to >= and =< to <=
   x <- gsub("=<", "<=", x, fixed = TRUE)
   x <- gsub("=>", ">=", x, fixed = TRUE)

R/sir.R

@@ -568,7 +568,7 @@ as.sir.default <- function(x,
     x[x %like% "dose"] <- "SDD"
     mtch <- grepl(paste0("(", S, "|", I, "|", R, "|", NI, "|", SDD, "|", WT, "|", NWT, "|", NS, "|[A-Z]+)"), x, perl = TRUE)
     x[!mtch] <- ""
-    x[mtch] <- trimws2(gsub("[^\\p{L}]", "", x[mtch], perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
+    x[mtch & x %unlike% "^[0-9+]$"] <- trimws2(gsub("[^\\p{L}]", "", x[mtch & x %unlike% "^[0-9+]$"], perl = TRUE)) # \p{L} is the Unicode category for all letters, including those with diacritics
     # apply regexes set by user
     x[x %like% S] <- "S"
     x[x %like% I] <- "I"

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"))
 })