(v3.0.1.9031) fix MDRO for non-RStudio terminal

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9030
+Version: 3.0.1.9031
-Date: 2026-03-07
+Date: 2026-03-08
 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 3.0.1.9030
+# AMR 3.0.1.9031
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -18,7 +18,6 @@
 * 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)
@@ -31,6 +30,7 @@
 * Fixed SIR and MIC coercion of combined values, e.g. `as.sir("<= 0.002; S") ` or `as.mic("S; 0.002")` (#252)
 
 ### Updates
+* `mdro()` now infers resistance for a _missing_ base drug column from an _available_ corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument `infer_from_combinations`, which defaults to `TRUE` (#209). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).
 * `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
 * `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
 * `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)

R/aa_helper_functions.R

@@ -387,6 +387,10 @@ import_fn <- function(name, pkg, error_on_fail = TRUE) {
   if (isTRUE(error_on_fail)) {
     stop_ifnot_installed(pkg)
   }
+  if (pkg == "rstudioapi" && tryCatch(!rstudioapi::isAvailable(), error = function(e) TRUE)) {
+    # only allow rstudioapi to be imported if RStudio is available
+    return(NULL)
+  }
   tryCatch(
     # don't use get() to avoid fetching non-API functions
     getExportedValue(name = name, ns = asNamespace(pkg)),
@@ -1220,10 +1224,14 @@ try_colour <- function(..., before, after, collapse = " ") {
   }
 }
 is_dark <- function() {
-  AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
+  AMR_env$current_theme <- NULL
+  current_theme_fn <- import_fn("getThemeInfo", "rstudioapi", error_on_fail = FALSE)
+  if (!is.null(current_theme_fn)) {
+    AMR_env$current_theme <- current_theme_fn()$editor
+  }
   if (!identical(AMR_env$current_theme, AMR_env$former_theme) || is.null(AMR_env$is_dark_theme)) {
     AMR_env$former_theme <- AMR_env$current_theme
-    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) TRUE)
+    AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(current_theme_fn()$dark), error = function(e) TRUE)
   }
   isTRUE(AMR_env$is_dark_theme)
 }

R/mdro.R

@@ -31,7 +31,7 @@
 #'
 #' Determine which isolates are multidrug-resistant organisms (MDRO) according to international, national, or custom guidelines.
 #' @param x A [data.frame] with antimicrobials columns, like `AMX` or `amox`. Can be left blank for automatic determination.
-#' @param guideline A specific guideline to follow, see sections *Supported international / national guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
+#' @param guideline A specific guideline to follow, see sections *Supported International / National Guidelines* and *Using Custom Guidelines* below. When left empty, the publication by Magiorakos *et al.* (see below) will be followed.
 #' @param esbl [logical] values, or a column name containing logical values, indicating the presence of an ESBL gene (or production of its proteins).
 #' @param carbapenemase [logical] values, or a column name containing logical values, indicating the presence of a carbapenemase gene (or production of its proteins).
 #' @param mecA [logical] values, or a column name containing logical values, indicating the presence of a *mecA* gene (or production of its proteins).
@@ -42,6 +42,7 @@
 #' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
 #' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
 #' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
+#' @param infer_from_combinations A [logical] to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does **not** imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to `TRUE`.
 #' @details
 #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
 #'
@@ -143,6 +144,7 @@ mdro <- function(x = NULL,
                  combine_SI = TRUE,
                  verbose = FALSE,
                  only_sir_columns = any(is.sir(x)),
+                 infer_from_combinations = TRUE,
                  ...) {
   if (is_null_or_grouped_tbl(x)) {
     # when `x` is left blank, auto determine it (get_current_data() searches underlying data within call)
@@ -165,7 +167,7 @@ mdro <- function(x = NULL,
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
   meet_criteria(verbose, allow_class = "logical", has_length = 1)
   meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
-
+  meet_criteria(infer_from_combinations, allow_class = "logical", has_length = 1)
 
   if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
     stop_("There were no SIR columns found in the data set, despite `only_sir_columns` being `TRUE`. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
@@ -480,49 +482,51 @@ mdro <- function(x = NULL,
   }
   cols_ab <- cols_ab[!duplicated(cols_ab)]
 
-  # Infer resistance for missing base drugs from available drug+inhibitor combination columns.
+  # Infer resistance for missing base drugs ----
-  # Clinical principle: resistance in drug+inhibitor (e.g., piperacillin/tazobactam = R)
+  if (isTRUE(infer_from_combinations)) {
-  # always implies resistance in the base drug (e.g., piperacillin = R), because the
+    .combos_in_data <- AB_BETALACTAMS_WITH_INHIBITOR[AB_BETALACTAMS_WITH_INHIBITOR %in% names(cols_ab)]
-  # enzyme inhibitor adds nothing when the organism is truly resistant to the base drug.
+    if (length(.combos_in_data) > 0) {
-  # NOTE: susceptibility in a combination does NOT imply susceptibility in the base drug
+      .base_drugs <- suppressMessages(
-  # (the inhibitor may be responsible), so synthetic proxy columns only propagate R, not S/I.
+        as.ab(gsub("/.*", "", ab_name(as.character(.combos_in_data), language = NULL)))
-  .combos_in_data <- AB_BETALACTAMS_WITH_INHIBITOR[AB_BETALACTAMS_WITH_INHIBITOR %in% names(cols_ab)]
+      )
-  if (length(.combos_in_data) > 0) {
+      .unique_bases <- unique(.base_drugs[!is.na(.base_drugs)])
-    .base_drugs <- suppressMessages(
+      for (.base in .unique_bases) {
-      as.ab(gsub("/.*", "", ab_name(as.character(.combos_in_data), language = NULL)))
+        .base_code <- as.character(.base)
-    )
+        if (!.base_code %in% names(cols_ab)) {
-    .unique_bases <- unique(.base_drugs[!is.na(.base_drugs)])
+          # Base drug column absent; find all available combo columns for this base drug
-    for (.base in .unique_bases) {
+          .combos <- .combos_in_data[!is.na(.base_drugs) & as.character(.base_drugs) == .base_code]
-      .base_code <- as.character(.base)
+          .combo_cols <- unname(cols_ab[as.character(.combos)])
-      if (!.base_code %in% names(cols_ab)) {
+          .combo_cols <- .combo_cols[!is.na(.combo_cols)]
-        # Base drug column absent; find all available combo columns for this base drug
+          if (length(.combo_cols) > 0) {
-        .combos <- .combos_in_data[!is.na(.base_drugs) & as.character(.base_drugs) == .base_code]
+            # Vectorised: if ANY combination is R, infer base drug as R; otherwise NA
-        .combo_cols <- unname(cols_ab[as.character(.combos)])
+            .sir_chars <- as.data.frame(
-        .combo_cols <- .combo_cols[!is.na(.combo_cols)]
+              lapply(x[, .combo_cols, drop = FALSE], function(col) as.character(as.sir(col))),
-        if (length(.combo_cols) > 0) {
+              stringsAsFactors = FALSE
-          # 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
             )
+            .new_col <- paste0(.base_code, ".inferred_sir_proxy_from#", paste0(.combos, collapse = "/"), "#")
+            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 (info == TRUE) {
+              message_(
+                "Inferring resistance for ",
+                ab_name(.base_code, language = NULL, tolower = TRUE),
+                " (", font_bold(.base_code, collapse = NULL), ", ", font_italic("missing"), ") from ",
+                vector_or(
+                  quotes = FALSE,
+                  last_sep = " and/or ",
+                  paste0(
+                    ab_name(.combos, language = NULL, tolower = TRUE),
+                    " (", font_bold(.combos, collapse = NULL), ", ", font_italic("available"), ")"
+                  )
+                )
+              )
+            }
           }
         }
       }
+      cols_ab <- cols_ab[!duplicated(names(cols_ab))]
     }
-    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"]
@@ -1937,7 +1941,8 @@ mdro <- function(x = NULL,
     # format data set
     colnames(x)[colnames(x) == col_mo] <- "microorganism"
     x$microorganism <- mo_name(x$microorganism, language = NULL)
-    x$guideline <- paste0(guideline$author, " - ", guideline$name, ", ", guideline$version, ")")
+    x$guideline <- paste0(guideline$author, " - ", guideline$name, ifelse(is.na(guideline$version), "", paste0(" (", guideline$version, ")")))
+    x$all_nonsusceptible_columns <- gsub(".inferred_sir_proxy_from#(.*?)#", " (inferred from \\1)", x$all_nonsusceptible_columns, perl = TRUE)
     x[, c(
       "row_number",
       "microorganism",

man/mdro.Rd

@@ -18,7 +18,8 @@
 mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
   carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
   info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
-  verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
+  verbose = FALSE, only_sir_columns = any(is.sir(x)),
+  infer_from_combinations = TRUE, ...)
 
 brmo(x = NULL, only_sir_columns = any(is.sir(x)), ...)
 
@@ -35,7 +36,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 \arguments{
 \item{x}{A \link{data.frame} with antimicrobials columns, like \code{AMX} or \code{amox}. Can be left blank for automatic determination.}
 
-\item{guideline}{A specific guideline to follow, see sections \emph{Supported international / national guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
+\item{guideline}{A specific guideline to follow, see sections \emph{Supported International / National Guidelines} and \emph{Using Custom Guidelines} below. When left empty, the publication by Magiorakos \emph{et al.} (see below) will be followed.}
 
 \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
 
@@ -61,6 +62,8 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
 
 \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}
 
+\item{infer_from_combinations}{A \link{logical} to indicate whether resistance for a missing base beta-lactam drug should be inferred from an available drug+inhibitor combination (e.g., piperacillin from piperacillin/tazobactam). The clinical basis is that resistance in a combination always implies resistance in the base drug, since the enzyme inhibitor provides no benefit when the organism is truly resistant. Only resistance is inferred; susceptibility in a combination does \strong{not} imply susceptibility in the base drug (the inhibitor may be responsible). Defaults to \code{TRUE}.}
+
 \item{...}{Column names of antimicrobials. To automatically detect antimicrobial column names, do not provide any named arguments; \code{\link[=guess_ab_col]{guess_ab_col()}} will then be used for detection. To manually specify a column, provide its name (case-insensitive) as an argument, e.g. \code{AMX = "amoxicillin"}. To skip a specific antimicrobial, set it to \code{NULL}, e.g. \code{TIC = NULL} to exclude ticarcillin. If a manually defined column does not exist in the data, it will be skipped with a warning.}
 }
 \value{

tests/testthat/test-mdro.R

@@ -313,14 +313,14 @@ test_that("test-mdro.R", {
   # 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)),
+    suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = TRUE)),
     "Inferring resistance"
   )
-  # With TZP=R, PIP is inferred R -> 4MRGN criteria met -> level 3 (> 1)
+  inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE))
-  result_no_pip <- suppressMessages(suppressWarnings(
+  not_inferred <- suppressWarnings(mdro(pseud_no_pip, guideline = "mrgn", info = FALSE, infer_from_combinations = FALSE))
-    mdro(pseud_no_pip, guideline = "mrgn", info = FALSE)
+  expect_equal(as.character(inferred), "4MRGN")
-  ))
+  expect_equal(as.character(not_inferred), "Negative")
-  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
@@ -328,18 +328,23 @@ test_that("test-mdro.R", {
   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))
+  expect_true(as.integer(result_tzp_s) < as.integer(inferred))
 
-  # Multiple combos for the same base drug: AMX can come from AMC (amoxicillin/clavulanic acid)
+  # Multiple combos for the same base drug: AMX can come from AMC (amoxi/clavulanic acid) and AXS (amoxi/sulbactam)
   ente_no_amx <- data.frame(
     mo = as.mo("Enterococcus faecium"),
-    AMC = as.sir("R"), # amoxicillin/clavulanic acid; no AMX column
+    AMC = as.sir("R"), # amoxicillin/clavulanic acid
+    AXS = as.sir("R"), # amoxicillin/sulbactam
     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
+  # Should have multiple columns in the verbose explanation
-  expect_inherits(suppressMessages(suppressWarnings(mdro(ente_no_amx, guideline = "EUCAST", info = FALSE))), c("factor", "ordered"))
+  out <- mdro(ente_no_amx, guideline = "EUCAST 3.3", info = FALSE, verbose = TRUE)
+  expect_identical(
+    out$all_nonsusceptible_columns,
+    "AMC, AMX (inferred from AMC/AXS), AXS, DAP, LNZ, TEC, VAN"
+  )
 })