Let aggregated analyses follow the guideline for the 'I' category in count_df(), proportion_df(), sir_df(), the plotting functions, antibiogram(), wisca(), and bug_drug_combinations(), deprecate combine_SI in favour of guideline, fix format() on bug_drug_combinations() counting I as resistant, and add a shared section 'Interpretation of SIR'

2026-11-15 22:20:47 +01:00 · 2026-10-15 09:58:21 +02:00
1 parent dbd95ffa46
commit 0efc8826c8
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9137
+Version: 3.0.1.9138
 Date: 2026-10-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9137
+# AMR 3.0.1.9138

 Planned as v3.1.0, mid October 2026.

@@ -25,7 +25,8 @@ Planned as v3.1.0, mid October 2026.
 * Parallel computing in `as.sir()`, `antibiogram()`, and `wisca()` now uses the `future` and `future.apply` packages, which is faster. A non-sequential plan (e.g., `future::plan(future::multisession)`) must be active before using `parallel = TRUE` (#281).
 * The options of `capped_mic_handling` in `as.sir()` have been redefined as `"none"`, `"conservative"`, `"standard"` (default), and `"lenient"`. The option `"inverse"` is no longer available (#243).
 * `as.sir()` now returns WT/NWT (Wildtype/Non-wildtype) instead of S/R when using ECOFF-based interpretation with `breakpoint_type = "ECOFF"`. WT/NWT results are fully supported in all resistance and susceptibility functions and in all plots (#254).
-* `count_df()`, `proportion_df()`, and `sir_df()` now follow the `AMR_guideline` option through their new `guideline` argument. With CLSI, `combine_SI = TRUE` merges 'I' with R into `"IR"` and returns `"S"` vs. `"IR"`, consistent with `count_susceptible()` and `susceptibility()`. Previously, these functions always merged 'I' with S, as with EUCAST. Use `guideline = "EUCAST"` for the old behaviour. This also applies to `ggplot_sir()`, `geom_sir()`, and `labels_sir_count()`, which got the same argument.
+* Aggregated analyses now follow the guideline for the 'I' category, set with the new `guideline` argument or the `AMR_guideline` option: EUCAST considers 'I' susceptible and CLSI considers 'I' resistant, while SDD and WT are always considered susceptible, and NWT and NS always resistant (see section *Interpretation of SIR* in `?as.sir`). This applies to `count_df()`, `proportion_df()`, `sir_df()`, `ggplot_sir()`, `geom_sir()`, and `labels_sir_count()`, which with CLSI now return `"S"` vs. `"IR"` instead of `"SI"` vs. `"R"`, and to `antibiogram()`, `wisca()`, and `format()` on the output of `bug_drug_combinations()`. Previously, these functions always considered 'I' susceptible, as with EUCAST. Use `guideline = "EUCAST"` for the old behaviour.
+* The `combine_SI` argument of these functions is deprecated in favour of `guideline`. While set, it is followed literally and takes precedence over `guideline`. Use `guideline = NULL` instead of `combine_SI = FALSE` to keep S, I, and R separate.

 ### New
 * **Updated clinical breakpoints**
@@ -110,7 +111,8 @@ Planned as v3.1.0, mid October 2026.
  * `wisca()` now follows Bielicki *et al.* (2016) more strictly by using $\text{Beta}(1, 9999)$ for intrinsically resistant pairs, forcing near-zero susceptibility regardless of observed data (based on EUCAST Expected Resistant Phenotypes)
  * Fixed a bug where both functions failed without the `antimicrobials` argument if `tidyselect` was not available, e.g., for binary installations without `dplyr`
 * Resistance and susceptibility calculation
-  * New argument `guideline` (default: EUCAST) in `susceptibility()`, `resistance()`, `count_df()`, `proportion_df()`, `sir_df()`, `ggplot_sir()`, `geom_sir()`, and `labels_sir_count()` to interpret the 'I' category correctly per guideline
+  * New argument `guideline` (default: the `AMR_guideline` option, otherwise EUCAST) in `susceptibility()`, `resistance()`, `count_df()`, `proportion_df()`, `sir_df()`, `ggplot_sir()`, `geom_sir()`, `labels_sir_count()`, `antibiogram()`, `wisca()`, and `bug_drug_combinations()` to interpret the 'I' category correctly per guideline. Functions that return results per category also accept `guideline = NULL` to keep S, I, and R separate, while functions that return a single proportion or count give an informative error.
+  * When EUCAST is assumed because neither the `guideline` argument nor the `AMR_guideline` option is set, a message explains how to change this, once per session and not in R Markdown or Quarto documents
  * `count_*()` and `proportion_*()` now handle WT, NWT, NS, and NI results correctly (#321)
 * MICs and disk diffusion
  * New argument `round_to_next_log2` in `as.mic()` and `rescale_mic()` to round values up to the nearest log2 dilution level (#255)
@@ -137,11 +139,14 @@ Planned as v3.1.0, mid October 2026.
 * `custom_eucast_rules()` has been renamed to `custom_interpretive_rules()`. The old name is now deprecated but still works (#268).
 * Logical comparison (`==`, `!=`) of the `sir` class with a `factor` is now possible on R >= 4.3
 * New argument `guideline` in `random_mic()` and `random_disk()`, defaulting to the `AMR_guideline` option (otherwise EUCAST), so that generated values are based on the latest breakpoints of one guideline instead of those of all guidelines and years combined
+* Fixed `format()` on the output of `bug_drug_combinations()`, which counted I and SDD as resistant with the default `combine_SI = TRUE`, contrary to its documentation. It now reads the guideline used in `bug_drug_combinations()`, which can be overridden with its own `guideline` argument, and also counts NS as resistant.
 * Fixed a bug in `g.test()` that returned the degrees of freedom as `argument` instead of `parameter`, so that they were not printed
 * Fixed a bug where R could crash after unloading the `data.table` package, and where suggested packages available on the machine that built the package were used even if they were not available to the user

 ### Other
 * Improved console messages with clickable links throughout the package, powered by `cli` if it is installed (#191, #265)
+* The section *Interpretation of SIR* (in `?as.sir`) now explains for all functions with a `guideline` argument for aggregated analyses how S, SDD, I, R, WT, NWT, NS, and NI are categorised per guideline. The handling of 'I' per MDRO guideline in `mdro()` will be revised in a future version (#323).
+* `labels_sir_count()` is now documented together with `ggplot_sir()`
 * The documentation of `get_AMR_locale()` now describes the actual order in which the language is determined: the `AMR_locale` option, then the `LANG` system variable, then `LANGUAGE` only if `LANG` is not set, and then the system locale
 * Revamped console output of `interpretive_rules()`, with section headers, S/I/R values styled as in the printing of `sir` columns in tibbles, and the summary of edits sorted by SIR level, using `cli` if it is installed (#259)
 * The printing of `custom_interpretive_rules()` and `custom_mdro_guideline()` now styles SIR values as in tibbles, i.e., the colour of `I` depends on the guideline. `WT`, `NWT`, and `NS` were previously shown as `SDD`, `I`, and `R`, and values other than `S` and `R` as `I`.
@@ -41,7 +41,7 @@
 #' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
 #' * `AMR_custom_mo` \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
 #' * `AMR_eucastrules` \cr A [character] to set the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
-#' * `AMR_guideline` \cr A [character] to set the default guideline used throughout the `AMR` package wherever a `guideline` argument is available. This option is used as the default in e.g. [as.sir()], [resistance()], [susceptibility()], [interpretive_rules()] and many plotting functions. **While unset**, the AMR package uses the latest implemented EUCAST guideline (currently `r AMR::clinical_breakpoints$guideline[1]`).
+#' * `AMR_guideline` \cr A [character] to set the default guideline used throughout the `AMR` package wherever a `guideline` argument is available. This option is used as the default in e.g. [as.sir()], [resistance()], [susceptibility()], [interpretive_rules()] and many plotting functions. **While unset**, the AMR package uses the latest implemented EUCAST guideline (currently `r AMR::clinical_breakpoints$guideline[1]`). In aggregated analyses, this option determines whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI), see section *Interpretation of SIR* in [as.sir()]; setting it also silences the message that EUCAST is assumed.
 #'
 #'   - For [as.sir()], this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`.
 #'
@@ -60,7 +60,8 @@
 #' @param col_mo Column name of the names or codes of the microorganisms (see [as.mo()]) - the default is the first column of class [`mo`]. Values will be coerced using [as.mo()].
 #' @param language Language to translate text, which defaults to the system language (see [get_AMR_locale()]).
 #' @param minimum The minimum allowed number of available (tested) isolates. Any isolate count lower than `minimum` will return `NA` with a warning. The default number of `30` isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see *Source*.
-#' @param combine_SI A [logical] to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is `TRUE`).
+#' @param combine_SI *(deprecated in favour of `guideline`)* A [logical]. If set, it takes precedence over `guideline`: `TRUE` considers S, SDD, and I susceptible, and `FALSE` only S.
+#' @param guideline A guideline name, `"EUCAST"` or `"CLSI"` (or any version thereof, e.g. `"CLSI 2025"`), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). 'SDD' is always considered susceptible. The default is the package option [`AMR_guideline`][AMR-options], or `"EUCAST"` if it is not set. See section *Interpretation of SIR* below.
 #' @param sep A separating character for antimicrobial columns in combination antibiograms.
 #' @param sort_columns A [logical] to indicate whether the antimicrobial columns must be sorted on name.
 #' @param wisca A [logical] to indicate whether a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) must be generated (default is `FALSE`). This will use a Bayesian decision model to estimate regimen coverage probabilities using [Monte Carlo simulations](https://en.wikipedia.org/wiki/Monte_Carlo_method). Per \doi{10.1093/jac/dkv397}, susceptibility priors are \eqn{\beta(0.5, 0.5)} (Jeffreys) and intrinsically resistant pairs (based on [intrinsic_resistant]) use \eqn{\beta(1, 9999)}.
@@ -137,7 +138,7 @@
 #'
 #' ### Inclusion in Combination Antibiograms
 #'
-#' For combination antibiograms, the results of the antimicrobials are combined using the same rules as [sir_combine()], see the section *Combination Therapy* below. Whether isolates must be tested for all antimicrobials can be set with the `only_all_tested` argument (default is `FALSE`). The 'I' and 'SDD' categories are considered susceptible if `combine_SI = TRUE` (default), which also determines whether a missing result can be ignored. To use a combination in other analyses as well, create a new variable with [sir_combine()].
+#' For combination antibiograms, the results of the antimicrobials are combined using the same rules as [sir_combine()], see the section *Combination Therapy* below. Whether isolates must be tested for all antimicrobials can be set with the `only_all_tested` argument (default is `FALSE`). Whether the 'I' category is considered susceptible follows the `guideline` argument, which also determines whether a missing result can be ignored. To use a combination in other analyses as well, create a new variable with [sir_combine()].
 #'
 #' ### Plotting
 #'
@@ -159,6 +160,7 @@
 #'
 #' For the full mathematical derivation and worked examples, see the [WISCA vignette](https://amr-for-r.org/articles/WISCA.html).
 #' @inheritSection sir_combine Combination Therapy
+#' @inheritSection as.sir Interpretation of SIR
 #' @references
 #' * Hebert C *et al.* (2012). **Demonstration of the weighted-incidence syndromic combination antibiogram: an empiric prescribing decision aid.** *Infection Control & Hospital Epidemiology* 33(4):381-388; \doi{10.1086/664768}
 #' * Bielicki JA *et al.* (2016). **Selecting appropriate empirical antibiotic regimens for paediatric bloodstream infections: application of a Bayesian decision model to local and pooled antimicrobial resistance surveillance data.** *Journal of Antimicrobial Chemotherapy* 71(3):794-802; \doi{10.1093/jac/dkv397}
@@ -312,7 +314,8 @@ wisca <- function(x,
                  formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
                  col_mo = NULL,
                  language = get_AMR_locale(),
-                  combine_SI = TRUE,
+                  combine_SI,
+                  guideline = getOption("AMR_guideline", "EUCAST"),
                  sep = " + ",
                  sort_columns = TRUE,
                  simulations = 1000,
@@ -321,6 +324,9 @@ wisca <- function(x,
                  info = interactive(),
                  parallel = FALSE,
                  ...) {
+  if (missing(guideline) && missing(combine_SI)) {
+    message_antibiogram_guideline_assumed(wisca = TRUE)
+  }
  antibiogram(
    x = x,
    antimicrobials = antimicrobials,
@@ -333,6 +339,7 @@ wisca <- function(x,
    col_mo = col_mo,
    language = language,
    combine_SI = combine_SI,
+    guideline = guideline,
    sep = sep,
    sort_columns = sort_columns,
    wisca = TRUE,
@@ -359,7 +366,8 @@ antibiogram <- function(x,
                        col_mo = NULL,
                        language = get_AMR_locale(),
                        minimum = 30,
-                        combine_SI = TRUE,
+                        combine_SI,
+                        guideline = getOption("AMR_guideline", "EUCAST"),
                        sep = " + ",
                        sort_columns = TRUE,
                        wisca = FALSE,
@@ -386,7 +394,8 @@ antibiogram.default <- function(x,
                                col_mo = NULL,
                                language = get_AMR_locale(),
                                minimum = 30,
-                                combine_SI = TRUE,
+                                combine_SI,
+                                guideline = getOption("AMR_guideline", "EUCAST"),
                                sep = " + ",
                                sort_columns = TRUE,
                                wisca = FALSE,
@@ -427,7 +436,18 @@ antibiogram.default <- function(x,
  meet_criteria(col_mo, allow_class = "character", has_length = 1, allow_NULL = TRUE, is_in = colnames(x))
  language <- validate_language(language)
  meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
-  meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+  fn <- ifelse(isTRUE(wisca), "wisca", "antibiogram")
+  if (!missing(combine_SI)) {
+    # deprecated argument, if set it must be followed literally, regardless of the guideline
+    meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+    deprecation_warning("combine_SI", "guideline", fn = fn, is_argument = TRUE, extra_msg = "As long as `combine_SI` is set, it takes precedence over `guideline`. Use `guideline = \"EUCAST\"` to consider S, SDD, and I susceptible, or `guideline = \"CLSI\"` to consider S and SDD susceptible.")
+    S_values <- c("S", "WT", if (isTRUE(combine_SI)) c("SDD", "I"))
+  } else {
+    if (missing(guideline)) {
+      message_antibiogram_guideline_assumed(wisca = wisca)
+    }
+    S_values <- get_susceptible_values(validate_sir_guideline(guideline, fn = fn))
+  }
  meet_criteria(sep, allow_class = "character", has_length = 1)
  meet_criteria(sort_columns, allow_class = "logical", has_length = 1)
  meet_criteria(simulations, allow_class = c("numeric", "integer"), has_length = 1, is_finite = TRUE, is_positive = TRUE)
@@ -604,10 +624,6 @@ antibiogram.default <- function(x,
        next
      } else {
        # determine whether this new column should contain S, I, R, or NA
-        S_values <- c("S", "WT")
-        if (isTRUE(combine_SI)) {
-          S_values <- c(S_values, "SDD", "I")
-        }
        # same rules as sir_combine(), after which the result is reduced to S or R
        combined <- as.character(sir_combine_engine(as.list(x[, abx, drop = FALSE]), S_values = S_values, only_all_tested = only_all_tested))
        combined[!is.na(combined)] <- ifelse(combined[!is.na(combined)] %in% S_values, "S", "R")
@@ -643,7 +659,8 @@ antibiogram.default <- function(x,
    bug_drug_combinations(
      col_mo = ".mo",
      FUN = function(x) x,
-      include_n_rows = TRUE
+      include_n_rows = TRUE,
+      guideline = NULL # only counts are used here, S_values determines what is susceptible
    )
  colnames(out)[colnames(out) == "total"] <- "n_tested"
  colnames(out)[colnames(out) == "total_rows"] <- "n_total"
@@ -652,10 +669,7 @@ antibiogram.default <- function(x,

  counts <- out

-  out$n_susceptible <- out$S + out$WT
-  if (isTRUE(combine_SI)) {
-    out$n_susceptible <- out$n_susceptible + out$I + out$SDD
-  }
+  out$n_susceptible <- rowSums(out[, S_values, drop = FALSE])
  if (all(out$n_tested < minimum, na.rm = TRUE) && wisca == FALSE) {
    warning_("All combinations had less than {.arg minimum} = ", minimum, " results, returning an empty antibiogram")
    return(as_original_data_class(data.frame(), class(x), extra_class = "antibiogram"))
@@ -1109,7 +1123,7 @@ antibiogram.default <- function(x,
  out <- structure(as_original_data_class(new_df, class(x), extra_class = "antibiogram"),
    has_syndromic_group = has_syndromic_group,
    antibiogram_groups = attr(x, "antibiogram_groups", exact = TRUE),
-    combine_SI = combine_SI,
+    combine_SI = "I" %in% S_values,
    wisca = wisca,
    conf_interval = conf_interval,
    simulations = if (isFALSE(wisca)) NULL else simulations,
@@ -1124,6 +1138,14 @@ antibiogram.default <- function(x,
  out
 }

+message_antibiogram_guideline_assumed <- function(wisca) {
+  term <- ifelse(isTRUE(wisca), "covered", "susceptible")
+  message_guideline_assumed(
+    ifelse(isTRUE(wisca), "wisca", "antibiogram"),
+    txt = paste0(", so S, SDD, and I count as ", term, ". Use {.code guideline = \"CLSI\"} to only count S and SDD as ", term, ".")
+  )
+}
+
 #' @method antibiogram grouped_df
 #' @export
 antibiogram.grouped_df <- function(x,
@@ -1138,7 +1160,8 @@ antibiogram.grouped_df <- function(x,
                                   col_mo = NULL,
                                   language = get_AMR_locale(),
                                   minimum = 30,
-                                   combine_SI = TRUE,
+                                   combine_SI,
+                                   guideline = getOption("AMR_guideline", "EUCAST"),
                                   sep = " + ",
                                   sort_columns = TRUE,
                                   wisca = FALSE,
@@ -1151,6 +1174,9 @@ antibiogram.grouped_df <- function(x,
  stop_ifnot(is.null(mo_transform), "{.arg mo_transform} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, which could include the pathogen information (though not necessary). Nonetheless, this makes {.arg mo_transform} redundant.", call = FALSE)
  stop_ifnot(is.null(syndromic_group), "{.arg syndromic_group} must not be set if creating an antibiogram using a grouped tibble. The groups will become the variables over which the antimicrobials are calculated, making {.arg syndromic_group} redundant.", call = FALSE)

+  if (missing(guideline) && missing(combine_SI)) {
+    message_antibiogram_guideline_assumed(wisca = wisca)
+  }
  groups <- attributes(x)$groups
  group_cols <- intersect(colnames(groups), colnames(x))
  # paste group together, will be split later in antibiogram.default()
@@ -1170,6 +1196,7 @@ antibiogram.grouped_df <- function(x,
    language = language,
    minimum = minimum,
    combine_SI = combine_SI,
+    guideline = guideline,
    sep = sep,
    sort_columns = sort_columns,
    wisca = wisca,
@@ -31,7 +31,8 @@
 #'
 #' Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use [format()] on the result to prettify it to a publishable/printable format, see *Examples*.
 #' @inheritParams eucast_rules
-#' @param combine_SI A [logical] to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is `TRUE`.
+#' @param guideline A guideline name, `"EUCAST"` or `"CLSI"` (or any version thereof, e.g. `"CLSI 2025"`), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI) when calculating resistance with [format()]. The default is the package option [`AMR_guideline`][AMR-options], or `"EUCAST"` if it is not set. In [bug_drug_combinations()], this can also be `NULL` or `FALSE`, after which [format()] requires its own `guideline` to be set. In [format()], the default is the guideline used in [bug_drug_combinations()], which can be overridden by setting it. See section *Interpretation of SIR* below.
+#' @param combine_SI *(deprecated in favour of `guideline`)* A [logical]. If set, it takes precedence over `guideline`: `TRUE` bases resistance on R only, and `FALSE` on SDD, I, and R.
 #' @param add_ab_group A [logical] to indicate where the group of the antimicrobials must be included as a first column.
 #' @param remove_intrinsic_resistant [logical] to indicate that rows and columns with 100% resistance for all tested antimicrobials must be removed from the table.
 #' @param FUN The function to call on the `mo` column to transform the microorganism codes - the default is [mo_shortname()].
@@ -40,10 +41,11 @@
 #' @param ... Arguments passed on to `FUN`.
 #' @inheritParams sir_df
 #' @inheritParams base::formatC
-#' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use `combine_SI = TRUE` (default) to test R vs. S+I and `combine_SI = FALSE` to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
+#' @inheritSection as.sir Interpretation of SIR
+#' @details The function [format()] calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Following the `guideline`, resistance is based on R (EUCAST) or on I and R (CLSI), see section *Interpretation of SIR* below. This table can also directly be used in R Markdown / Quarto without the need for e.g. [knitr::kable()].
 #' @export
 #' @rdname bug_drug_combinations
-#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", "WT, "NWT", and "total".
+#' @return The function [bug_drug_combinations()] returns a [data.frame] with columns "mo", "ab", "S", "SDD", "I", "R", "NI", "WT", "NWT", "NS", and "total".
 #' @examples
 #' # example_isolates is a data set available in the AMR package.
 #' # run ?example_isolates for more info.
@@ -72,8 +74,11 @@ bug_drug_combinations <- function(x,
                                  col_mo = NULL,
                                  FUN = mo_shortname,
                                  include_n_rows = FALSE,
+                                  guideline = getOption("AMR_guideline", "EUCAST"),
                                  ...) {
  meet_criteria(x, allow_class = "data.frame")
+  guideline_assumed <- missing(guideline)
+  guideline <- validate_sir_guideline(guideline, fn = "bug_drug_combinations", allow_none = TRUE)
  x <- ascertain_sir_classes(x, "x")
  meet_criteria(col_mo, allow_class = "character", is_in = colnames(x), has_length = 1, allow_NULL = TRUE)
  meet_criteria(FUN, allow_class = "function", has_length = 1)
@@ -202,6 +207,9 @@ bug_drug_combinations <- function(x,
  out <- out %pm>% pm_arrange(mo, ab)
  class(out) <- c("bug_drug_combinations", if (data_has_groups) "grouped" else NULL, class(out))
  rownames(out) <- NULL
+  # the guideline is used by format() to calculate resistance, FALSE means that 'I' must not be merged
+  attr(out, "guideline") <- if (is.null(guideline)) FALSE else guideline
+  attr(out, "guideline_assumed") <- guideline_assumed
  out
 }

@@ -212,7 +220,8 @@ format.bug_drug_combinations <- function(x,
                                         translate_ab = "name (ab, atc)",
                                         language = get_AMR_locale(),
                                         minimum = 30,
-                                         combine_SI = TRUE,
+                                         combine_SI,
+                                         guideline = attr(x, "guideline"),
                                         add_ab_group = TRUE,
                                         remove_intrinsic_resistant = FALSE,
                                         decimal.mark = getOption("OutDec"),
@@ -222,7 +231,26 @@ format.bug_drug_combinations <- function(x,
  meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
  language <- validate_language(language)
  meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
-  meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+  if (!missing(combine_SI)) {
+    # deprecated argument, if set it must be followed literally, regardless of the guideline
+    meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+    deprecation_warning("combine_SI", "guideline", fn = "format", is_argument = TRUE, extra_msg = "As long as `combine_SI` is set, it takes precedence over `guideline`. Use `guideline = \"EUCAST\"` to base resistance on R only, or `guideline = \"CLSI\"` to base resistance on I and R.")
+    R_values <- c("R", "NWT", "NS", if (isFALSE(combine_SI)) c("SDD", "I"))
+  } else {
+    guideline_assumed <- FALSE
+    if (missing(guideline)) {
+      guideline_assumed <- !isFALSE(attr(x, "guideline_assumed"))
+      if (is.null(guideline)) {
+        # e.g., created with an older version of this package
+        guideline <- getOption("AMR_guideline", "EUCAST")
+      }
+    }
+    guideline <- validate_sir_guideline(guideline, fn = "bug_drug_combinations")
+    if (isTRUE(guideline_assumed)) {
+      message_guideline_assumed("bug_drug_combinations", txt = " when calculating resistance in {.fun format} (R vs. S+SDD+I). Use {.code guideline = \"CLSI\"} for I+R vs. S+SDD.")
+    }
+    R_values <- c("R", "NWT", "NS", if (identical(guideline, "CLSI")) "I")
+  }
  meet_criteria(add_ab_group, allow_class = "logical", has_length = 1)
  meet_criteria(remove_intrinsic_resistant, allow_class = "logical", has_length = 1)
  meet_criteria(decimal.mark, allow_class = "character", has_length = 1)
@@ -265,10 +293,7 @@ format.bug_drug_combinations <- function(x,
    x <- subset(x, R != total)
  }

-  x$isolates <- x$R + x$NWT
-  if (combine_SI == TRUE) {
-    x$isolates <- x$isolates + x$I + x$SDD
-  }
+  x$isolates <- rowSums(x[, R_values, drop = FALSE])

  give_ab_name <- function(ab, format, language) {
    format <- tolower(format)
@@ -33,11 +33,6 @@
 #'
 #' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
 #' @param ... One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.sir()] if needed.
-#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
-#'   * EUCAST: [count_susceptible()] \eqn{= N_{S} + N_{I}}, [count_resistant()] \eqn{= N_{R}}
-#'   * CLSI: [count_susceptible()] \eqn{= N_{S} + N_{SDD}}, [count_resistant()] \eqn{= N_{I} + N_{R}}
-#'
-#' You can also use e.g. [count_R()] or [count_S()] instead, to be explicit.
 #' @inheritParams proportion
 #' @inheritSection as.sir Interpretation of SIR
 #' @details These functions are meant to count isolates. Use the [resistance()]/[susceptibility()] functions to calculate microbial resistance/susceptibility.
@@ -126,16 +121,10 @@ count_resistant <- function(...,
                            only_all_tested = FALSE,
                            guideline = getOption("AMR_guideline", "EUCAST")) {
  # other arguments for meet_criteria are handled by sir_calc()
-  if (guideline %like% "EUCAST") {
-    guideline <- "EUCAST"
-  } else if (guideline %like% "CLSI") {
-    guideline <- "CLSI"
-  }
-  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
-  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun count_resistant}](AMR::count_resistant)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
-    message_("This message will be shown once per session.")
+  if (missing(guideline)) {
+    message_guideline_assumed("count_resistant", txt = ". Use {.code guideline = \"CLSI\"} to consider it resistant.")
  }
+  guideline <- validate_sir_guideline(guideline, fn = "count_resistant")
  tryCatch(
    sir_calc(...,
      ab_result = c(
@@ -156,16 +145,10 @@ count_susceptible <- function(...,
                              only_all_tested = FALSE,
                              guideline = getOption("AMR_guideline", "EUCAST")) {
  # other arguments for meet_criteria are handled by sir_calc()
-  if (guideline %like% "EUCAST") {
-    guideline <- "EUCAST"
-  } else if (guideline %like% "CLSI") {
-    guideline <- "CLSI"
-  }
-  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
-  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun count_susceptible}](AMR::count_susceptible)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
-    message_("This message will be shown once per session.")
+  if (missing(guideline)) {
+    message_guideline_assumed("count_susceptible", txt = ". Use {.code guideline = \"CLSI\"} to consider it resistant.")
  }
+  guideline <- validate_sir_guideline(guideline, fn = "count_susceptible")
  tryCatch(
    sir_calc(...,
      ab_result = c(
@@ -267,15 +250,15 @@ n_sir <- count_all
 count_df <- function(data,
                     translate_ab = "name",
                     language = get_AMR_locale(),
-                     combine_SI = TRUE,
+                     combine_SI,
                     guideline = getOption("AMR_guideline", "EUCAST")) {
+  guideline <- get_aggregation_guideline(guideline, missing(guideline), combine_SI, missing(combine_SI), fn = "count_df")
  tryCatch(
    sir_calc_df(
      type = "count",
      data = data,
      translate_ab = translate_ab,
      language = language,
-      combine_SI = combine_SI,
      confidence_level = 0.95, # doesn't matter, will be removed
      guideline = guideline
    ),
@@ -49,6 +49,7 @@
 #' @param x.title Text to show as x axis description.
 #' @param y.title Text to show as y axis description.
 #' @param ... Other arguments passed on to [geom_sir()] or, in case of [scale_sir_colours()], named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See *Examples*.
+#' @inheritSection as.sir Interpretation of SIR
 #' @details At default, the names of antimicrobials will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` argument. See [count_df()].
 #'
 #' [geom_sir()] will take any variable from the data that has an [`sir`] class (created with [as.sir()]) using [sir_df()] and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antimicrobials on the x axis.
@@ -171,7 +172,7 @@ ggplot_sir <- function(data,
                       breaks = seq(0, 1, 0.1),
                       limits = NULL,
                       translate_ab = "name",
-                       combine_SI = TRUE,
+                       combine_SI,
                       minimum = 30,
                       language = get_AMR_locale(),
                       guideline = getOption("AMR_guideline", "EUCAST"),
@@ -203,7 +204,7 @@ ggplot_sir <- function(data,
  meet_criteria(breaks, allow_class = c("numeric", "integer"))
  meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
  meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
-  meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+  guideline <- get_aggregation_guideline(guideline, missing(guideline), combine_SI, missing(combine_SI), fn = "ggplot_sir")
  meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
  language <- validate_language(language)
  meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
@@ -243,7 +244,7 @@ ggplot_sir <- function(data,
    geom_sir(
      position = position, x = x, fill = fill, translate_ab = translate_ab,
      minimum = minimum, language = language,
-      combine_SI = combine_SI, guideline = guideline, ...
+      guideline = guideline, ...
    ) +
    theme_sir()

@@ -263,7 +264,6 @@ ggplot_sir <- function(data,
      translate_ab = translate_ab,
      minimum = minimum,
      language = language,
-      combine_SI = combine_SI,
      guideline = guideline,
      datalabels.size = datalabels.size,
      datalabels.colour = datalabels.colour
@@ -293,7 +293,7 @@ geom_sir <- function(position = NULL,
                     translate_ab = "name",
                     minimum = 30,
                     language = get_AMR_locale(),
-                     combine_SI = TRUE,
+                     combine_SI,
                     guideline = getOption("AMR_guideline", "EUCAST"),
                     ...) {
  x <- x[1]
@@ -305,7 +305,7 @@ geom_sir <- function(position = NULL,
  meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
  meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
  language <- validate_language(language)
-  meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+  guideline <- get_aggregation_guideline(guideline, missing(guideline), combine_SI, missing(combine_SI), fn = "geom_sir")

  y <- "value"
  if (missing(position) || is.null(position)) {
@@ -337,7 +337,6 @@ geom_sir <- function(position = NULL,
        translate_ab = translate_ab,
        language = language,
        minimum = minimum,
-        combine_SI = combine_SI,
        guideline = guideline
      )
    },
@@ -40,7 +40,7 @@
 #' @param vanB [logical] values, or a column name containing logical values, indicating the presence of a *vanB* gene (or production of its proteins).
 #' @inheritParams eucast_rules
 #' @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 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. In a future version, the handling of 'I' will follow the selected MDRO guideline ([#323](https://github.com/msberends/AMR/issues/323)).
 #' @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
@@ -1546,14 +1546,14 @@ theme_sir <- function() {
    )
 }

-#' @rdname plot
+#' @rdname ggplot_sir
 #' @export
 labels_sir_count <- function(position = NULL,
                             x = "antibiotic",
                             translate_ab = "name",
                             minimum = 30,
                             language = get_AMR_locale(),
-                             combine_SI = TRUE,
+                             combine_SI,
                             guideline = getOption("AMR_guideline", "EUCAST"),
                             datalabels.size = 3,
                             datalabels.colour = "grey15") {
@@ -1563,7 +1563,7 @@ labels_sir_count <- function(position = NULL,
  meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
  meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
  language <- validate_language(language)
-  meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
+  guideline <- get_aggregation_guideline(guideline, missing(guideline), combine_SI, missing(combine_SI), fn = "labels_sir_count")
  meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
  meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)

@@ -1586,7 +1586,6 @@ labels_sir_count <- function(position = NULL,
      transformed <- sir_df(
        data = x,
        translate_ab = translate_ab,
-        combine_SI = combine_SI,
        minimum = minimum,
        language = language,
        guideline = guideline
@@ -38,13 +38,9 @@
 #' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a [logical] to indicate that isolates must be tested for all antimicrobials, see section *Combination Therapy* below. Use [sir_combine()] to create a new variable for a combination therapy.
 #' @param data A [data.frame] containing columns with class [`sir`] (see [as.sir()]).
 #' @param translate_ab A column name of the [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()].
-#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
-#'   * EUCAST: [susceptibility()] \eqn{= \%S + \%I}, [resistance()] \eqn{= \%R}
-#'   * CLSI: [susceptibility()] \eqn{= \%S + \%SDD}, [resistance()] \eqn{= \%I + \%R}
-#'
-#' You can also use e.g. [proportion_R()] or [proportion_S()] instead, to be explicit. For [proportion_df()], [count_df()], and [sir_df()], the guideline determines how 'I' is merged when `combine_SI = TRUE`.
+#' @param guideline A guideline name, `"EUCAST"` or `"CLSI"` (or any version thereof, e.g. `"CLSI 2025"`), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). The default is the package option [`AMR_guideline`][AMR-options], or `"EUCAST"` if it is not set. For functions that return results per category, i.e., [count_df()], [proportion_df()], [sir_df()], [ggplot_sir()], [geom_sir()], and [labels_sir_count()], this can also be `NULL` or `FALSE` to keep S, I, and R separate. See section *Interpretation of SIR* below.
 #' @inheritParams ab_property
-#' @param combine_SI A [logical] to indicate whether the 'I' category must be merged with another category, so the output only consists of susceptible vs. resistant - the default is `TRUE`. Following the `guideline` argument, the output then consists of `"SI"` (S+SDD+I) vs. `"R"` with EUCAST, and of `"S"` (S+SDD) vs. `"IR"` (I+R) with CLSI.
+#' @param combine_SI *(deprecated in favour of `guideline`)* A [logical]. If set, it takes precedence over `guideline`: `TRUE` merges S, SDD, and I into `"SI"` vs. `"R"`, and `FALSE` keeps S, I, and R separate.
 #' @param ab_result Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".
 #' @param confidence_level The confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using [binom.test()], i.e., the Clopper-Pearson method.
 #' @param side The side of the confidence interval to return. The default is `"both"` for a length 2 vector, but can also be (abbreviated as) `"min"`/`"left"`/`"lower"`/`"less"` or `"max"`/`"right"`/`"higher"`/`"greater"`.
@@ -199,16 +195,10 @@ resistance <- function(...,
                       only_all_tested = FALSE,
                       guideline = getOption("AMR_guideline", "EUCAST")) {
  # other arguments for meet_criteria are handled by sir_calc()
-  if (guideline %like% "EUCAST") {
-    guideline <- "EUCAST"
-  } else if (guideline %like% "CLSI") {
-    guideline <- "CLSI"
-  }
-  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
-  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun resistance}](AMR::resistance)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
-    message_("This message will be shown once per session.")
+  if (missing(guideline)) {
+    message_guideline_assumed("resistance", txt = ". Use {.code guideline = \"CLSI\"} to consider it resistant.")
  }
+  guideline <- validate_sir_guideline(guideline, fn = "resistance")
  tryCatch(
    sir_calc(...,
      ab_result = c(
@@ -233,16 +223,10 @@ susceptibility <- function(...,
                           only_all_tested = FALSE,
                           guideline = getOption("AMR_guideline", "EUCAST")) {
  # other arguments for meet_criteria are handled by sir_calc()
-  if (guideline %like% "EUCAST") {
-    guideline <- "EUCAST"
-  } else if (guideline %like% "CLSI") {
-    guideline <- "CLSI"
-  }
-  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
-  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
-    message_("{.help [{.fun susceptibility}](AMR::susceptibility)} assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
-    message_("This message will be shown once per session.")
+  if (missing(guideline)) {
+    message_guideline_assumed("susceptibility", txt = ". Use {.code guideline = \"CLSI\"} to consider it resistant.")
  }
+  guideline <- validate_sir_guideline(guideline, fn = "susceptibility")
  tryCatch(
    sir_calc(...,
      ab_result = c(
@@ -430,9 +414,10 @@ proportion_df <- function(data,
                          language = get_AMR_locale(),
                          minimum = 30,
                          as_percent = FALSE,
-                          combine_SI = TRUE,
+                          combine_SI,
                          confidence_level = 0.95,
                          guideline = getOption("AMR_guideline", "EUCAST")) {
+  guideline <- get_aggregation_guideline(guideline, missing(guideline), combine_SI, missing(combine_SI), fn = "proportion_df")
  tryCatch(
    sir_calc_df(
      type = "proportion",
@@ -441,7 +426,6 @@ proportion_df <- function(data,
      language = language,
      minimum = minimum,
      as_percent = as_percent,
-      combine_SI = combine_SI,
      confidence_level = confidence_level,
      guideline = guideline
    ),
@@ -173,7 +173,25 @@ VALID_SIR_LEVELS <- c("S", "SDD", "I", "R", "NI", "WT", "NWT", "NS")
 #' @section Interpretation of SIR:
 #' In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (<https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/>).
 #'
-#' This AMR package follows insight; use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
+#' In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a `guideline` argument for this purpose use these categories:
+#'
+#' | `guideline` | Susceptible | Resistant |
+#' |---|---|---|
+#' | `"EUCAST"` | S, SDD, I, WT | R, NWT, NS |
+#' | `"CLSI"` | S, SDD, WT | I, R, NWT, NS |
+#'
+#' The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+#'
+#' The `guideline` argument can be:
+#'
+#' * **Left unset**, to use the package option [`AMR_guideline`][AMR-options], or `"EUCAST"` if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+#' * **`"EUCAST"`**, or any EUCAST version such as `"EUCAST 2025"`, to consider 'I' susceptible, e.g., to return `"SI"` vs. `"R"` in [proportion_df()].
+#' * **`"CLSI"`**, or any CLSI version such as `"CLSI 2025"`, to consider 'I' resistant, e.g., to return `"S"` vs. `"IR"` in [proportion_df()].
+#' * **`NULL` or `FALSE`**, to keep S, I, and R separate. This is only possible in functions that return results per category: [count_df()], [proportion_df()], [sir_df()], [ggplot_sir()], [geom_sir()], [labels_sir_count()], and [bug_drug_combinations()]. Functions that return a single proportion or count, such as [susceptibility()], [count_resistant()], [antibiogram()], [wisca()], and [format()] on the result of [bug_drug_combinations()], require 'I' to be considered either susceptible or resistant, and return an error.
+#'
+#' Use [susceptibility()] and [resistance()] (or [count_susceptible()] and [count_resistant()]) to follow the guideline, or e.g. [proportion_SI()] and [proportion_R()] to be explicit regardless of the guideline.
+#'
+#' The `combine_SI` argument of the functions that return results per category, [antibiogram()], and [wisca()] is deprecated in favour of `guideline`. If set, it is followed literally and takes precedence over `guideline`.
 #' @return Ordered [factor] with new class `sir`
 #' @aliases sir
 #' @export
@@ -35,6 +35,55 @@ dots2vars <- function(...) {
  paste0(dots[dots != "."], collapse = "+")
 }

+validate_sir_guideline <- function(guideline, fn, allow_none = FALSE) {
+  # returns "EUCAST" or "CLSI" to consider 'I' susceptible or resistant, or NULL to not merge 'I' at all, see the section 'Interpretation of SIR' in ?as.sir
+  if (is.null(guideline) || isFALSE(guideline)) {
+    stop_ifnot(
+      allow_none,
+      "{.arg guideline} must be {.val EUCAST} or {.val CLSI} in {.help [{.fun ", fn, "}](AMR::", fn, ")}, since a single proportion or count requires the 'I' category to be considered either susceptible (EUCAST) or resistant (CLSI). See the section 'Interpretation of SIR' in {.help [{.fun as.sir}](AMR::as.sir)}.",
+      call = FALSE
+    )
+    return(NULL)
+  }
+  stop_ifnot(
+    is.character(guideline) && length(guideline) == 1 && !is.na(guideline) && (guideline %like% "EUCAST" || guideline %like% "CLSI"),
+    "{.arg guideline} must be {.val EUCAST} or {.val CLSI}", ifelse(allow_none, ", or {.code NULL} to keep S, I, and R separate,", ""), " in {.help [{.fun ", fn, "}](AMR::", fn, ")}. See the section 'Interpretation of SIR' in {.help [{.fun as.sir}](AMR::as.sir)}.",
+    call = FALSE
+  )
+  if (guideline %like% "EUCAST") "EUCAST" else "CLSI"
+}
+
+message_guideline_assumed <- function(fn, txt) {
+  # informs once per session that EUCAST is assumed, only to be called when the `guideline` argument is missing
+  # - not when the AMR_guideline option is set, since that is a deliberate choice
+  # - not when knitting R Markdown or Quarto documents, so it will not end up in reports
+  if (is.null(getOption("AMR_guideline")) && !isTRUE(getOption("knitr.in.progress")) && message_not_thrown_before(fn, "guideline_assumed", entire_session = TRUE)) {
+    message_(
+      "{.help [{.fun ", fn, "}](AMR::", fn, ")} assumes the EUCAST guideline and thus considers the 'I' category susceptible", txt,
+      " Set the {.arg guideline} argument, or set the {.code AMR_guideline} option to change the default (see {.topic [AMR-options](AMR::AMR-options)}). This message is shown once per session."
+    )
+  }
+}
+
+get_aggregation_guideline <- function(guideline, guideline_missing, combine_SI, combine_SI_missing, fn) {
+  # for functions that return results per category: returns "EUCAST" ("SI" vs. "R"), "CLSI" ("S" vs. "IR"), or NULL (S, I, and R separately)
+  if (!combine_SI_missing) {
+    # deprecated argument, if set it must be followed literally, regardless of the guideline
+    meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = 1)
+    deprecation_warning("combine_SI", "guideline", fn = fn, is_argument = TRUE, extra_msg = "As long as `combine_SI` is set, it takes precedence over `guideline`. Use `guideline = \"EUCAST\"` to merge 'I' with S, `guideline = \"CLSI\"` to merge 'I' with R, or `guideline = NULL` to keep S, I, and R separate.")
+    if (isTRUE(combine_SI)) {
+      return("EUCAST")
+    } else {
+      return(NULL)
+    }
+  }
+  guideline <- validate_sir_guideline(guideline, fn = fn, allow_none = TRUE)
+  if (isTRUE(guideline_missing) && !is.null(guideline)) {
+    message_guideline_assumed(fn, txt = paste0(" (S+SDD+I vs. R). Use {.code guideline = \"CLSI\"} for S+SDD vs. I+R, or {.code guideline = NULL} to keep S, I, and R separate."))
+  }
+  guideline
+}
+
 sir_calc <- function(...,
                     ab_result,
                     minimum = 0,
@@ -219,9 +268,8 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
                        language = get_AMR_locale(),
                        minimum = 30,
                        as_percent = FALSE,
-                        combine_SI = TRUE,
                        confidence_level = 0.95,
-                        guideline = getOption("AMR_guideline", "EUCAST")) {
+                        guideline = "EUCAST") { # must be "EUCAST", "CLSI", or NULL, see get_aggregation_guideline()
  meet_criteria(type, is_in = c("proportion", "count", "both"), has_length = 1)
  meet_criteria(data, allow_class = "data.frame")
  data <- ascertain_sir_classes(data, "data")
@@ -229,16 +277,10 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
  language <- validate_language(language)
  meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
  meet_criteria(as_percent, allow_class = "logical", has_length = 1)
-  meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
  meet_criteria(confidence_level, allow_class = "numeric", has_length = 1)
-  meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if (guideline %like% "EUCAST") {
-    guideline <- "EUCAST"
-  } else if (guideline %like% "CLSI") {
-    guideline <- "CLSI"
-  }
-  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
-  # with EUCAST, 'I' is merged with S into 'SI', with CLSI, 'I' is merged with R into 'IR'
+  meet_criteria(guideline, allow_class = "character", has_length = 1, is_in = c("EUCAST", "CLSI"), allow_NULL = TRUE)
+  # with EUCAST, 'I' is merged with S into 'SI', with CLSI, 'I' is merged with R into 'IR', and with NULL, 'I' is not merged
+  combine_SI <- !is.null(guideline)
  combined_levels <- if (identical(guideline, "CLSI")) c("S", "IR") else c("SI", "R")

  translate_ab <- get_translate_ab(translate_ab)
@@ -38,7 +38,8 @@
 #' @param ... Two or more vectors (or columns) with antimicrobial interpretations, or a data frame with such columns. They will be transformed internally with [as.sir()] if needed. All vectors must be of the same length.
 #' @param method Either `"most_susceptible"` (default) to return the most susceptible result, as for combination therapy, or `"most_resistant"` to return the most resistant result, as for resistance within a group of antimicrobials. See *Combination Therapy* below.
 #' @param only_all_tested A [logical] to indicate that isolates must be tested for all antimicrobials. If `TRUE`, the result is `NA` for isolates with a missing result for any of the antimicrobials. If `FALSE` (default), a missing result only leads to `NA` if a result for the missing antimicrobial could have changed the result, see *Combination Therapy* below.
-#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`, to determine whether the 'I' category is considered susceptible. This only affects isolates with a missing result for any of the antimicrobials when `only_all_tested = FALSE`, see *Combination Therapy* below. The default can be changed with the `AMR_guideline` option, see [AMR-options].
+#' @param guideline A guideline name, `"EUCAST"` or `"CLSI"` (or any version thereof, e.g. `"CLSI 2025"`), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). This only affects isolates with a missing result for any of the antimicrobials when `only_all_tested = FALSE`, see *Combination Therapy* below. The default is the package option [`AMR_guideline`][AMR-options], or `"EUCAST"` if it is not set. See section *Interpretation of SIR* below.
+#' @inheritSection as.sir Interpretation of SIR
 #' @section Combination Therapy:
 #' Results are ordered from susceptible to resistant: S (and WT), SDD, I, R (and NWT, NS). With `method = "most_susceptible"` (in [sir_combine()]), the most susceptible result of the antimicrobials is returned, and with `method = "most_resistant"`, the most resistant result. The value `"NI"` (non-interpretable) is considered a missing result.
 #'
@@ -82,7 +83,7 @@
 #'   proportion_S() + proportion_I() + proportion_R() = 1
 #' ```
 #'
-#' In [antibiogram()] and [wisca()], the result of the combination therapy (`"most_susceptible"`) is used, the 'I' and 'SDD' categories are considered susceptible if `combine_SI = TRUE` (default), and the result is then reduced to S or R.
+#' In [antibiogram()] and [wisca()], the result of the combination therapy (`"most_susceptible"`) is used, the 'I' category is considered susceptible or not following the `guideline` argument ('SDD' is always considered susceptible), and the result is then reduced to S or R.
 #' @return A [`sir`] vector with the same length as the input.
 #' @seealso [count()] and [proportion()] for counting and calculating susceptibility of (combinations of) antimicrobials, and [antibiogram()] for combination antibiograms.
 #' @export
@@ -142,13 +143,8 @@
 sir_combine <- function(..., method = c("most_susceptible", "most_resistant"), only_all_tested = FALSE, guideline = getOption("AMR_guideline", "EUCAST")) {
  method <- match.arg(method)
  meet_criteria(only_all_tested, allow_class = "logical", has_length = 1)
-  meet_criteria(guideline, allow_class = "character", has_length = 1)
-  if (guideline %like% "EUCAST") {
-    guideline <- "EUCAST"
-  } else if (guideline %like% "CLSI") {
-    guideline <- "CLSI"
-  }
-  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  guideline_missing <- missing(guideline)
+  guideline <- validate_sir_guideline(guideline, fn = "sir_combine")

  # unpack data frames, so that e.g. sir_combine(df[, c("GEN", "TOB")], CIP) works
  cols <- list()
@@ -166,12 +162,11 @@ sir_combine <- function(..., method = c("most_susceptible", "most_resistant"), o

  out <- sir_combine_engine(cols, S_values = get_susceptible_values(guideline), only_all_tested = only_all_tested, method = method)

-  if (isFALSE(only_all_tested) && is.null(getOption("AMR_guideline")) && missing(guideline)) {
+  if (isFALSE(only_all_tested) && is.null(getOption("AMR_guideline")) && guideline_missing) {
    # only notify about the assumed guideline if it affected the result
    out_clsi <- sir_combine_engine(cols, S_values = get_susceptible_values("CLSI"), only_all_tested = only_all_tested, method = method)
-    if (!identical(out, out_clsi) && message_not_thrown_before("sir_combine", "eucast_default", entire_session = TRUE)) {
-      message_("{.help [{.fun sir_combine}](AMR::sir_combine)} assumes the EUCAST guideline and thus considers the 'I' category susceptible, which affected the result for 'I' results combined with a missing result. Set the {.arg guideline} argument or the {.code AMR_guideline} option to either \"CLSI\" or \"EUCAST\", see {.topic [AMR-options](AMR::AMR-options)}.")
-      message_("This message will be shown once per session.")
+    if (!identical(out, out_clsi)) {
+      message_guideline_assumed("sir_combine", txt = ", which affected the result for 'I' results combined with a missing result. Use {.code guideline = \"CLSI\"} to consider it resistant.")
    }
  }
  out
@@ -34,9 +34,10 @@ sir_df <- function(data,
                   language = get_AMR_locale(),
                   minimum = 30,
                   as_percent = FALSE,
-                   combine_SI = TRUE,
+                   combine_SI,
                   confidence_level = 0.95,
                   guideline = getOption("AMR_guideline", "EUCAST")) {
+  guideline <- get_aggregation_guideline(guideline, missing(guideline), combine_SI, missing(combine_SI), fn = "sir_df")
  tryCatch(
    sir_calc_df(
      type = "both",
@@ -45,7 +46,6 @@ sir_df <- function(data,
      language = language,
      minimum = minimum,
      as_percent = as_percent,
-      combine_SI = combine_SI,
      confidence_level = confidence_level,
      guideline = guideline
    ),
@@ -69,6 +69,7 @@ as.data.frame.deprecated_amr_dataset <- function(x, ...) {
 # currently deprecated arguments at least:
 # - `antibiotics` in `antibiogram()`
 # - `converse_capped_values` in `as.sir()`
+# - `combine_SI` in `count_df()`, `proportion_df()`, `sir_df()`, `ggplot_sir()`, `geom_sir()`, `labels_sir_count()`, `antibiogram()`, `wisca()`, and `format()` for `bug_drug_combinations()`

 #' @rdname AMR-deprecated
 #' @export
@@ -18,7 +18,7 @@ This is an overview of all the package-specific options you can set in the \code
 \item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
 \item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
 \item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
-\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2026).
+\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2026). In aggregated analyses, this option determines whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI), see section \emph{Interpretation of SIR} in \code{\link[=as.sir]{as.sir()}}; setting it also silences the message that EUCAST is assumed.
 \itemize{
 \item For \code{\link[=as.sir]{as.sir()}}, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., \code{"CLSI"} or \code{"EUCAST"}) or the name including a year (e.g., \code{"CLSI 2019"}). Supported guidelines are EUCAST 2011 to 2026, and CLSI 2011 to 2026.
 \item For \code{\link[=resistance]{resistance()}} and \code{\link[=susceptibility]{susceptibility()}}, this setting determines how the \code{"I"} (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, \code{"I"} is considered \emph{resistant} in susceptibility calculations; under EUCAST, \code{"I"} is considered \emph{susceptible} in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
@@ -20,7 +20,8 @@ wisca(
  formatting_type = getOption("AMR_antibiogram_formatting_type", 14),
  col_mo = NULL,
  language = get_AMR_locale(),
-  combine_SI = TRUE,
+  combine_SI,
+  guideline = getOption("AMR_guideline", "EUCAST"),
  sep = " + ",
  sort_columns = TRUE,
  simulations = 1000,
@@ -44,7 +45,8 @@ antibiogram(
  col_mo = NULL,
  language = get_AMR_locale(),
  minimum = 30,
-  combine_SI = TRUE,
+  combine_SI,
+  guideline = getOption("AMR_guideline", "EUCAST"),
  sep = " + ",
  sort_columns = TRUE,
  wisca = FALSE,
@@ -121,7 +123,9 @@ wisca_plot(

 \item{language}{Language to translate text, which defaults to the system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}).}

-\item{combine_SI}{A \link{logical} to indicate whether all susceptibility should be determined by results of either S, SDD, or I, instead of only S (default is \code{TRUE}).}
+\item{combine_SI}{\emph{(deprecated in favour of \code{guideline})} A \link{logical}. If set, it takes precedence over \code{guideline}: \code{TRUE} considers S, SDD, and I susceptible, and \code{FALSE} only S.}
+
+\item{guideline}{A guideline name, \code{"EUCAST"} or \code{"CLSI"} (or any version thereof, e.g. \code{"CLSI 2025"}), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). 'SDD' is always considered susceptible. The default is the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if it is not set. See section \emph{Interpretation of SIR} below.}

 \item{sep}{A separating character for antimicrobial columns in combination antibiograms.}

@@ -243,7 +247,7 @@ your_data \%>\%

 \subsection{Inclusion in Combination Antibiograms}{

-For combination antibiograms, the results of the antimicrobials are combined using the same rules as \code{\link[=sir_combine]{sir_combine()}}, see the section \emph{Combination Therapy} below. Whether isolates must be tested for all antimicrobials can be set with the \code{only_all_tested} argument (default is \code{FALSE}). The 'I' and 'SDD' categories are considered susceptible if \code{combine_SI = TRUE} (default), which also determines whether a missing result can be ignored. To use a combination in other analyses as well, create a new variable with \code{\link[=sir_combine]{sir_combine()}}.
+For combination antibiograms, the results of the antimicrobials are combined using the same rules as \code{\link[=sir_combine]{sir_combine()}}, see the section \emph{Combination Therapy} below. Whether isolates must be tested for all antimicrobials can be set with the \code{only_all_tested} argument (default is \code{FALSE}). Whether the 'I' category is considered susceptible follows the \code{guideline} argument, which also determines whether a missing result can be ignored. To use a combination in other analyses as well, create a new variable with \code{\link[=sir_combine]{sir_combine()}}.
 }

 \subsection{Plotting}{
@@ -310,7 +314,33 @@ With \code{only_all_tested = TRUE}, all these functions count the result of the
  proportion_S() + proportion_I() + proportion_R() = 1
 }\if{html}{\out{</div>}}

-In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' and 'SDD' categories are considered susceptible if \code{combine_SI = TRUE} (default), and the result is then reduced to S or R.
+In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' category is considered susceptible or not following the \code{guideline} argument ('SDD' is always considered susceptible), and the result is then reduced to S or R.
+}
+
+\section{Interpretation of SIR}{
+
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
+
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \examples{
@@ -296,7 +296,26 @@ The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRU

 In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).

-This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \section{Download Our Reference Data}{
@@ -10,6 +10,7 @@ bug_drug_combinations(
  col_mo = NULL,
  FUN = mo_shortname,
  include_n_rows = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST"),
  ...
 )

@@ -18,7 +19,8 @@ bug_drug_combinations(
  translate_ab = "name (ab, atc)",
  language = get_AMR_locale(),
  minimum = 30,
-  combine_SI = TRUE,
+  combine_SI,
+  guideline = attr(x, "guideline"),
  add_ab_group = TRUE,
  remove_intrinsic_resistant = FALSE,
  decimal.mark = getOption("OutDec"),
@@ -35,6 +37,8 @@ bug_drug_combinations(

 \item{include_n_rows}{A \link{logical} to indicate if the total number of rows must be included in the output.}

+\item{guideline}{A guideline name, \code{"EUCAST"} or \code{"CLSI"} (or any version thereof, e.g. \code{"CLSI 2025"}), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI) when calculating resistance with \code{\link[=format]{format()}}. The default is the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if it is not set. In \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, this can also be \code{NULL} or \code{FALSE}, after which \code{\link[=format]{format()}} requires its own \code{guideline} to be set. In \code{\link[=format]{format()}}, the default is the guideline used in \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, which can be overridden by setting it. See section \emph{Interpretation of SIR} below.}
+
 \item{...}{Arguments passed on to \code{FUN}.}

 \item{translate_ab}{A \link{character} of length 1 containing column names of the \link{antimicrobials} data set.}
@@ -43,7 +47,7 @@ bug_drug_combinations(

 \item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}

-\item{combine_SI}{A \link{logical} to indicate whether values S, SDD, and I should be summed, so resistance will be based on only R - the default is \code{TRUE}.}
+\item{combine_SI}{\emph{(deprecated in favour of \code{guideline})} A \link{logical}. If set, it takes precedence over \code{guideline}: \code{TRUE} bases resistance on R only, and \code{FALSE} on SDD, I, and R.}

 \item{add_ab_group}{A \link{logical} to indicate where the group of the antimicrobials must be included as a first column.}

@@ -57,14 +61,40 @@ bug_drug_combinations(
    decimal point.}
 }
 \value{
-The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "SDD", "I", "R", "WT, "NWT", and "total".
+The function \code{\link[=bug_drug_combinations]{bug_drug_combinations()}} returns a \link{data.frame} with columns "mo", "ab", "S", "SDD", "I", "R", "NI", "WT", "NWT", "NS", and "total".
 }
 \description{
 Determine antimicrobial resistance (AMR) of all bug-drug combinations in your data set where at least 30 (default) isolates are available per species. Use \code{\link[=format]{format()}} on the result to prettify it to a publishable/printable format, see \emph{Examples}.
 }
 \details{
-The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Use \code{combine_SI = TRUE} (default) to test R vs. S+I and \code{combine_SI = FALSE} to test R+I vs. S. This table can also directly be used in R Markdown / Quarto without the need for e.g. \code{\link[knitr:kable]{knitr::kable()}}.
+The function \code{\link[=format]{format()}} calculates the resistance per bug-drug combination and returns a table ready for reporting/publishing. Following the \code{guideline}, resistance is based on R (EUCAST) or on I and R (CLSI), see section \emph{Interpretation of SIR} below. This table can also directly be used in R Markdown / Quarto without the need for e.g. \code{\link[knitr:kable]{knitr::kable()}}.
 }
+\section{Interpretation of SIR}{
+
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
+
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
+}
+
 \examples{
 # example_isolates is a data set available in the AMR package.
 # run ?example_isolates for more info.
@@ -44,7 +44,7 @@ count_df(
  data,
  translate_ab = "name",
  language = get_AMR_locale(),
-  combine_SI = TRUE,
+  combine_SI,
  guideline = getOption("AMR_guideline", "EUCAST")
 )
 }
@@ -53,13 +53,7 @@ count_df(

 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below. Use \code{\link[=sir_combine]{sir_combine()}} to create a new variable for a combination therapy.}

-\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
-\itemize{
-\item EUCAST: \code{\link[=count_susceptible]{count_susceptible()}} \eqn{= N_{S} + N_{I}}, \code{\link[=count_resistant]{count_resistant()}} \eqn{= N_{R}}
-\item CLSI: \code{\link[=count_susceptible]{count_susceptible()}} \eqn{= N_{S} + N_{SDD}}, \code{\link[=count_resistant]{count_resistant()}} \eqn{= N_{I} + N_{R}}
-}
-
-You can also use e.g. \code{\link[=count_R]{count_R()}} or \code{\link[=count_S]{count_S()}} instead, to be explicit.}
+\item{guideline}{A guideline name, \code{"EUCAST"} or \code{"CLSI"} (or any version thereof, e.g. \code{"CLSI 2025"}), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). The default is the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if it is not set. For functions that return results per category, i.e., \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, and \code{\link[=labels_sir_count]{labels_sir_count()}}, this can also be \code{NULL} or \code{FALSE} to keep S, I, and R separate. See section \emph{Interpretation of SIR} below.}

 \item{data}{A \link{data.frame} containing columns with class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}}).}

@@ -67,7 +61,7 @@ You can also use e.g. \code{\link[=count_R]{count_R()}} or \code{\link[=count_S]

 \item{language}{Language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}

-\item{combine_SI}{A \link{logical} to indicate whether the 'I' category must be merged with another category, so the output only consists of susceptible vs. resistant - the default is \code{TRUE}. Following the \code{guideline} argument, the output then consists of \code{"SI"} (S+SDD+I) vs. \code{"R"} with EUCAST, and of \code{"S"} (S+SDD) vs. \code{"IR"} (I+R) with CLSI.}
+\item{combine_SI}{\emph{(deprecated in favour of \code{guideline})} A \link{logical}. If set, it takes precedence over \code{guideline}: \code{TRUE} merges S, SDD, and I into \code{"SI"} vs. \code{"R"}, and \code{FALSE} keeps S, I, and R separate.}
 }
 \value{
 An \link{integer}
@@ -88,7 +82,26 @@ The function \code{\link[=count_df]{count_df()}} takes any variable from \code{d

 In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).

-This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \section{Combination Therapy}{
@@ -132,7 +145,7 @@ With \code{only_all_tested = TRUE}, all these functions count the result of the
  proportion_S() + proportion_I() + proportion_R() = 1
 }\if{html}{\out{</div>}}

-In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' and 'SDD' categories are considered susceptible if \code{combine_SI = TRUE} (default), and the result is then reduced to S or R.
+In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' category is considered susceptible or not following the \code{guideline} argument ('SDD' is always considered susceptible), and the result is then reduced to S or R.
 }

 \examples{
@@ -1,8 +1,9 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/ggplot_sir.R
+% Please edit documentation in R/ggplot_sir.R, R/plotting.R
 \name{ggplot_sir}
 \alias{ggplot_sir}
 \alias{geom_sir}
+\alias{labels_sir_count}
 \title{AMR Plots with \code{ggplot2}}
 \usage{
 ggplot_sir(
@@ -14,7 +15,7 @@ ggplot_sir(
  breaks = seq(0, 1, 0.1),
  limits = NULL,
  translate_ab = "name",
-  combine_SI = TRUE,
+  combine_SI,
  minimum = 30,
  language = get_AMR_locale(),
  guideline = getOption("AMR_guideline", "EUCAST"),
@@ -39,10 +40,22 @@ geom_sir(
  translate_ab = "name",
  minimum = 30,
  language = get_AMR_locale(),
-  combine_SI = TRUE,
+  combine_SI,
  guideline = getOption("AMR_guideline", "EUCAST"),
  ...
 )
+
+labels_sir_count(
+  position = NULL,
+  x = "antibiotic",
+  translate_ab = "name",
+  minimum = 30,
+  language = get_AMR_locale(),
+  combine_SI,
+  guideline = getOption("AMR_guideline", "EUCAST"),
+  datalabels.size = 3,
+  datalabels.colour = "grey15"
+)
 }
 \arguments{
 \item{data}{A \link{data.frame} with column(s) of class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}}).}
@@ -61,19 +74,13 @@ geom_sir(

 \item{translate_ab}{A column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}.}

-\item{combine_SI}{A \link{logical} to indicate whether the 'I' category must be merged with another category, so the output only consists of susceptible vs. resistant - the default is \code{TRUE}. Following the \code{guideline} argument, the output then consists of \code{"SI"} (S+SDD+I) vs. \code{"R"} with EUCAST, and of \code{"S"} (S+SDD) vs. \code{"IR"} (I+R) with CLSI.}
+\item{combine_SI}{\emph{(deprecated in favour of \code{guideline})} A \link{logical}. If set, it takes precedence over \code{guideline}: \code{TRUE} merges S, SDD, and I into \code{"SI"} vs. \code{"R"}, and \code{FALSE} keeps S, I, and R separate.}

 \item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}

 \item{language}{Language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}

-\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
-\itemize{
-\item EUCAST: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%I}, \code{\link[=resistance]{resistance()}} \eqn{= \%R}
-\item CLSI: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%SDD}, \code{\link[=resistance]{resistance()}} \eqn{= \%I + \%R}
-}
-
-You can also use e.g. \code{\link[=proportion_R]{proportion_R()}} or \code{\link[=proportion_S]{proportion_S()}} instead, to be explicit. For \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=count_df]{count_df()}}, and \code{\link[=sir_df]{sir_df()}}, the guideline determines how 'I' is merged when \code{combine_SI = TRUE}.}
+\item{guideline}{A guideline name, \code{"EUCAST"} or \code{"CLSI"} (or any version thereof, e.g. \code{"CLSI 2025"}), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). The default is the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if it is not set. For functions that return results per category, i.e., \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, and \code{\link[=labels_sir_count]{labels_sir_count()}}, this can also be \code{NULL} or \code{FALSE} to keep S, I, and R separate. See section \emph{Interpretation of SIR} below.}

 \item{nrow}{(when using \code{facet}) number of rows.}

@@ -116,6 +123,32 @@ Additional functions include:

 \code{\link[=ggplot_sir]{ggplot_sir()}} is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (\verb{\%>\%}). See \emph{Examples}.
 }
+\section{Interpretation of SIR}{
+
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
+
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
+}
+
 \examples{
 \donttest{
 if (require("ggplot2") && require("dplyr")) {
@@ -72,7 +72,7 @@ eucast_exceptional_phenotypes(

 \item{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 \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.}

-\item{combine_SI}{A \link{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 \code{\link[=mdro]{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 \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.}
+\item{combine_SI}{A \link{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 \code{\link[=mdro]{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 \code{combine_SI = FALSE}, resistance is considered when isolates are R or I. In a future version, the handling of 'I' will follow the selected MDRO guideline (\href{https://github.com/msberends/AMR/issues/323}{#323}).}

 \item{verbose}{A \link{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.}

@@ -157,7 +157,26 @@ Custom guidelines can be set with the \code{\link[=custom_mdro_guideline]{custom

 In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).

-This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \examples{
@@ -22,7 +22,6 @@
 \alias{scale_sir_colours}
 \alias{scale_sir_colors}
 \alias{theme_sir}
-\alias{labels_sir_count}
 \title{Plotting Helpers for AMR Data Analysis}
 \usage{
 scale_x_mic(keep_operators = "edges", mic_range = NULL, ...)
@@ -151,18 +150,6 @@ scale_sir_colours(
 )

 theme_sir()
-
-labels_sir_count(
-  position = NULL,
-  x = "antibiotic",
-  translate_ab = "name",
-  minimum = 30,
-  language = get_AMR_locale(),
-  combine_SI = TRUE,
-  guideline = getOption("AMR_guideline", "EUCAST"),
-  datalabels.size = 3,
-  datalabels.colour = "grey15"
-)
 }
 \arguments{
 \item{keep_operators}{A \link{character} specifying how to handle operators (such as \code{>} and \code{<=}) in the input. Accepts one of three values: \code{"all"} (or \code{TRUE}) to keep all operators, \code{"none"} (or \code{FALSE}) to remove all operators, or \code{"edges"} to keep operators only at both ends of the range.}
@@ -204,18 +191,6 @@ labels_sir_count(
 \item{limits}{A \link{numeric} vector of length two providing limits of the scale, use \code{NA} to refer to the existing minimum or maximum.}

 \item{aesthetics}{Aesthetics to apply the colours to - the default is "fill" but can also be (a combination of) "alpha", "colour", "fill", "linetype", "shape" or "size".}
-
-\item{position}{Position adjustment of bars, either \code{"fill"}, \code{"stack"} or \code{"dodge"}.}
-
-\item{translate_ab}{A column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}.}
-
-\item{minimum}{The minimum allowed number of available (tested) isolates. Any isolate count lower than \code{minimum} will return \code{NA} with a warning. The default number of \code{30} isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see \emph{Source}.}
-
-\item{combine_SI}{A \link{logical} to indicate whether the 'I' category must be merged with another category, so the output only consists of susceptible vs. resistant - the default is \code{TRUE}. Following the \code{guideline} argument, the output then consists of \code{"SI"} (S+SDD+I) vs. \code{"R"} with EUCAST, and of \code{"S"} (S+SDD) vs. \code{"IR"} (I+R) with CLSI.}
-
-\item{datalabels.size}{Size of the datalabels.}
-
-\item{datalabels.colour}{Colour of the datalabels.}
 }
 \value{
 The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
@@ -58,7 +58,7 @@ proportion_df(
  language = get_AMR_locale(),
  minimum = 30,
  as_percent = FALSE,
-  combine_SI = TRUE,
+  combine_SI,
  confidence_level = 0.95,
  guideline = getOption("AMR_guideline", "EUCAST")
 )
@@ -69,7 +69,7 @@ sir_df(
  language = get_AMR_locale(),
  minimum = 30,
  as_percent = FALSE,
-  combine_SI = TRUE,
+  combine_SI,
  confidence_level = 0.95,
  guideline = getOption("AMR_guideline", "EUCAST")
 )
@@ -83,13 +83,7 @@ sir_df(

 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below. Use \code{\link[=sir_combine]{sir_combine()}} to create a new variable for a combination therapy.}

-\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
-\itemize{
-\item EUCAST: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%I}, \code{\link[=resistance]{resistance()}} \eqn{= \%R}
-\item CLSI: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%SDD}, \code{\link[=resistance]{resistance()}} \eqn{= \%I + \%R}
-}
-
-You can also use e.g. \code{\link[=proportion_R]{proportion_R()}} or \code{\link[=proportion_S]{proportion_S()}} instead, to be explicit. For \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=count_df]{count_df()}}, and \code{\link[=sir_df]{sir_df()}}, the guideline determines how 'I' is merged when \code{combine_SI = TRUE}.}
+\item{guideline}{A guideline name, \code{"EUCAST"} or \code{"CLSI"} (or any version thereof, e.g. \code{"CLSI 2025"}), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). The default is the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if it is not set. For functions that return results per category, i.e., \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, and \code{\link[=labels_sir_count]{labels_sir_count()}}, this can also be \code{NULL} or \code{FALSE} to keep S, I, and R separate. See section \emph{Interpretation of SIR} below.}

 \item{ab_result}{Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".}

@@ -105,7 +99,7 @@ You can also use e.g. \code{\link[=proportion_R]{proportion_R()}} or \code{\link

 \item{language}{Language of the returned text - the default is the current system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with the package option \code{\link[=AMR-options]{AMR_locale}}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}

-\item{combine_SI}{A \link{logical} to indicate whether the 'I' category must be merged with another category, so the output only consists of susceptible vs. resistant - the default is \code{TRUE}. Following the \code{guideline} argument, the output then consists of \code{"SI"} (S+SDD+I) vs. \code{"R"} with EUCAST, and of \code{"S"} (S+SDD) vs. \code{"IR"} (I+R) with CLSI.}
+\item{combine_SI}{\emph{(deprecated in favour of \code{guideline})} A \link{logical}. If set, it takes precedence over \code{guideline}: \code{TRUE} merges S, SDD, and I into \code{"SI"} vs. \code{"R"}, and \code{FALSE} keeps S, I, and R separate.}
 }
 \value{
 A \link{double} or, when \code{as_percent = TRUE}, a \link{character}.
@@ -132,7 +126,26 @@ The function \code{\link[=proportion_df]{proportion_df()}} takes any variable fr

 In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).

-This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \section{Combination Therapy}{
@@ -176,7 +189,7 @@ With \code{only_all_tested = TRUE}, all these functions count the result of the
  proportion_S() + proportion_I() + proportion_R() = 1
 }\if{html}{\out{</div>}}

-In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' and 'SDD' categories are considered susceptible if \code{combine_SI = TRUE} (default), and the result is then reduced to S or R.
+In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' category is considered susceptible or not following the \code{guideline} argument ('SDD' is always considered susceptible), and the result is then reduced to S or R.
 }

 \examples{
@@ -116,7 +116,26 @@ Valid options for the statistical model (argument \code{model}) are:

 In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).

-This AMR package follows insight; use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \examples{
@@ -18,7 +18,7 @@ sir_combine(

 \item{only_all_tested}{A \link{logical} to indicate that isolates must be tested for all antimicrobials. If \code{TRUE}, the result is \code{NA} for isolates with a missing result for any of the antimicrobials. If \code{FALSE} (default), a missing result only leads to \code{NA} if a result for the missing antimicrobial could have changed the result, see \emph{Combination Therapy} below.}

-\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}, to determine whether the 'I' category is considered susceptible. This only affects isolates with a missing result for any of the antimicrobials when \code{only_all_tested = FALSE}, see \emph{Combination Therapy} below. The default can be changed with the \code{AMR_guideline} option, see \link{AMR-options}.}
+\item{guideline}{A guideline name, \code{"EUCAST"} or \code{"CLSI"} (or any version thereof, e.g. \code{"CLSI 2025"}), to determine whether the 'I' category is considered susceptible (EUCAST) or resistant (CLSI). This only affects isolates with a missing result for any of the antimicrobials when \code{only_all_tested = FALSE}, see \emph{Combination Therapy} below. The default is the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if it is not set. See section \emph{Interpretation of SIR} below.}
 }
 \value{
 A \code{\link{sir}} vector with the same length as the input.
@@ -73,7 +73,33 @@ With \code{only_all_tested = TRUE}, all these functions count the result of the
  proportion_S() + proportion_I() + proportion_R() = 1
 }\if{html}{\out{</div>}}

-In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' and 'SDD' categories are considered susceptible if \code{combine_SI = TRUE} (default), and the result is then reduced to S or R.
+In \code{\link[=antibiogram]{antibiogram()}} and \code{\link[=wisca]{wisca()}}, the result of the combination therapy (\code{"most_susceptible"}) is used, the 'I' category is considered susceptible or not following the \code{guideline} argument ('SDD' is always considered susceptible), and the result is then reduced to S or R.
+}
+
+\section{Interpretation of SIR}{
+
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I, and R (\url{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}).
+
+In aggregated analyses, such as proportions, counts, antibiograms, and plots, the 'I' category must be considered either susceptible or resistant. In epidemiological AMR data analysis, this follows the guideline: EUCAST considers 'I' susceptible, while CLSI considers 'I' resistant. The dose-dependent susceptibility of CLSI ('SDD') is always considered susceptible, as it equals what EUCAST defines as 'I'. All functions with a \code{guideline} argument for this purpose use these categories:\tabular{lll}{
+   \code{guideline} \tab Susceptible \tab Resistant \cr
+   \code{"EUCAST"} \tab S, SDD, I, WT \tab R, NWT, NS \cr
+   \code{"CLSI"} \tab S, SDD, WT \tab I, R, NWT, NS \cr
+}
+
+
+The values 'WT' (wild type) and 'NWT' (non-wild type) result from epidemiological cut-off values (ECOFFs) instead of clinical breakpoints. Since they are no clinical categories, 'WT' is always considered susceptible and 'NWT' always resistant, regardless of the guideline. The value 'NS' (non-susceptible) is always considered resistant, and 'NI' (non-interpretable) is always considered a missing result.
+
+The \code{guideline} argument can be:
+\itemize{
+\item \strong{Left unset}, to use the package option \code{\link[=AMR-options]{AMR_guideline}}, or \code{"EUCAST"} if this option is not set. In the latter case, a message is shown once per session (but not in R Markdown or Quarto documents); set the option to silence it.
+\item \strong{\code{"EUCAST"}}, or any EUCAST version such as \code{"EUCAST 2025"}, to consider 'I' susceptible, e.g., to return \code{"SI"} vs. \code{"R"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{"CLSI"}}, or any CLSI version such as \code{"CLSI 2025"}, to consider 'I' resistant, e.g., to return \code{"S"} vs. \code{"IR"} in \code{\link[=proportion_df]{proportion_df()}}.
+\item \strong{\code{NULL} or \code{FALSE}}, to keep S, I, and R separate. This is only possible in functions that return results per category: \code{\link[=count_df]{count_df()}}, \code{\link[=proportion_df]{proportion_df()}}, \code{\link[=sir_df]{sir_df()}}, \code{\link[=ggplot_sir]{ggplot_sir()}}, \code{\link[=geom_sir]{geom_sir()}}, \code{\link[=labels_sir_count]{labels_sir_count()}}, and \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}. Functions that return a single proportion or count, such as \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=count_resistant]{count_resistant()}}, \code{\link[=antibiogram]{antibiogram()}}, \code{\link[=wisca]{wisca()}}, and \code{\link[=format]{format()}} on the result of \code{\link[=bug_drug_combinations]{bug_drug_combinations()}}, require 'I' to be considered either susceptible or resistant, and return an error.
+}
+
+Use \code{\link[=susceptibility]{susceptibility()}} and \code{\link[=resistance]{resistance()}} (or \code{\link[=count_susceptible]{count_susceptible()}} and \code{\link[=count_resistant]{count_resistant()}}) to follow the guideline, or e.g. \code{\link[=proportion_SI]{proportion_SI()}} and \code{\link[=proportion_R]{proportion_R()}} to be explicit regardless of the guideline.
+
+The \code{combine_SI} argument of the functions that return results per category, \code{\link[=antibiogram]{antibiogram()}}, and \code{\link[=wisca]{wisca()}} is deprecated in favour of \code{guideline}. If set, it is followed literally and takes precedence over \code{guideline}.
 }

 \examples{
@@ -30,6 +30,16 @@
 test_that("test-antibiogram.R", {
  skip_on_cran()

+  # 'I' follows the guideline, see section 'Interpretation of SIR' in ?as.sir
+  get_gen <- function(...) suppressWarnings(antibiogram(example_isolates, antimicrobials = "GEN", ab_transform = NULL, formatting_type = 1, ...))$GEN
+  gen_eucast <- get_gen(guideline = "EUCAST")
+  gen_clsi <- get_gen(guideline = "CLSI")
+  expect_true(all(gen_eucast >= gen_clsi, na.rm = TRUE) && any(gen_eucast > gen_clsi, na.rm = TRUE))
+  expect_error(antibiogram(example_isolates, antimicrobials = "GEN", guideline = NULL))
+  # the deprecated combine_SI must be followed literally if set, regardless of the guideline
+  expect_identical(get_gen(combine_SI = TRUE, guideline = "CLSI"), gen_eucast)
+  expect_identical(get_gen(combine_SI = FALSE, guideline = "EUCAST"), gen_clsi) # identical since example_isolates contains no SDD
+
  # Traditional antibiogram ----------------------------------------------


@@ -35,6 +35,24 @@ test_that("test-bug/drug.R", {
  expect_output(suppressMessages(print(b)))
  expect_true(is.data.frame(format(b)))
  expect_true(is.data.frame(format(b, add_ab_group = FALSE)))
+
+  # format() calculates resistance following the guideline, taken from bug_drug_combinations() unless set
+  b_eucast <- suppressMessages(bug_drug_combinations(example_isolates, FUN = function(x) x, guideline = "EUCAST"))
+  b_clsi <- suppressMessages(bug_drug_combinations(example_isolates, FUN = function(x) x, guideline = "CLSI"))
+  expect_identical(attr(b_clsi, "guideline"), "CLSI")
+  cons_gen <- subset(b_eucast, mo == "B_STPHY_CONS" & ab == "GEN")
+  n_R <- cons_gen$R + cons_gen$NWT + cons_gen$NS
+  n_IR <- n_R + cons_gen$I
+  get_cons_gen <- function(f) f[f$Drug %like% "GEN", "B_STPHY_CONS", drop = TRUE]
+  expect_true(grepl(paste0("(", n_R, "/", cons_gen$total, ")"), get_cons_gen(format(b_eucast, translate_ab = "ab", language = "en")), fixed = TRUE))
+  expect_true(grepl(paste0("(", n_IR, "/", cons_gen$total, ")"), get_cons_gen(format(b_clsi, translate_ab = "ab", language = "en")), fixed = TRUE))
+  expect_identical(format(b_eucast, guideline = "CLSI"), format(b_clsi))
+  # with guideline = NULL, format() requires its own guideline
+  b_none <- suppressMessages(bug_drug_combinations(example_isolates, FUN = function(x) x, guideline = NULL))
+  expect_error(format(b_none))
+  expect_identical(format(b_none, guideline = "CLSI"), format(b_clsi))
+  # the deprecated combine_SI must be followed literally if set, regardless of the guideline
+  expect_identical(suppressWarnings(format(b_clsi, combine_SI = TRUE)), format(b_eucast))
  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
    expect_true(example_isolates %>%
      group_by(ward) %>%
@@ -111,14 +111,27 @@ test_that("test-count.R", {
    old_opts <- options(AMR_guideline = "CLSI")
    expect_identical(count_df(example_isolates[, "AMX"]), count_df(example_isolates[, "AMX"], guideline = "CLSI"))
    options(old_opts)
+    # guideline = NULL or FALSE keeps S, I, and R separate
    expect_equal(
-      example_isolates %>% select(AMX) %>% count_df(combine_SI = FALSE) %>% pull(value),
+      example_isolates %>% select(AMX) %>% count_df(guideline = NULL) %>% pull(value),
      c(
        suppressWarnings(example_isolates$AMX %>% count_S()),
        example_isolates$AMX %>% count_I(),
        example_isolates$AMX %>% count_R()
      )
    )
+    expect_identical(count_df(example_isolates[, "AMX"], guideline = FALSE), count_df(example_isolates[, "AMX"], guideline = NULL))
+    expect_error(count_df(example_isolates[, "AMX"], guideline = "WHO"))
+    expect_error(count_susceptible(example_isolates$AMX, guideline = NULL))
+    # the deprecated combine_SI must be followed literally if set, regardless of the guideline
+    expect_identical(
+      suppressWarnings(count_df(example_isolates[, "AMX"], combine_SI = TRUE, guideline = "CLSI")),
+      count_df(example_isolates[, "AMX"], guideline = "EUCAST")
+    )
+    expect_identical(
+      suppressWarnings(count_df(example_isolates[, "AMX"], combine_SI = FALSE, guideline = "CLSI")),
+      count_df(example_isolates[, "AMX"], guideline = NULL)
+    )

    # grouping in sir_calc_df() (= backbone of sir_df())
    expect_true("ward" %in% (example_isolates %>%
@@ -101,6 +101,16 @@ test_that("test-ggplot_sir.R", {
      levels(ggplot_sir(example_isolates[, c("AMC", "CIP")], guideline = "CLSI")$layers[[1]]$data(example_isolates[, c("AMC", "CIP")])$interpretation),
      c("S", "IR")
    )
+    # S, I, and R are kept separate with guideline = NULL
+    expect_identical(
+      levels(ggplot_sir(example_isolates[, c("AMC", "CIP")], guideline = NULL)$layers[[1]]$data(example_isolates[, c("AMC", "CIP")])$interpretation),
+      c("S", "I", "R")
+    )
+    # the deprecated combine_SI must be followed literally if set, regardless of the guideline
+    expect_identical(
+      levels(suppressWarnings(ggplot_sir(example_isolates[, c("AMC", "CIP")], combine_SI = TRUE, guideline = "CLSI"))$layers[[1]]$data(example_isolates[, c("AMC", "CIP")])$interpretation),
+      c("SI", "R")
+    )

    # support for scale_type ab and mo
    expect_inherits(
@@ -122,7 +122,7 @@ test_that("test-proportion.R", {
      )
    )
    expect_equal(
-      example_isolates %>% select(AMX) %>% proportion_df(combine_SI = FALSE) %>% pull(value),
+      example_isolates %>% select(AMX) %>% proportion_df(guideline = NULL) %>% pull(value),
      c(
        example_isolates$AMX %>% proportion_S(),
        example_isolates$AMX %>% proportion_I(),
@@ -130,6 +130,12 @@ test_that("test-proportion.R", {
      )
    )

+    expect_error(susceptibility(example_isolates$AMX, guideline = NULL))
+    expect_identical(
+      suppressWarnings(sir_df(example_isolates[, "AMX"], combine_SI = TRUE, guideline = "CLSI")),
+      sir_df(example_isolates[, "AMX"], guideline = "EUCAST")
+    )
+
    # expect_warning(example_isolates %>% group_by(ward) %>% summarise(across(KAN, sir_confidence_interval)))
  }

@@ -229,7 +229,7 @@ wisca_plot(wisca_out, wisca_plot_type = "posterior_coverage")

 - `simulations = 1000`: number of Monte Carlo draws
 - `conf_interval = 0.95`: coverage interval width
- `combine_SI = TRUE`: count "I" and "SDD" as susceptible
+- `guideline = "EUCAST"` (or the `AMR_guideline` option): count "I" and "SDD" as covered; use `guideline = "CLSI"` to count only "SDD" as covered

 ## Practical considerations