(v3.0.1.9151) Fix inconsistencies in the plotting functions and correct the translations of the interpretation categories

Plotting: - Base colours and legends of interpreted MIC and disk values on the interpretation itself instead of matching colours - Fix SDD in autoplot() for disks, the colours of barplot() for SIR values, and barplot() for MICs ignoring language and expand - Match a named colours_SIR by name; let keep_operators = TRUE/FALSE in scale_*_mic() behave as "all"/"none" - Let a named values in scale_*_sir() replace the colours it names, warn in scale_x_sir(), and pass other arguments on - Let the default of eucast_I follow the guideline option, also for EUCAST before 2019 - Support unquoted column names in facet_sir() without evaluating them - Correct the documentation and examples Translations: - Add SDD, NS, WT and NWT, and correct S, I, R and NI in 18 languages - Sources of the terms for 'I': NAK via German laboratories (de), SZU national reference laboratory (cs), lex.dk (da), Karolinska University Hospital (sv), COESANT (es), Nordlab (fi), CA-SFM (fr); no by analogy with da and sv - Not verified against an official source: ar, bn, el, hi, id, ja, ko, pl, ro, ru, sw, tr, uk, ur, vi, zh Tests: - Let the grouped antibiogram test use English so it passes in other locales
2026-11-15 22:20:47 +01:00 · 2026-10-15 22:25:20 +02:00
1 parent b63263cc56
commit 43accd35d1
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.1.9150
+Version: 3.0.1.9151
 Date: 2026-10-15
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@@ -1,4 +1,4 @@
-# AMR 3.0.1.9150
+# AMR 3.0.1.9151

 Planned as v3.1.0, mid October 2026.

@@ -129,6 +129,19 @@ Planned as v3.1.0, mid October 2026.
  * New argument `round_to_next_log2` in `as.mic()` and `rescale_mic()` to round values up to the nearest log2 dilution level (#255)
  * `as.mic()` now handles values in scientific notation (e.g., `1e-3`) correctly
  * Input validation of `as.disk()` is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter. Values higher than 50 mm now return `NA` with a warning, instead of being set to 50 mm.
+* Plotting (`plot()`, `barplot()`, and `autoplot()` for MIC, disk diffusion and SIR values, and the `scale_*_mic()` and `scale_*_sir()` functions)
+  * The colours and legend labels of interpreted MIC and disk values are now based on the interpretation itself instead of matching colours, so that the legend of `plot()` no longer shows SDD when `colours_SIR` gives SDD the colour of S (e.g., with one or three colours), and NI and NS are labelled too
+  * Fixed `autoplot()` for disk diffusion values, which left SDD bars without colour and legend entry
+  * Fixed `barplot()` for MIC values, which ignored the `language` and `expand` arguments, and which now also has the `include_PKPD` and `breakpoint_type` arguments
+  * Fixed `barplot()` for SIR values, which gave NI, WT, and NWT the wrong colours, and always showed empty bars for WT, NWT, and NS. `barplot()` and `autoplot()` for SIR values now always show S and R, and all other values (such as SDD, I, WT, NWT, and NS) only when they occur. Data with only WT and NWT shows these two.
+  * `autoplot()` for disk diffusion values now validates `include_PKPD` and `breakpoint_type`, and `plot()` and `autoplot()` for SIR values now validate `language`
+  * The y axis of `plot()` and `barplot()` now has a readable number of tick marks for large counts, instead of one per count
+  * A named `colours_SIR` is now matched by name in all plotting functions, and needs at least the names S, I and R. SDD gets the colour of S if not set. Previously, the colours of S/I and I/R were taken by position, and a named vector of three colours gave missing colours.
+  * `keep_operators = TRUE` and `FALSE` in the `scale_*_mic()` functions now behave like `"all"` and `"none"`, as in `as.mic()`
+  * Fixed the `scale_*_sir()` functions failing when `values` was set. A named `values` (e.g., `values = c(S = "green")`) now replaces the colours of the SIR values it names, and `scale_x_sir()` warns that it ignores `values`.
+  * Fixed `scale_x_sir()` ignoring other arguments, such as `name`
+  * The `scale_*_sir()` functions now call 'I' "Intermediate" by default if the `AMR_guideline` option is set to EUCAST before 2019
+  * `facet_sir()` now accepts unquoted column names, e.g., `facet_sir(antibiotic)`
 * MDRO determination (`mdro()`)
  * Resistance can now be inferred from a drug/inhibitor combination when the column of the base drug is absent (e.g., piperacillin inferred from piperacillin/tazobactam). This is controlled with the new argument `infer_from_combinations` (default: `TRUE`) (#209).
  * BRMO classification now includes bacterial complexes (#275)
@@ -142,6 +155,8 @@ Planned as v3.1.0, mid October 2026.
  * Translating is now around 50 times faster, with identical results, as the translations are prepared once per language and applied to all values at once. This also makes `ab_group()` faster in other languages.
  * Translations are no longer translated again (e.g., "Ticarcillinee" in Dutch and "groupee" in French), and parts of combination names are no longer left untranslated
  * Fixed Italian names of CoNS and CoPS (#256), Dutch names of antimicrobials, and output of `sir_df()` in other languages (#272)
+  * Added translations of "Susceptible dose-dependent", "Non-susceptible", "Wildtype", and "Non-wildtype", which were previously shown half translated in plots
+  * Corrected the translations of the interpretation categories (S, I, R, and NI) in 18 languages, which were partly incorrect (e.g., Ukrainian words in Russian, "temporary" for Intermediate in Finnish, and "intermediate product" in Czech), and made them consistent with the newly added categories. Where available, the terms of national antimicrobial susceptibility testing committees and laboratories are used, e.g., "Sensibel bei erhöhter Exposition" (German), "Sensible, cuando se incrementa la exposición" (Spanish), and "Känslig vid ökad exponering" (Swedish).
 * Interpretive rules (`interpretive_rules()`, `eucast_rules()`, and `clsi_rules()`)
  * Considerably faster, around 11 to 18 times, with identical results
  * The number of added and changed values now only counts values that were actually written, so that values left untouched due to `overwrite = FALSE` or `add_if_missing = FALSE` are no longer reported as changes or additions, also not in the output of `verbose = TRUE` (#259)
@@ -158,6 +173,7 @@ Planned as v3.1.0, mid October 2026.
 * 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()`
+* Corrected the documentation of `colours_SIR` and `eucast_I` in the plotting functions, and an example of `scale_colour_sir()` in which the title was not applied
 * 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`.
@@ -138,6 +138,7 @@ TAXONOMY_VERSION <- list(

 globalVariables(c(
  ".coverage",
+  ".data",
  ".GenericCallEnv",
  ".lower",
  ".mo",
@@ -32,18 +32,18 @@
 #' @description
 #' Functions to plot classes `sir`, `mic` and `disk`, with support for base \R and `ggplot2`.
 #'
-#' Especially the `scale_*_mic()` functions are relevant wrappers to plot MIC values for `ggplot2`. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
+#' Especially the `scale_*_mic()` functions are relevant wrappers to plot MIC values for `ggplot2`. They allow custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
 #' @param x,object Values created with [as.mic()], [as.disk()] or [as.sir()] (or their `random_*` variants, such as [random_mic()]).
 #' @param mo Any (vector of) text that can be coerced to a valid microorganism code with [as.mo()].
 #' @param ab Any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()].
 #' @param guideline Interpretation guideline to use - the default is the latest included EUCAST guideline, see *Details*.
 #' @param main,title Title of the plot.
 #' @param xlab,ylab Axis title.
-#' @param colours_SIR Colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.
+#' @param colours_SIR Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with at least the names S, I and R. With three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.
 #' @param language Language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see [get_AMR_locale()]) and can be overwritten by setting the package option [`AMR_locale`][AMR-options], e.g. `options(AMR_locale = "de")`, see [translate]. Use `language = NULL` to prevent translation.
 #' @param expand A [logical] to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.
 #' @param 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".
-#' @param eucast_I A [logical] to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be `TRUE` if the default [AMR interpretation guideline][as.sir()] is set to EUCAST (which is the default). With `FALSE`, it will be interpreted as "Intermediate".
+#' @param eucast_I A [logical] to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be `TRUE` if the default [AMR interpretation guideline][as.sir()] is set to EUCAST 2019 or later (which is the default). With `FALSE`, it will be interpreted as "Intermediate".
 #' @inheritParams as.sir
 #' @param mic_range A manual range to rescale the MIC values (using [rescale_mic()]), e.g., `mic_range = c(0.001, 32)`. Use `NA` to prevent rescaling on one side, e.g., `mic_range = c(NA, 32)`. **Note:** This rescales values but does not filter them - use the ggplot2 `limits` argument separately to exclude values from the plot.
 #' @inheritParams as.mic
@@ -52,7 +52,7 @@
 #' @details
 #' ### The `scale_*_mic()` Functions
 #'
-#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale.
+#' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale.
 #'
 #' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [mic][as.mic()].
 #'
@@ -60,7 +60,7 @@
 #'
 #' ### The `scale_*_sir()` Functions
 #'
-#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`).
+#' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`).
 #'
 #' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [sir][as.sir()].
 #'
@@ -74,9 +74,9 @@
 #' * [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
 #' * [scale_sir_colours()] allows to set colours to any aesthetic, even for `shape` or `linetype`.
 #' * [theme_sir()] is a [ggplot2 theme][ggplot2::theme()] with minimal distraction.
-#' * [labels_sir_count()] print datalabels on the bars with percentage and number of isolates, using [ggplot2::geom_text()].
+#' * [labels_sir_count()] prints data labels on the bars with percentage and number of isolates, using [ggplot2::geom_text()].
 #'
-#' The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
+#' The interpretation of "I" will be named "Susceptible, incr. exp." (susceptible, increased exposure) for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
 #'
 #' For interpreting MIC values as well as disk diffusion diameters, the default guideline is `r AMR::clinical_breakpoints$guideline[1]`, unless the package option [`AMR_guideline`][AMR-options] is set. See [as.sir()] for more information.
 #' @name plot
@@ -102,7 +102,7 @@
 #' }
 #'
 #' if (require("ggplot2")) {
-#'   # support for 27 languages, various guidelines, and many options
+#'   # support for all languages in ?translate, various guidelines, and many options
 #'   autoplot(some_disk_values,
 #'     mo = "Escherichia coli", ab = "cipro",
 #'     guideline = "CLSI", language = "no",
@@ -199,8 +199,8 @@
 #'   ) +
 #'     theme_minimal() +
 #'     geom_boxplot(fill = NA, colour = "grey30") +
-#'     geom_jitter(width = 0.25)
-#'   labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
+#'     geom_jitter(width = 0.25) +
+#'     labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
 #'
 #'   mic_sir_plot
 #' }
@@ -209,7 +209,7 @@
 #'     scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
 #'     scale_colour_sir(
 #'       language = "pt", # Portuguese
-#'       name = "Support in 28 languages"
+#'       name = "Support in many languages"
 #'     )
 #' }
 #' }
@@ -231,6 +231,11 @@ NULL
 scale_type.mic <- function(x) c("mic", "discrete")

 create_scale_mic <- function(aest, keep_operators, mic_range = NULL, ...) {
+  if (isTRUE(keep_operators)) {
+    keep_operators <- "all"
+  } else if (isFALSE(keep_operators)) {
+    keep_operators <- "none"
+  }
  ggplot_fn <- getExportedValue(paste0("scale_", aest, "_continuous"),
    ns = asNamespace("ggplot2")
  )
@@ -416,26 +421,28 @@ scale_type.sir <- function(x) c("sir", "discrete")

 create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
  args <- list(...)
-  args[c("value", "labels", "limits")] <- NULL
+  user_values <- args$values
+  args[c("values", "labels", "limits")] <- NULL

  colours_SIR <- expand_SIR_colours(colours_SIR, unname = FALSE)

  if (identical(aesthetics, "x")) {
+    if (!is.null(user_values)) {
+      warning_("The argument {.arg values} is ignored in {.help [{.fun scale_x_sir}](AMR::scale_x_sir)}, as it sets no colours.")
+    }
    ggplot_fn <- ggplot2::scale_x_discrete
  } else {
    ggplot_fn <- ggplot2::scale_discrete_manual
-    args <- c(
-      args,
-      list(
-        aesthetics = aesthetics,
-        values = c(colours_SIR,
-          NI = "grey30",
-          WT = unname(colours_SIR[1]),
-          NWT = unname(colours_SIR[4]),
-          NS = unname(colours_SIR[4])
-        )
+    values <- c(plot_sir_colour_values(colours_SIR), colours_SIR[c("SI", "IR")])
+    if (!is.null(user_values)) {
+      # 'values' as in ggplot2 replaces the colours of the SIR values it names
+      stop_ifnot(
+        !is.null(names(user_values)) && all(names(user_values) %in% names(values)),
+        "{.arg values} must be named with any of: ", vector_or(names(values), quotes = FALSE, sort = FALSE), ". Use {.arg colours_SIR} for unnamed colours."
      )
-    )
+      values[names(user_values)] <- user_values
+    }
+    args <- c(args, list(aesthetics = aesthetics, values = values))
  }
  scale <- do.call(ggplot_fn, args)

@@ -482,12 +489,12 @@ scale_x_sir <- function(colours_SIR = c(
                          R = "#ED553B"
                        ),
                        language = get_AMR_locale(),
-                        eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
+                        eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
                        ...) {
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
  meet_criteria(eucast_I, allow_class = "logical", has_length = 1)
-  create_scale_sir(aesthetics = "x", colours_SIR = colours_SIR, language = language, eucast_I = eucast_I)
+  create_scale_sir(aesthetics = "x", colours_SIR = colours_SIR, language = language, eucast_I = eucast_I, ...)
 }

 #' @rdname plot
@@ -499,7 +506,7 @@ scale_colour_sir <- function(colours_SIR = c(
                               R = "#ED553B"
                             ),
                             language = get_AMR_locale(),
-                             eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
+                             eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
                             ...) {
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
@@ -528,7 +535,7 @@ scale_fill_sir <- function(colours_SIR = c(
                             R = "#ED553B"
                           ),
                           language = get_AMR_locale(),
-                           eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
+                           eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
                           ...) {
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
@@ -581,9 +588,6 @@ plot.mic <- function(x,
  main <- gsub(" +", " ", paste0(main, collapse = " "))
  colours_SIR <- expand_SIR_colours(colours_SIR)

-  # wildtype/Non-wildtype
-  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
-
  x <- plotrange_as_table(x, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
    x = x,
@@ -598,58 +602,7 @@ plot.mic <- function(x,
    breakpoint_type = breakpoint_type,
    ...
  )
-  barplot(x,
-    col = cols_sub$cols,
-    main = main,
-    ylim = c(0, max(x) * ifelse(any(colours_SIR %in% cols_sub$cols), 1.1, 1)),
-    ylab = ylab,
-    xlab = xlab,
-    axes = FALSE
-  )
-  axis(2, seq(0, max(x)))
-  if (!is.null(cols_sub$sub)) {
-    mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
-  }
-
-  if (any(colours_SIR %in% cols_sub$cols)) {
-    legend_txt <- character(0)
-    legend_col <- character(0)
-    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(S) Susceptible")
-      legend_col <- colours_SIR[1]
-    }
-    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(WT) Wildtype")
-      legend_col <- colours_SIR[1]
-    }
-    if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
-      legend_col <- c(legend_col, colours_SIR[2])
-    }
-    if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
-      legend_col <- c(legend_col, colours_SIR[3])
-    }
-    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(R) Resistant")
-      legend_col <- c(legend_col, colours_SIR[4])
-    }
-    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(NWT) Non-wildtype")
-      legend_col <- c(legend_col, colours_SIR[4])
-    }
-
-    legend("top",
-      x.intersp = 0.5,
-      legend = translate_into_language(legend_txt, language = language),
-      fill = legend_col,
-      horiz = TRUE,
-      cex = 0.75,
-      box.lwd = 0,
-      box.col = "#FFFFFF55",
-      bg = "#FFFFFF55"
-    )
-  }
+  plot_base_sir_bars(x = x, cols_sub = cols_sub, colours_SIR = colours_SIR, language = language, main = main, ylab = ylab, xlab = xlab, reverse_legend = FALSE)
 }

 #' @method barplot mic
@@ -670,16 +623,20 @@ barplot.mic <- function(height,
                        ),
                        language = get_AMR_locale(),
                        expand = TRUE,
+                        include_PKPD = getOption("AMR_include_PKPD", TRUE),
+                        breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                        ...) {
-  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
-  meet_criteria(ylab, allow_class = "character", has_length = 1)
-  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
  meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
  meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ylab, allow_class = "character", has_length = 1)
+  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
  meet_criteria(expand, allow_class = "logical", has_length = 1)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
+  meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)

  main <- gsub(" +", " ", paste0(main, collapse = " "))

@@ -687,13 +644,17 @@ barplot.mic <- function(height,

  plot(
    x = height,
-    main = main,
-    ylab = ylab,
-    xlab = xlab,
    mo = mo,
    ab = ab,
    guideline = guideline,
+    main = main,
+    ylab = ylab,
+    xlab = xlab,
    colours_SIR = colours_SIR,
+    language = language,
+    expand = expand,
+    include_PKPD = include_PKPD,
+    breakpoint_type = breakpoint_type,
    ...
  )
 }
@@ -742,9 +703,6 @@ autoplot.mic <- function(object,

  colours_SIR <- expand_SIR_colours(colours_SIR)

-  # wildtype/Non-wildtype
-  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
-
  object <- as.mic(object) # make sure that currently implemented MIC levels are used
  x <- plotrange_as_table(object, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
@@ -760,58 +718,7 @@ autoplot.mic <- function(object,
    breakpoint_type = breakpoint_type,
    ...
  )
-  df <- as.data.frame(x, stringsAsFactors = TRUE)
-  colnames(df) <- c("mic", "count")
-  df$cols <- cols_sub$cols
-  df$cols[df$cols == colours_SIR[1] & !is_wt_nwt] <- "(S) Susceptible"
-  df$cols[df$cols == colours_SIR[1] & is_wt_nwt] <- "(WT) Wildtype"
-  df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
-  df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
-  df$cols[df$cols == colours_SIR[4] & !is_wt_nwt] <- "(R) Resistant"
-  df$cols[df$cols == colours_SIR[4] & is_wt_nwt] <- "(NWT) Non-wildtype"
-  df$cols <- factor(translate_into_language(df$cols, language = language),
-    levels = translate_into_language(
-      c(
-        "(S) Susceptible",
-        "(SDD) Susceptible dose-dependent",
-        paste("(I)", plot_name_of_I(cols_sub$guideline)),
-        "(R) Resistant",
-        "(WT) Wildtype",
-        "(NWT) Non-wildtype"
-      ),
-      language = language
-    ),
-    ordered = TRUE
-  )
-  p <- ggplot2::ggplot(df)
-
-  if (any(colours_SIR %in% cols_sub$cols)) {
-    vals <- c(
-      "(S) Susceptible" = colours_SIR[1],
-      "(SDD) Susceptible dose-dependent" = colours_SIR[2],
-      "(I) Susceptible, incr. exp." = colours_SIR[3],
-      "(I) Intermediate" = colours_SIR[3],
-      "(R) Resistant" = colours_SIR[4],
-      "(NI) Non-interpretable" = "grey30",
-      "(WT) Wildtype" = colours_SIR[1],
-      "(NWT) Non-wildtype" = colours_SIR[4]
-    )
-    names(vals) <- translate_into_language(names(vals), language = language)
-    p <- p +
-      ggplot2::geom_col(ggplot2::aes(x = mic, y = count, fill = cols)) +
-      # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
-      ggplot2::scale_fill_manual(
-        values = vals,
-        name = NULL,
-        limits = force
-      )
-  } else {
-    p <- p +
-      ggplot2::geom_col(ggplot2::aes(x = mic, y = count))
-  }
-
-  p +
-    ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
+  plot_ggplot_sir_bars(x = x, method = "mic", cols_sub = cols_sub, colours_SIR = colours_SIR, language = language, title = title, ylab = ylab, xlab = xlab)
 }

 #' @method fortify mic
@@ -849,12 +756,12 @@ plot.disk <- function(x,
                      include_PKPD = getOption("AMR_include_PKPD", TRUE),
                      breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                      ...) {
-  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
-  meet_criteria(ylab, allow_class = "character", has_length = 1)
-  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
  meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
  meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ylab, allow_class = "character", has_length = 1)
+  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
  meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -864,9 +771,6 @@ plot.disk <- function(x,
  main <- gsub(" +", " ", paste0(main, collapse = " "))
  colours_SIR <- expand_SIR_colours(colours_SIR)

-  # wildtype/Non-wildtype
-  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
-
  x <- plotrange_as_table(x, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
    x = x,
@@ -881,58 +785,8 @@ plot.disk <- function(x,
    breakpoint_type = breakpoint_type,
    ...
  )
-
-  barplot(x,
-    col = cols_sub$cols,
-    main = main,
-    ylim = c(0, max(x) * ifelse(any(colours_SIR %in% cols_sub$cols), 1.1, 1)),
-    ylab = ylab,
-    xlab = xlab,
-    axes = FALSE
-  )
-  axis(2, seq(0, max(x)))
-  if (!is.null(cols_sub$sub)) {
-    mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
-  }
-
-  if (any(colours_SIR %in% cols_sub$cols)) {
-    legend_txt <- character(0)
-    legend_col <- character(0)
-    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
-      legend_txt <- "(R) Resistant"
-      legend_col <- colours_SIR[4]
-    }
-    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
-      legend_txt <- "(NWT) Non-wildtype"
-      legend_col <- colours_SIR[4]
-    }
-    if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
-      legend_col <- c(legend_col, colours_SIR[3])
-    }
-    if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
-      legend_col <- c(legend_col, colours_SIR[2])
-    }
-    if (!is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(S) Susceptible")
-      legend_col <- c(legend_col, colours_SIR[1])
-    }
-    if (is_wt_nwt & any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(WT) Wildtype")
-      legend_col <- c(legend_col, colours_SIR[1])
-    }
-    legend("top",
-      x.intersp = 0.5,
-      legend = translate_into_language(legend_txt, language = language),
-      fill = legend_col,
-      horiz = TRUE,
-      cex = 0.75,
-      box.lwd = 0,
-      box.col = "#FFFFFF55",
-      bg = "#FFFFFF55"
-    )
-  }
+  # zone diameters run from resistant to susceptible, so the legend does too
+  plot_base_sir_bars(x = x, cols_sub = cols_sub, colours_SIR = colours_SIR, language = language, main = main, ylab = ylab, xlab = xlab, reverse_legend = TRUE)
 }

 #' @method barplot disk
@@ -956,12 +810,12 @@ barplot.disk <- function(height,
                         include_PKPD = getOption("AMR_include_PKPD", TRUE),
                         breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                         ...) {
-  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
-  meet_criteria(ylab, allow_class = "character", has_length = 1)
-  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
  meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
  meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(ylab, allow_class = "character", has_length = 1)
+  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
  meet_criteria(expand, allow_class = "logical", has_length = 1)
@@ -972,12 +826,12 @@ barplot.disk <- function(height,

  plot(
    x = height,
-    main = main,
-    ylab = ylab,
-    xlab = xlab,
    mo = mo,
    ab = ab,
    guideline = guideline,
+    main = main,
+    ylab = ylab,
+    xlab = xlab,
    colours_SIR = colours_SIR,
    language = language,
    expand = expand,
@@ -1010,15 +864,17 @@ autoplot.disk <- function(object,
                          breakpoint_type = getOption("AMR_breakpoint_type", "human"),
                          ...) {
  stop_ifnot_installed("ggplot2")
-  meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
-  meet_criteria(ylab, allow_class = "character", has_length = 1)
-  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
  meet_criteria(ab, allow_class = c("ab", "character"), allow_NULL = TRUE)
  meet_criteria(guideline, allow_class = "character", has_length = 1)
+  meet_criteria(title, allow_class = "character", allow_NULL = TRUE)
+  meet_criteria(ylab, allow_class = "character", has_length = 1)
+  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
  language <- validate_language(language)
  meet_criteria(expand, allow_class = "logical", has_length = 1)
+  meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
+  meet_criteria(breakpoint_type, allow_class = "character", is_in = AMR::clinical_breakpoints$type, has_length = 1)

  if ("main" %in% names(list(...))) {
    title <- list(...)$main
@@ -1029,9 +885,6 @@ autoplot.disk <- function(object,

  colours_SIR <- expand_SIR_colours(colours_SIR)

-  # wildtype/Non-wildtype
-  is_wt_nwt <- identical(breakpoint_type, "ECOFF")
-
  x <- plotrange_as_table(object, expand = expand)
  cols_sub <- plot_colours_subtitle_guideline(
    x = x,
@@ -1046,56 +899,7 @@ autoplot.disk <- function(object,
    breakpoint_type = breakpoint_type,
    ...
  )
-  df <- as.data.frame(x, stringsAsFactors = TRUE)
-  colnames(df) <- c("disk", "count")
-  df$cols <- cols_sub$cols
-  df$cols[df$cols == colours_SIR[1] & !is_wt_nwt] <- "(S) Susceptible"
-  df$cols[df$cols == colours_SIR[1] & is_wt_nwt] <- "(WT) Wildtype"
-  df$cols[df$cols == colours_SIR[2]] <- "(SDD) Susceptible dose-dependent"
-  df$cols[df$cols == colours_SIR[3]] <- paste("(I)", plot_name_of_I(cols_sub$guideline))
-  df$cols[df$cols == colours_SIR[4] & !is_wt_nwt] <- "(R) Resistant"
-  df$cols[df$cols == colours_SIR[4] & is_wt_nwt] <- "(NWT) Non-wildtype"
-  df$cols <- factor(translate_into_language(df$cols, language = language),
-    levels = translate_into_language(
-      c(
-        "(S) Susceptible",
-        paste("(I)", plot_name_of_I(cols_sub$guideline)),
-        "(R) Resistant",
-        "(WT) Wildtype",
-        "(NWT) Non-wildtype"
-      ),
-      language = language
-    ),
-    ordered = TRUE
-  )
-  p <- ggplot2::ggplot(df)
-  if (any(colours_SIR %in% cols_sub$cols)) {
-    vals <- c(
-      "(S) Susceptible" = colours_SIR[1],
-      "(SDD) Susceptible dose-dependent" = colours_SIR[2],
-      "(I) Susceptible, incr. exp." = colours_SIR[3],
-      "(I) Intermediate" = colours_SIR[3],
-      "(R) Resistant" = colours_SIR[4],
-      "(NI) Non-interpretable" = "grey30",
-      "(WT) Wildtype" = colours_SIR[1],
-      "(NWT) Non-wildtype" = colours_SIR[4]
-    )
-    names(vals) <- translate_into_language(names(vals), language = language)
-    p <- p +
-      ggplot2::geom_col(ggplot2::aes(x = disk, y = count, fill = cols)) +
-      # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
-      ggplot2::scale_fill_manual(
-        values = vals,
-        name = NULL,
-        limits = force
-      )
-  } else {
-    p <- p +
-      ggplot2::geom_col(ggplot2::aes(x = disk, y = count))
-  }
-
-  p +
-    ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
+  plot_ggplot_sir_bars(x = x, method = "disk", cols_sub = cols_sub, colours_SIR = colours_SIR, language = language, title = title, ylab = ylab, xlab = xlab)
 }

 #' @method fortify disk
@@ -1122,6 +926,7 @@ plot.sir <- function(x,
  meet_criteria(ylab, allow_class = "character", has_length = 1)
  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(main, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  language <- validate_language(language)

  data <- as.data.frame(table(x), stringsAsFactors = FALSE)
  colnames(data) <- c("x", "n")
@@ -1196,29 +1001,19 @@ barplot.sir <- function(height,
  meet_criteria(expand, allow_class = "logical", has_length = 1)

  colours_SIR <- expand_SIR_colours(colours_SIR)
-
-  # add SDD and N to colours
-  colours_SIR <- c(colours_SIR, "grey30")
  main <- gsub(" +", " ", paste0(main, collapse = " "))

  x <- table(height)
-  if (all(height %in% c("WT", "NWT"), na.rm = TRUE)) {
-    colours_SIR <- colours_SIR[c(1, 4)]
-    x <- x[names(x) %in% c("WT", "NWT")]
-  } else {
-    # remove missing I, SDD, and N
-    colours_SIR <- colours_SIR[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
-    x <- x[!(names(x) %in% c("SDD", "I", "NI") & x == 0)]
-  }
+  x <- x[plot_sir_levels_to_keep(height, x)]
  # plot it
  barplot(x,
-    col = colours_SIR,
+    col = unname(plot_sir_colour_values(colours_SIR)[names(x)]),
    xlab = xlab,
    main = main,
    ylab = ylab,
    axes = FALSE
  )
-  axis(2, seq(0, max(x)))
+  axis(2, plot_count_ticks(max(x)))
 }

 #' @method autoplot sir
@@ -1242,6 +1037,7 @@ autoplot.sir <- function(object,
  meet_criteria(ylab, allow_class = "character", has_length = 1)
  meet_criteria(xlab, allow_class = "character", has_length = 1)
  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
+  language <- validate_language(language)

  if ("main" %in% names(list(...))) {
    title <- list(...)$main
@@ -1254,25 +1050,12 @@ autoplot.sir <- function(object,

  df <- as.data.frame(table(object), stringsAsFactors = TRUE)
  colnames(df) <- c("x", "n")
-  df <- df[!(df$n == 0 & df$x %in% c("SDD", "I", "NI")), , drop = FALSE]
-  if (all(object %in% c("WT", "NWT"), na.rm = TRUE)) {
-    df <- df[which(df$x %in% c("WT", "NWT")), ]
-  } else {
-    df <- df[which(!df$x %in% c("WT", "NWT", "NS")), ]
-  }
+  df <- df[plot_sir_levels_to_keep(object, stats::setNames(df$n, df$x)), , drop = FALSE]
  ggplot2::ggplot(df) +
    ggplot2::geom_col(ggplot2::aes(x = x, y = n, fill = x)) +
    # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
    ggplot2::scale_fill_manual(
-      values = c(
-        "S" = colours_SIR[1],
-        "SDD" = colours_SIR[2],
-        "I" = colours_SIR[3],
-        "R" = colours_SIR[4],
-        "NI" = "grey30",
-        "WT" = colours_SIR[1],
-        "NWT" = colours_SIR[4]
-      ),
+      values = plot_sir_colour_values(colours_SIR),
      limits = force
    ) +
    ggplot2::labs(title = title, x = xlab, y = ylab) +
@@ -1290,6 +1073,106 @@ fortify.sir <- function(object, ...) {
  )
 }

+# colours for all values of VALID_SIR_LEVELS, named by level, based on the output of expand_SIR_colours() (in the order S, SDD, I, R, SI, IR)
+plot_sir_colour_values <- function(colours_SIR) {
+  c(
+    S = unname(colours_SIR[1]),
+    SDD = unname(colours_SIR[2]),
+    I = unname(colours_SIR[3]),
+    R = unname(colours_SIR[4]),
+    NI = "grey30",
+    WT = unname(colours_SIR[1]),
+    NWT = unname(colours_SIR[4]),
+    NS = unname(colours_SIR[4])
+  )
+}
+
+# legend labels for all values of VALID_SIR_LEVELS, named by level
+plot_sir_label_values <- function(guideline) {
+  c(
+    S = "(S) Susceptible",
+    SDD = "(SDD) Susceptible dose-dependent",
+    I = paste("(I)", plot_name_of_I(guideline)),
+    R = "(R) Resistant",
+    NI = "(NI) Non-interpretable",
+    WT = "(WT) Wildtype",
+    NWT = "(NWT) Non-wildtype",
+    NS = "(NS) Non-susceptible"
+  )
+}
+
+# for bar plots of SIR values: keep S and R, and other levels only if they occur; keep only WT and NWT if the data contains nothing else
+plot_sir_levels_to_keep <- function(values, counts) {
+  values <- as.character(values[!is.na(values)])
+  if (length(values) > 0 && all(values %in% c("WT", "NWT"))) {
+    names(counts) %in% c("WT", "NWT")
+  } else {
+    names(counts) %in% c("S", "R") | counts > 0
+  }
+}
+
+# integer tick marks for an axis with counts, around 5 ticks as with pretty()
+plot_count_ticks <- function(max_count) {
+  ticks <- pretty(c(0, max_count))
+  ticks[ticks == round(ticks)]
+}
+
+plot_base_sir_bars <- function(x, cols_sub, colours_SIR, language, main, ylab, xlab, reverse_legend) {
+  # SIR values that occur in the data, in the order of VALID_SIR_LEVELS
+  in_legend <- VALID_SIR_LEVELS[VALID_SIR_LEVELS %in% as.character(cols_sub$sir[cols_sub$count > 0])]
+  if (isTRUE(reverse_legend)) {
+    in_legend <- rev(in_legend)
+  }
+  barplot(x,
+    col = cols_sub$cols,
+    main = main,
+    ylim = c(0, max(x) * ifelse(length(in_legend) > 0, 1.1, 1)),
+    ylab = ylab,
+    xlab = xlab,
+    axes = FALSE
+  )
+  axis(2, plot_count_ticks(max(x)))
+  if (!is.null(cols_sub$sub)) {
+    mtext(side = 3, line = 0.5, adj = 0.5, cex = 0.75, cols_sub$sub)
+  }
+  if (length(in_legend) > 0) {
+    legend("top",
+      x.intersp = 0.5,
+      legend = translate_into_language(unname(plot_sir_label_values(cols_sub$guideline)[in_legend]), language = language),
+      fill = unname(plot_sir_colour_values(colours_SIR)[in_legend]),
+      horiz = TRUE,
+      cex = 0.75,
+      box.lwd = 0,
+      box.col = "#FFFFFF55",
+      bg = "#FFFFFF55"
+    )
+  }
+}
+
+plot_ggplot_sir_bars <- function(x, method, cols_sub, colours_SIR, language, title, ylab, xlab) {
+  df <- as.data.frame(x, stringsAsFactors = TRUE)
+  colnames(df) <- c(method, "count")
+  if (any(!is.na(cols_sub$sir))) {
+    labels <- plot_sir_label_values(cols_sub$guideline)
+    labels[] <- translate_into_language(labels, language = language)
+    df$cols <- factor(unname(labels[as.character(cols_sub$sir)]), levels = unname(labels), ordered = TRUE)
+    p <- ggplot2::ggplot(df) +
+      ggplot2::geom_col(ggplot2::aes(x = .data[[method]], y = count, fill = cols)) +
+      # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
+      ggplot2::scale_fill_manual(
+        values = stats::setNames(unname(plot_sir_colour_values(colours_SIR)[names(labels)]), labels),
+        name = NULL,
+        limits = force,
+        na.value = "#BEBEBE"
+      )
+  } else {
+    p <- ggplot2::ggplot(df) +
+      ggplot2::geom_col(ggplot2::aes(x = .data[[method]], y = count))
+  }
+  p +
+    ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
+}
+
 plotrange_as_table <- function(x, expand, keep_operators = "all", mic_range = NULL) {
  x <- x[!is.na(x)]
  if (is.mic(x)) {
@@ -1332,17 +1215,10 @@ plotrange_as_table <- function(x, expand, keep_operators = "all", mic_range = NU
  as.table(x)
 }

-ggplot2_get_from_dots <- function(arg, default, ...) {
-  dots <- list(...)
-  if (!arg %in% names(dots)) {
-    default
-  } else {
-    dots[[arg]]
-  }
-}
-
 plot_name_of_I <- function(guideline) {
-  if (guideline %unlike% "CLSI" && as.double(gsub("[^0-9]+", "", guideline)) >= 2019) {
+  # a guideline without a year, such as "EUCAST", is the latest version
+  year <- suppressWarnings(as.double(gsub("[^0-9]+", "", guideline)))
+  if (guideline %unlike% "CLSI" && (is.na(year) || year >= 2019)) {
    # interpretation since 2019
    "Susceptible, incr. exp."
  } else {
@@ -1393,18 +1269,12 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
      ref_tbl <- paste0('"', unique(AMR_env$sir_interpretation_history$ref_table), '"', collapse = "/")
      guideline_txt <- paste0("(", guideline_txt, ": ", ref_tbl, ")")
    }
-    cols <- character(length = length(sir))
-    cols[is.na(sir)] <- "#BEBEBE"
-    cols[sir == "S"] <- colours_SIR[1]
-    cols[sir == "SDD"] <- colours_SIR[2]
-    cols[sir == "I"] <- colours_SIR[3]
-    cols[sir == "R"] <- colours_SIR[4]
-    cols[sir == "NI"] <- "grey30"
-    cols[sir == "WT"] <- colours_SIR[1]
-    cols[sir == "NWT"] <- colours_SIR[4]
-    cols[sir == "NS"] <- colours_SIR[4]
+    sir <- as.character(sir)
+    cols <- unname(plot_sir_colour_values(colours_SIR)[sir])
+    cols[is.na(cols)] <- "#BEBEBE"
    sub <- bquote(.(abname) ~ "-" ~ italic(.(moname)) ~ .(guideline_txt))
  } else {
+    sir <- rep(NA_character_, length(x))
    cols <- "#BEBEBE"
    sub <- NULL
  }
@@ -1412,28 +1282,24 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
  # restore previous interpretations to backup
  AMR_env$sir_interpretation_history <- sir_history

-  list(cols = cols, count = as.double(x), sub = sub, guideline = guideline)
+  list(cols = cols, sir = sir, count = as.double(x), sub = sub, guideline = guideline)
 }

 #' @rdname plot
 #' @export
 facet_sir <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
+  # support unquoted column names, such as facet_sir(antibiotic), without evaluating them
+  if (!missing(facet) && is.symbol(substitute(facet))) {
+    facet <- as.character(substitute(facet))
+  }
  facet <- facet[1]
  stop_ifnot_installed("ggplot2")
  meet_criteria(facet, allow_class = "character", has_length = 1)
  meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)

-  facet_deparse <- deparse(substitute(facet))
-  if (facet_deparse != "facet") {
-    facet <- facet_deparse
-  }
-  if (facet %like% '".*"') {
-    facet <- substr(facet, 2, nchar(facet) - 1)
-  }
-
-  if (tolower(facet) %in% tolower(c("SIR", "sir", "interpretations", "result"))) {
+  if (tolower(facet) %in% c("sir", "interpretations", "result")) {
    facet <- "interpretation"
-  } else if (tolower(facet) %in% tolower(c("ab", "abx", "antimicrobials"))) {
+  } else if (tolower(facet) %in% c("ab", "abx", "antimicrobials")) {
    facet <- "antibiotic"
  }

@@ -1608,26 +1474,25 @@ expand_SIR_colours <- function(colours_SIR, unname = TRUE) {
      colours_SIR <- rep(colours_SIR, 4)
    } else if (length(colours_SIR) == 3) {
      # old method for AMR < 3.0.1 which allowed for 3 colours
-      # fill in green for SDD as extra colour
+      # fill in the colour of S for SDD
      colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
    }
-    if (length(colours_SIR) == 4) {
-      # add colours for SI (same as S) and IR (same as R)
-      colours_SIR <- c(colours_SIR[1:4], colours_SIR[1], colours_SIR[4])
-    }
-    names(colours_SIR) <- sir_order
+    names(colours_SIR) <- sir_order[1:4]
  } else {
-    # named input: match and reorder
+    # named input: match by name
    stop_ifnot(
      all(names(colours_SIR) %in% sir_order),
-      "Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(levels(NA_sir_), quotes = FALSE, sort = FALSE), "."
+      "Unknown names in {.arg colours_SIR}. Expected any of: ", vector_or(sir_order, quotes = FALSE, sort = FALSE), "."
+    )
+    stop_ifnot(
+      all(c("S", "I", "R") %in% names(colours_SIR)),
+      "A named {.arg colours_SIR} must contain at least the names S, I and R."
    )
-    if (length(colours_SIR) == 4) {
-      # add colours for SI (same as S) and IR (same as R)
-      colours_SIR <- c(colours_SIR[1:4], SI = unname(colours_SIR[1]), IR = unname(colours_SIR[4]))
-    }
-    colours_SIR <- colours_SIR[sir_order]
  }
+  # SDD and SI get the colour of S, and IR gets the colour of R, unless set
+  colours_SIR[setdiff(c("SDD", "SI"), names(colours_SIR))] <- colours_SIR[["S"]]
+  colours_SIR[setdiff("IR", names(colours_SIR))] <- colours_SIR[["R"]]
+  colours_SIR <- colours_SIR[sir_order]

  if (unname) {
    colours_SIR <- unname(colours_SIR)
@@ -39,13 +39,17 @@ vegetative	TRUE	TRUE	FALSE	FALSE	vegetative	نباتي/خضري	উদ্ভি
 ([([ ]*?)Group\\b	TRUE	TRUE	FALSE	FALSE	\\1Group	\\1 مجموعة	\\1গ্রুপ	([([]*?)组	\\1Skupina	\\1Gruppe	\\1Groep	\\1Ryhmä	\\1Groupe	\\1Gruppe	([([ ]*;)ομάδα	\\1समूह	\\1Grup	\\1Gruppo	\\1グループ	\\1그룹	\\1Gruppe	([([ ]*?)Grupa	\\1Grupo	\\1Grup	\\1Группа	\\1Grupo	\\1 Kundi	\\1Grupp	([([ ]*?)Grup	\\1Група	\\1گروپ	\\1Nhóm
 no .*growth	FALSE	FALSE	FALSE	FALSE	no .*growth	لا يوجد نمو	কোনও বৃদ্ধি নেই	无.*生长	žádný .*růst	ingen .*vækst	geen .*groei	ei .*kasvua	pas .*croissance	keine(|n|m|r|s)|nicht .*wachstum	όχι .*αύξηση	कोई वृद्धि नहीं	Tidak ada pertumbuhan	sem .*crescimento	成長なし	성장 없음	nei .*vekst	brak .*wzrostu	sem .*crescimento	fără creștere	отсутствие.*роста	no .*crecimientonon	Hakuna ukuaji	ingen .*tillväxt	büyüme yok	відсутність .*росту	کسی قسم کی افزائش نہیں	Không có phát triển
 no|not	FALSE	FALSE	FALSE	FALSE	no|not	لا	না|নয়	不|不	ne	nej|ikke	geen|niet	ei	non	keine?	no|not	नहीं	tidak|bukan	sem	no|ない	없음	nei|ikke	nie|nie	sem	nu	нет?	no|sin	hapana	nej|inte	hayır|değil|hayir|degil	ні	نہیں|نہ	không
-Intermediate	TRUE	FALSE	FALSE	FALSE	Intermediate	متوسط	মধ্যবর্তী	中级	Meziprodukt	Mellemliggende	Intermediair	Väliaikainen	Intermédiaire	Mittlere	Ενδιάμεση	मध्यम	Intermediat	Intermedio	中間体	중간	Mellomliggende	Pośrednia	Intermediário	Intermediar	Проміжний	Intermedio	Kati	Mellanliggande	Orta seviye	Знижена чутливість	درمیانی	Trung gian
-Susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	Susceptible, incr. exp.	حساس، يحتاج تعرض زائد	সংবেদনশীল, অতিরিক্ত এক্সপোজার প্রয়োজন	易感，暴露增加	Vnímavý, zvýšená expozice	Modtagelig, øget eksponering	Gevoelig bij verhoogde blootstelling	Altis, lisääntynyt altistuminen	Sensible, à forte posologie	Empfindlich, erhöhte Belastung	Ευάλωτος, αυξημένη έκθεση	संवेदनशील, अधिक संपर्क	Rentan, perlu paparan tambahan	Sensibile, esposizione aumentata	感受性、曝露量増加	감수성, 노출 증가 필요	Mottakelig, økt eksponering	Podatne, zwiększone narażenie	Suscetível, exposição aumentada	Susceptibil, expunere crescută	Чутливий, підвищена експозиція	Susceptible, mayor exposición	Inayokubali, huhitaji mfiduo zaidi	Mottaglig, ökad exponering	Duyarlı, artmış maruziyet	Чутливий до підвищеної експозиції	حساس، مزید نمائش درکار	Nhạy cảm, cần tăng phơi nhiễm
-susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	susceptible, incr. exp.	حساس، يحتاج تعرض زائد	সংবেদনশীল, অতিরিক্ত এক্সপোজার প্রয়োজন	易感，接触增加	Vnímavý, zvýšená expozice	Modtagelig, øget eksponering	Gevoelig bij verhoogde blootstelling	Altis, lisääntynyt altistuminen	Sensible, à forte posologie	Empfindlich, erhöhte Belastung	Ευαίσθητος, αυξημένη έκθεση	संवेदनशील, अधिक संपर्क	rentan, perlu paparan tambahan	Sensibile, esposizione aumentata	影響を受けやすい、露出が増える	감수성, 노출 증가 필요	Mottakelig, økt eksponering	Podatne, zwiększone narażenie	Suscetível, exposição aumentada	Susceptibil, expunere crescută	Чутливий, підвищена експозиція	Susceptible, mayor exposición	inayokubali, huhitaji mfiduo zaidi	Mottaglig, ökad exponering	Duyarlı, artmış maruziyet	Чутливий до підвищеної експозиції	حساس، مزید نمائش درکار	nhạy cảm, cần tăng phơi nhiễm
-Susceptible	TRUE	FALSE	FALSE	FALSE	Susceptible	حساس	সংবেদনশীল	易受影响	Vnímavý	Modtagelig	Gevoelig	Altis	Sensible	Empfindlich	Ευαίσθητο	संवेदनशील	Rentan	Sensibile	影響を受けやすい	감수성 있음	Mottakelig	Podatny	Suscetível	Susceptibil	Чутливий	Susceptible	Inayokubali	Mottaglig	Duyarlı	Чутливий	حساس	Nhạy cảm
-Incr. exposure	TRUE	FALSE	FALSE	FALSE	Incr. exposure	زيادة التعرض	অতিরিক্ত এক্সপোজার	暴露增加	Zvýšená expozice	Øget eksponering	Verhoogde blootstelling	Lisääntynyt altistuminen	Forte posologie	Erhöhte Belastung	Αυξημένη έκθεση	अधिक संपर्क	Paparan tambahan	Esposizione aumentata	曝露量増加	노출 증가	Økt eksponering	Większe narażenie	Exposição aumentada	Expunere crescută	Підвищена експозиція	Mayor exposición	Mfiduo zaidi	Ökad exponering	Artmış maruziyet	Підвищена експозиція	زیادہ نمائش	Tăng phơi nhiễm
-Resistant	TRUE	FALSE	FALSE	FALSE	Resistant	مقاوم	প্রতিরোধী	耐药性	Rezistentní	Resistent	Resistent	Kestävä	Résistant	Resistent	Ανθεκτικός	प्रतिरोधी	Tahan	Resistente	耐性	내성	Resistent	Odporny	Resistente	Rezistent	Стійкий	Resistente	Sugu	Resistent	Dayanıklı	Стійкий	مزاحم	Kháng
-Non-interpretable	TRUE	FALSE	FALSE	FALSE	Non-interpretable	غير قابل للتفسير	ব্যাখ্যাতীত	无法解释	Nelze interpretovat	Ufortolkelig	Niet interpreteerbaar	Ei tulkittavissa	Non interprétable	Nicht interpretierbar	Μη ερμηνεύσιμο	अव्याख्यायनीय	Tidak dapat ditafsirkan	Non interpretabile	解釈不可	해석 불가	Utolkelig ikke	Niemożliwe do interpretacji	Não interpretável	Neinterpretabil	Непереводимо	No interpretable	Haieleweki	Inte tolkningsbar	Yorumlanamaz	Непридатний до інтерпретації	غیر قابل تشریح	Không diễn giải được
+Intermediate	TRUE	FALSE	FALSE	FALSE	Intermediate	متوسط	মধ্যবর্তী	中介	Intermediární	Intermediær	Intermediair	Kohtalaisen herkkä	Intermédiaire	Intermediär	Ενδιάμεσο	मध्यम	Intermediet	Intermedio	中間	중간	Intermediær	Średnio wrażliwy	Intermediário	Intermediar	Промежуточный	Intermedio	Kati	Intermediär	Orta duyarlı	Проміжний	درمیانی	Trung gian
+Susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	Susceptible, incr. exp.	حساس، يحتاج تعرض زائد	সংবেদনশীল, অতিরিক্ত এক্সপোজার প্রয়োজন	敏感，增加暴露	Citlivý, zvýšená expozice	Følsom ved øget eksponering	Gevoelig bij verhoogde blootstelling	Herkkä riittävän suurella annostuksella	Sensible à forte posologie	Sensibel bei erhöhter Exposition	Ευαίσθητο, αυξημένη έκθεση	संवेदनशील, अधिक संपर्क	Sensitif, paparan ditingkatkan	Sensibile, esposizione aumentata	感性、曝露量増加	감수성, 노출 증가 필요	Følsom ved økt eksponering	Wrażliwy, zwiększona ekspozycja	Suscetível, exposição aumentada	Sensibil, expunere crescută	Чувствительный при увеличенной экспозиции	Sensible, cuando se incrementa la exposición	Inayoathirika, mfiduo zaidi	Känslig vid ökad exponering	Duyarlı, artmış maruziyet	Чутливий при підвищеній експозиції	حساس، مزید نمائش درکار	Nhạy cảm, cần tăng phơi nhiễm
+susceptible, incr. exp.	FALSE	TRUE	FALSE	FALSE	susceptible, incr. exp.	حساس، يحتاج تعرض زائد	সংবেদনশীল, অতিরিক্ত এক্সপোজার প্রয়োজন	敏感，增加暴露	citlivý, zvýšená expozice	følsom ved øget eksponering	gevoelig bij verhoogde blootstelling	herkkä riittävän suurella annostuksella	sensible à forte posologie	sensibel bei erhöhter Exposition	ευαίσθητο, αυξημένη έκθεση	संवेदनशील, अधिक संपर्क	sensitif, paparan ditingkatkan	sensibile, esposizione aumentata	感性、曝露量増加	감수성, 노출 증가 필요	følsom ved økt eksponering	wrażliwy, zwiększona ekspozycja	suscetível, exposição aumentada	sensibil, expunere crescută	чувствительный при увеличенной экспозиции	sensible, cuando se incrementa la exposición	inayoathirika, mfiduo zaidi	känslig vid ökad exponering	duyarlı, artmış maruziyet	чутливий при підвищеній експозиції	حساس، مزید نمائش درکار	nhạy cảm, cần tăng phơi nhiễm
+Susceptible	TRUE	FALSE	FALSE	FALSE	Susceptible	حساس	সংবেদনশীল	敏感	Citlivý	Følsom	Gevoelig	Herkkä	Sensible	Sensibel	Ευαίσθητο	संवेदनशील	Sensitif	Sensibile	感性	감수성	Følsom	Wrażliwy	Suscetível	Sensibil	Чувствительный	Sensible	Inayoathirika	Känslig	Duyarlı	Чутливий	حساس	Nhạy cảm
+Incr. exposure	TRUE	FALSE	FALSE	FALSE	Incr. exposure	زيادة التعرض	অতিরিক্ত এক্সপোজার	增加暴露	Zvýšená expozice	Øget eksponering	Verhoogde blootstelling	Riittävän suuri annostus	Forte posologie	Erhöhte Exposition	Αυξημένη έκθεση	अधिक संपर्क	Paparan ditingkatkan	Esposizione aumentata	曝露量増加	노출 증가	Økt eksponering	Zwiększona ekspozycja	Exposição aumentada	Expunere crescută	Увеличенная экспозиция	Mayor exposición	Mfiduo zaidi	Ökad exponering	Artmış maruziyet	Підвищена експозиція	زیادہ نمائش	Tăng phơi nhiễm
+Resistant	TRUE	FALSE	FALSE	FALSE	Resistant	مقاوم	প্রতিরোধী	耐药	Rezistentní	Resistent	Resistent	Resistentti	Résistant	Resistent	Ανθεκτικό	प्रतिरोधी	Resisten	Resistente	耐性	내성	Resistent	Oporny	Resistente	Rezistent	Резистентный	Resistente	Sugu	Resistent	Dirençli	Резистентний	مزاحم	Kháng
+Non-interpretable	TRUE	FALSE	FALSE	FALSE	Non-interpretable	غير قابل للتفسير	ব্যাখ্যাতীত	无法判读	Nelze interpretovat	Ufortolkelig	Niet interpreteerbaar	Ei tulkittavissa	Non interprétable	Nicht interpretierbar	Μη ερμηνεύσιμο	अव्याख्यायनीय	Tidak dapat ditafsirkan	Non interpretabile	解釈不可	해석 불가	Ikke tolkbar	Niemożliwe do interpretacji	Não interpretável	Neinterpretabil	Не интерпретируемый	No interpretable	Haieleweki	Ej tolkningsbar	Yorumlanamaz	Непридатний до інтерпретації	غیر قابل تشریح	Không diễn giải được
+Susceptible dose-dependent	TRUE	FALSE	FALSE	FALSE	Susceptible dose-dependent	حساس حسب الجرعة	ডোজ-নির্ভর সংবেদনশীল	剂量依赖性敏感	Citlivý v závislosti na dávce	Følsom, dosisafhængig	Gevoelig, dosisafhankelijk	Herkkä, annoksesta riippuva	Sensible dose-dépendant	Sensibel, dosisabhängig	Ευαίσθητο εξαρτώμενο από τη δόση	खुराक-निर्भर संवेदनशील	Sensitif tergantung dosis	Sensibile dose-dipendente	用量依存的感性	용량 의존적 감수성	Følsom, doseavhengig	Wrażliwy zależnie od dawki	Suscetível dose-dependente	Sensibil dependent de doză	Дозозависимо чувствительный	Sensible dependiente de la dosis	Inayoathirika kulingana na dozi	Känslig, dosberoende	Doza bağlı duyarlı	Дозозалежно чутливий	خوراک پر منحصر حساس	Nhạy cảm phụ thuộc liều
+Non-susceptible	TRUE	FALSE	FALSE	FALSE	Non-susceptible	غير حساس	অসংবেদনশীল	不敏感	Necitlivý	Ikke-følsom	Niet-gevoelig	Ei herkkä	Non sensible	Nicht sensibel	Μη ευαίσθητο	असंवेदनशील	Tidak sensitif	Non sensibile	非感性	비감수성	Ikke-følsom	Niewrażliwy	Não suscetível	Nesensibil	Нечувствительный	No sensible	Isiyoathirika	Ej känslig	Duyarlı değil	Нечутливий	غیر حساس	Không nhạy cảm
+Non-wildtype	TRUE	FALSE	FALSE	FALSE	Non-wildtype	غير النمط البري	অ-বন্য প্রকার	非野生型	Jiný než divoký typ	Ikke-vildtype	Niet-wildtype	Ei-villityyppi	Type non sauvage	Nicht-Wildtyp	Μη άγριος τύπος	गैर-वन्य प्रकार	Bukan tipe liar	Tipo non selvatico	非野生型	비야생형	Ikke-villtype	Typ inny niż dziki	Tipo não selvagem	Tip non-sălbatic	Не дикий тип	Tipo no salvaje	Si aina ya asili	Icke-vildtyp	Yabanıl tip dışı	Не дикий тип	غیر جنگلی قسم	Không phải kiểu hoang dã
+Wildtype	TRUE	FALSE	FALSE	FALSE	Wildtype	النمط البري	বন্য প্রকার	野生型	Divoký typ	Vildtype	Wildtype	Villityyppi	Type sauvage	Wildtyp	Άγριος τύπος	वन्य प्रकार	Tipe liar	Tipo selvatico	野生型	야생형	Villtype	Typ dziki	Tipo selvagem	Tip sălbatic	Дикий тип	Tipo salvaje	Aina ya asili	Vildtyp	Yabanıl tip	Дикий тип	جنگلی قسم	Kiểu hoang dã
 antibiotic	TRUE	TRUE	FALSE	FALSE	antibiotic	مضاد حيوي	অ্যান্টিবায়োটিক	抗生素	antibiotikum	antibiotikum	antibioticum	antibiootti	antibiotique	Antibiotikum	αντιβιοτικό	प्रतिजैविक	Antibiotik	antibiotico	抗生物質	항생제	Antibiotikum	antybiotyk	antibiótico	antibiotic	антибиотик	antibiótico	antibayotiki	antibiotika	Antibiyotik	антибіотик	اینٹی بایوٹک	Kháng sinh
 Antibiotic	TRUE	TRUE	FALSE	FALSE	Antibiotic	مضاد حيوي	অ্যান্টিবায়োটিক	抗生素	Antibiotikum	Antibiotikum	Antibioticum	Antibiootti	Antibiotique	Antibiotikum	Αντιβιοτικό	प्रतिजैविक	Antibiotik	Antibiotico	抗生物質	항생제	Antibiotikum	Antybiotyk	Antibiótico	Antibiotic	Антибиотик	Antibiótico	Antibayotiki	Antibiotika	Antibiyotik	Антибіотик	اینٹی بایوٹک	Kháng sinh
 Drug	TRUE	TRUE	FALSE	FALSE	Drug	دواء	ড্রাগ	药物	Lék	Lægemiddel	Middel	Lääke	Médicament	Medikament	Φάρμακο	दवा	Obat	Droga	薬剤	약물	Legemiddel	Lek	Droga	Medicament	Лекарство	Fármaco	Dawa	Läkemedel	İlaç	Лікарський засіб	Dوا	Nhóm thuốc
@@ -35,21 +35,21 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
 scale_x_sir(
  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
  language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
+  eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
  ...
 )

 scale_colour_sir(
  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
  language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
+  eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
  ...
 )

 scale_fill_sir(
  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
  language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
+  eucast_I = plot_name_of_I(getOption("AMR_guideline", "EUCAST")) != "Intermediate",
  ...
 )

@@ -158,11 +158,11 @@ theme_sir()

 \item{...}{Arguments passed on to methods.}

-\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of three values (in the order S, I and R). The default colours are colour-blind friendly.}
+\item{colours_SIR}{Colours to use for filling in the bars, must be a vector of one, three or four values (in the order S, SDD, I and R), or a named vector with at least the names S, I and R. With three values or without a name SDD, SDD gets the colour of S. The default colours are colour-blind friendly.}

 \item{language}{Language to be used to translate 'Susceptible', 'Increased exposure'/'Intermediate' and 'Resistant' - the default is system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can be overwritten by setting the package option \code{\link[=AMR-options]{AMR_locale}}, e.g. \code{options(AMR_locale = "de")}, see \link{translate}. Use \code{language = NULL} to prevent translation.}

-\item{eucast_I}{A \link{logical} to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be \code{TRUE} if the default \link[=as.sir]{AMR interpretation guideline} is set to EUCAST (which is the default). With \code{FALSE}, it will be interpreted as "Intermediate".}
+\item{eucast_I}{A \link{logical} to indicate whether the 'I' must be interpreted as "Susceptible, under increased exposure". Will be \code{TRUE} if the default \link[=as.sir]{AMR interpretation guideline} is set to EUCAST 2019 or later (which is the default). With \code{FALSE}, it will be interpreted as "Intermediate".}

 \item{x, object}{Values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.sir]{as.sir()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}}).}

@@ -198,12 +198,12 @@ The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} mo
 \description{
 Functions to plot classes \code{sir}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.

-Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allows custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
+Especially the \verb{scale_*_mic()} functions are relevant wrappers to plot MIC values for \code{ggplot2}. They allow custom MIC ranges and to plot intermediate log2 levels for missing MIC values.
 }
 \details{
 \subsection{The \verb{scale_*_mic()} Functions}{

-The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} functions allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale.
+The functions \code{\link[=scale_x_mic]{scale_x_mic()}}, \code{\link[=scale_y_mic]{scale_y_mic()}}, \code{\link[=scale_colour_mic]{scale_colour_mic()}}, and \code{\link[=scale_fill_mic]{scale_fill_mic()}} allow to plot the \link[=as.mic]{mic} class (MIC values) on a continuous, logarithmic scale.

 There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class \link[=as.mic]{mic}.

@@ -212,7 +212,7 @@ When manually added though, they allow to rescale the MIC range with an 'inside'

 \subsection{The \verb{scale_*_sir()} Functions}{

-The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} functions allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI < WT < NWT < NS).
+The functions \code{\link[=scale_x_sir]{scale_x_sir()}}, \code{\link[=scale_colour_sir]{scale_colour_sir()}}, and \code{\link[=scale_fill_sir]{scale_fill_sir()}} allow to plot the \link[=as.sir]{sir} class in the right order (S < SDD < I < R < NI < WT < NWT < NS).

 There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class \link[=as.sir]{sir}.

@@ -227,10 +227,10 @@ This package contains more functions that extend the \code{ggplot2} package, to
 \item \code{\link[=scale_y_percent]{scale_y_percent()}} transforms the y axis to a 0 to 100\% range using \code{\link[ggplot2:scale_y_continuous]{ggplot2::scale_y_continuous()}}.
 \item \code{\link[=scale_sir_colours]{scale_sir_colours()}} allows to set colours to any aesthetic, even for \code{shape} or \code{linetype}.
 \item \code{\link[=theme_sir]{theme_sir()}} is a \link[ggplot2:theme]{ggplot2 theme} with minimal distraction.
-\item \code{\link[=labels_sir_count]{labels_sir_count()}} print datalabels on the bars with percentage and number of isolates, using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
+\item \code{\link[=labels_sir_count]{labels_sir_count()}} prints data labels on the bars with percentage and number of isolates, using \code{\link[ggplot2:geom_text]{ggplot2::geom_text()}}.
 }

-The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
+The interpretation of "I" will be named "Susceptible, incr. exp." (susceptible, increased exposure) for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.

 For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2026, unless the package option \code{\link[=AMR-options]{AMR_guideline}} is set. See \code{\link[=as.sir]{as.sir()}} for more information.
 }
@@ -254,7 +254,7 @@ if (require("ggplot2")) {
 }

 if (require("ggplot2")) {
-  # support for 27 languages, various guidelines, and many options
+  # support for all languages in ?translate, various guidelines, and many options
  autoplot(some_disk_values,
    mo = "Escherichia coli", ab = "cipro",
    guideline = "CLSI", language = "no",
@@ -351,8 +351,8 @@ if (require("ggplot2")) {
  ) +
    theme_minimal() +
    geom_boxplot(fill = NA, colour = "grey30") +
-    geom_jitter(width = 0.25)
-  labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
+    geom_jitter(width = 0.25) +
+    labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")

  mic_sir_plot
 }
@@ -361,7 +361,7 @@ if (require("ggplot2")) {
    scale_y_mic(mic_range = c(0.005, 32), name = "Our MICs!") +
    scale_colour_sir(
      language = "pt", # Portuguese
-      name = "Support in 28 languages"
+      name = "Support in many languages"
    )
 }
 }
@@ -49,7 +49,10 @@ test_that("test-antibiogram.R", {
  expect_false(identical(as.data.frame(wisca_all), as.data.frame(wisca_known)))
  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
    ab_grouped <- tryCatch(
-      example_isolates %>% group_by(ward) %>% antibiogram(antimicrobials = "GEN", minimum = 0, formatting_type = 1, guideline = "EUCAST"),
+      # pathogen names are translated, so test in English, which must also hold on systems in another language
+      example_isolates %>%
+        group_by(ward) %>%
+        antibiogram(antimicrobials = "GEN", minimum = 0, formatting_type = 1, guideline = "EUCAST", language = "en"),
      warning = function(w) conditionMessage(w)
    )
    expect_inherits(ab_grouped, "antibiogram")
@@ -114,5 +114,90 @@ test_that("test-plotting.R", {
        scale_x_sir(),
      "gg"
    )
+
+    # named colours are matched by name, and SDD, S/I and I/R follow S and R
+    expect_identical(AMR:::expand_SIR_colours(c(R = "r", I = "i", SDD = "d", S = "s")), c("s", "d", "i", "r", "s", "r"))
+    expect_identical(AMR:::expand_SIR_colours(c(S = "s", I = "i", R = "r")), c("s", "s", "i", "r", "s", "r"))
+    expect_identical(AMR:::expand_SIR_colours(c("s", "i", "r")), c("s", "s", "i", "r", "s", "r"))
+    expect_error(AMR:::expand_SIR_colours(c(S = "s", I = "i", X = "r")))
+
+    # colours of SIR bar plots follow the SIR values
+    sir_values <- as.sir(c("S", "S", "R", "NI", "NS"))
+    keep <- AMR:::plot_sir_levels_to_keep(sir_values, table(sir_values))
+    expect_identical(names(table(sir_values))[keep], c("S", "R", "NI", "NS"))
+    p <- autoplot(sir_values)
+    expect_identical(as.character(p$data$x), c("S", "R", "NI", "NS"))
+    expect_identical(unique(ggplot_build(p)$data[[1]]$fill), c("#3CAEA3", "#ED553B", "grey30"))
+
+    # SDD in disk diffusion plots
+    p <- autoplot(as.disk(15:30), mo = "Escherichia coli", ab = "cefepime", guideline = "CLSI 2025", language = "en")
+    expect_true("(SDD) Susceptible dose-dependent" %in% as.character(p$data$cols))
+    expect_false(anyNA(p$data$cols))
+
+    # colours and labels are named by, and cover, all SIR levels
+    expect_identical(names(AMR:::plot_sir_colour_values(AMR:::expand_SIR_colours("red"))), AMR:::VALID_SIR_LEVELS)
+    expect_identical(names(AMR:::plot_sir_label_values("EUCAST")), AMR:::VALID_SIR_LEVELS)
+
+    # arguments are passed on
+    expect_identical(scale_x_sir(name = "Interpretation")$name, "Interpretation")
+    expect_identical(scale_fill_sir(values = c(S = "black"))$palette(1)[["S"]], "black")
+    expect_identical(scale_fill_sir(values = c(S = "black"))$palette(1)[["R"]], "#ED553B")
+    expect_error(scale_fill_sir(values = c("black", "white", "grey")))
+    expect_warning(scale_x_sir(values = c(S = "black")))
+    expect_identical(AMR:::plot_count_ticks(3), c(0, 1, 2, 3))
+    expect_identical(AMR:::plot_name_of_I("EUCAST"), "Susceptible, incr. exp.")
+    expect_identical(AMR:::plot_name_of_I("EUCAST 2018"), "Intermediate")
+
+    # unquoted column names in facet_sir() are not evaluated, also not if an object with that name exists
+    antibiotic <- "some other column"
+    expect_identical(facet_sir(antibiotic)$params$facets, facet_sir("antibiotic")$params$facets)
+
+    # the default of eucast_I follows the guideline option
+    expect_identical(scale_fill_sir(language = "en")$labels("I"), "(I) Susceptible, incr. exp.")
+    old_option <- options(AMR_guideline = "EUCAST 2018")
+    expect_identical(scale_fill_sir(language = "en")$labels("I"), "(I) Intermediate")
+    options(old_option)
+
+    # keep_operators = TRUE/FALSE equals "all"/"none"
+    mic_labels <- function(keep_operators) {
+      p <- ggplot(data.frame(m = as.mic(c(">=8", "2", "<=0.5"))), aes(m, 1)) +
+        geom_point() +
+        scale_x_mic(keep_operators = keep_operators)
+      ggplot_build(p)$layout$panel_params[[1]]$x$get_labels()
+    }
+    expect_identical(mic_labels(TRUE), mic_labels("all"))
+    expect_identical(mic_labels(FALSE), mic_labels("none"))
+    expect_false(identical(mic_labels(TRUE), mic_labels(FALSE)))
  }
+
+  # base R plots: texts in the legend (drawn with text()) and bar names (drawn with axis())
+  recorded_strings <- function(expr, fn) {
+    pdf(NULL)
+    dev.control("enable")
+    on.exit(dev.off())
+    force(expr)
+    unlist(lapply(recordPlot()[[1]], function(call) {
+      if (identical(call[[2]][[1]]$name, fn)) {
+        as.character(call[[2]][[if (fn == "C_text") 3 else 4]])
+      }
+    }))
+  }
+  mic_values <- as.mic(c(0.25, 0.25, 4, 32))
+
+  # the legend is based on the interpretation, so SDD is not shown when it has the colour of S
+  expect_identical(
+    recorded_strings(plot(mic_values, mo = "Escherichia coli", ab = "AMC", language = "en", colours_SIR = c("green", "yellow", "red")), "C_text"),
+    c("(S) Susceptible", "(R) Resistant")
+  )
+  # zone diameters run from resistant to susceptible, and so does the legend
+  expect_identical(
+    recorded_strings(plot(as.disk(15:30), mo = "Escherichia coli", ab = "cefepime", guideline = "CLSI 2025", language = "en"), "C_text"),
+    c("(R) Resistant", "(SDD) Susceptible dose-dependent", "(S) Susceptible")
+  )
+  # barplot() for MIC values passes on language and expand
+  expect_identical(
+    recorded_strings(barplot(mic_values, mo = "Escherichia coli", ab = "AMC", language = "nl"), "C_text"),
+    c("(S) Gevoelig", "(R) Resistent")
+  )
+  expect_true(length(recorded_strings(barplot(mic_values, expand = TRUE), "C_axis")) > length(recorded_strings(barplot(mic_values, expand = FALSE), "C_axis")))
 })