(v3.0.0.9008) fix ggplot_sir(), support lighter green for SDD

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0.9004
+Version: 3.0.0.9008
-Date: 2025-06-13
+Date: 2025-07-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,15 +1,20 @@
-# AMR 3.0.0.9004
+# AMR 3.0.0.9008
+
+This is primarily a bugfix release, though we added one nice feature too.
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of MIC and SIR data in modelling pipelines via `recipes`
   - `step_mic_log2()` to transform `<mic>` columns with log2, and `step_sir_numeric()` to convert `<sir>` columns to numeric
-  - `tidyselect` helpers: `all_mic()`, `all_mic_predictors()`, `all_sir()`, `all_sir_predictors()`
+  - New `tidyselect` helpers: `all_mic()`, `all_mic_predictors()`, `all_sir()`, `all_sir_predictors()`
-  - Enables seamless use of MIC and SIR data in modelling pipelines via `recipes`
 
 ### Changed
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
+* Fixed a bug in `antibiogram()` to allow column names containing the `+` character (#222)
 * Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space
 * Fixed a bug in `eucast_rules()` for using specific custom rules
+* Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
+* Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
+* Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent)
 * Fixed some specific Dutch translations for antimicrobials
 * Updated `random_mic()` and `random_disk()` to set skewedness of the distribution and allow multiple microorganisms
 

R/aa_helper_functions.R

@@ -63,31 +63,6 @@ pm_left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
   merged
 }
 
-# support where() like tidyverse (this function will also be used when running `antibiogram()`):
-where <- function(fn) {
-  # based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
-  if (!is.function(fn)) {
-    stop_("`", deparse(substitute(fn)), "()` is not a valid predicate function.")
-  }
-  df <- pm_select_env$.data
-  cols <- pm_select_env$get_colnames()
-  if (is.null(df)) {
-    df <- get_current_data("where", call = FALSE)
-    cols <- colnames(df)
-  }
-  preds <- unlist(lapply(
-    df,
-    function(x, fn) {
-      do.call("fn", list(x))
-    },
-    fn
-  ))
-  if (!is.logical(preds)) stop_("`where()` must be used with functions that return `TRUE` or `FALSE`.")
-  data_cols <- cols
-  cols <- data_cols[preds]
-  which(data_cols %in% cols)
-}
-
 # copied and slightly rewritten from {poorman} under permissive license (2021-10-15)
 # https://github.com/nathaneastwood/poorman, MIT licensed, Nathan Eastwood, 2020
 case_when_AMR <- function(...) {
@@ -814,7 +789,7 @@ meet_criteria <- function(object, # can be literally `list(...)` for `allow_argu
 
   # if object is missing, or another error:
   tryCatch(invisible(object),
-    error = function(e) AMR_env$meet_criteria_error_txt <- e$message
+    error = function(e) AMR_env$meet_criteria_error_txt <- conditionMessage(e)
   )
   if (!is.null(AMR_env$meet_criteria_error_txt)) {
     error_txt <- AMR_env$meet_criteria_error_txt
@@ -1319,6 +1294,10 @@ font_green_bg <- function(..., collapse = " ") {
   # this is #3caea3 (picked to be colourblind-safe with other SIR colours)
   try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;79m", after = "\033[49m", collapse = collapse)
 }
+font_green_lighter_bg <- function(..., collapse = " ") {
+  # this is #8FD6C4 (picked to be colourblind-safe with other SIR colours)
+  try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;158m", after = "\033[49m", collapse = collapse)
+}
 font_purple_bg <- function(..., collapse = " ") {
   try_colour(font_black(..., collapse = collapse, adapt = FALSE), before = "\033[48;5;89m", after = "\033[49m", collapse = collapse)
 }
@@ -1636,6 +1615,36 @@ get_n_cores <- function(max_cores = Inf) {
   n_cores
 }
 
+# Support `where()` if tidyselect not installed ----
+if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
+  # tidyselect::where() exists, load the namespace to make `where()`s work across the package in default arguments
+  loadNamespace("tidyselect")
+} else {
+  where <- function(fn) {
+    # based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32
+    if (!is.function(fn)) {
+      stop_("`", deparse(substitute(fn)), "()` is not a valid predicate function.")
+    }
+    df <- pm_select_env$.data
+    cols <- pm_select_env$get_colnames()
+    if (is.null(df)) {
+      df <- get_current_data("where", call = FALSE)
+      cols <- colnames(df)
+    }
+    preds <- unlist(lapply(
+      df,
+      function(x, fn) {
+        do.call("fn", list(x))
+      },
+      fn
+    ))
+    if (!is.logical(preds)) stop_("`where()` must be used with functions that return `TRUE` or `FALSE`.")
+    data_cols <- cols
+    cols <- data_cols[preds]
+    which(data_cols %in% cols)
+  }
+}
+
 # Faster data.table implementations ----
 
 match <- function(x, table, ...) {
@@ -1655,52 +1664,6 @@ match <- function(x, table, ...) {
   }
 }
 
-# nolint start
-
-# Register S3 methods ----
-# copied from vctrs::s3_register by their permission:
-# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
-s3_register <- function(generic, class, method = NULL) {
-  stopifnot(is.character(generic), length(generic) == 1)
-  stopifnot(is.character(class), length(class) == 1)
-  pieces <- strsplit(generic, "::")[[1]]
-  stopifnot(length(pieces) == 2)
-  package <- pieces[[1]]
-  generic <- pieces[[2]]
-  caller <- parent.frame()
-  get_method_env <- function() {
-    top <- topenv(caller)
-    if (isNamespace(top)) {
-      asNamespace(environmentName(top))
-    } else {
-      caller
-    }
-  }
-  get_method <- function(method, env) {
-    if (is.null(method)) {
-      get(paste0(generic, ".", class), envir = get_method_env())
-    } else {
-      method
-    }
-  }
-  method_fn <- get_method(method)
-  stopifnot(is.function(method_fn))
-  setHook(packageEvent(package, "onLoad"), function(...) {
-    ns <- asNamespace(package)
-    method_fn <- get_method(method)
-    registerS3method(generic, class, method_fn, envir = ns)
-  })
-  if (!isNamespaceLoaded(package)) {
-    return(invisible())
-  }
-  envir <- asNamespace(package)
-  if (exists(generic, envir)) {
-    registerS3method(generic, class, method_fn, envir = envir)
-  }
-  invisible()
-}
-
-
 # Support old R versions ----
 # these functions were not available in previous versions of R
 # see here for the full list: https://github.com/r-lib/backports

R/aa_helper_pm_functions.R

@@ -952,7 +952,19 @@ pm_select_env$get_nrow <- function() nrow(pm_select_env$.data)
 pm_select_env$get_ncol <- function() ncol(pm_select_env$.data)
 
 pm_select <- function(.data, ...) {
-  col_pos <- pm_select_positions(.data, ..., .group_pos = TRUE)
+  # col_pos <- pm_select_positions(.data, ..., .group_pos = TRUE),
+  col_pos <- tryCatch(pm_select_positions(.data, ..., .group_pos = TRUE), error = function(e) NULL)
+  if (is.null(col_pos)) {
+    # try with tidyverse
+    select_dplyr <- import_fn("select", "dplyr", error_on_fail = FALSE)
+    if (!is.null(select_dplyr)) {
+      col_pos <- which(colnames(.data) %in% colnames(select_dplyr(.data, ...)))
+    } else {
+      # this will throw an error as it did, but dplyr is not available, so no other option
+      col_pos <- pm_select_positions(.data, ..., .group_pos = TRUE)
+    }
+  }
+
   map_names <- names(col_pos)
   map_names_length <- nchar(map_names)
   if (any(map_names_length == 0L)) {

R/ab.R

@@ -184,7 +184,8 @@ as.ab <- function(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
   x_new[known_codes_cid] <- AMR_env$AB_lookup$ab[match(x[known_codes_cid], AMR_env$AB_lookup$cid)]
   previously_coerced <- x %in% AMR_env$ab_previously_coerced$x
   x_new[previously_coerced & is.na(x_new)] <- AMR_env$ab_previously_coerced$ab[match(x[is.na(x_new) & x %in% AMR_env$ab_previously_coerced$x], AMR_env$ab_previously_coerced$x)]
-  if (any(previously_coerced) && isTRUE(info) && message_not_thrown_before("as.ab", entire_session = TRUE)) {
+  previously_coerced_mention <- x %in% AMR_env$ab_previously_coerced$x & !x %in% AMR_env$AB_lookup$ab & !x %in% AMR_env$AB_lookup$generalised_name
+  if (any(previously_coerced_mention) && isTRUE(info) && message_not_thrown_before("as.ab", entire_session = TRUE)) {
     message_(
       "Returning previously coerced ",
       ifelse(length(unique(which(x[which(previously_coerced)] %in% x_bak_clean))) > 1, "value for an antimicrobial", "values for various antimicrobials"),

R/ab_property.R

@@ -445,7 +445,7 @@ ab_validate <- function(x, property, ...) {
     # try to catch an error when inputting an invalid argument
     # so the 'call.' can be set to FALSE
     tryCatch(x[1L] %in% AMR_env$AB_lookup[1, property, drop = TRUE],
-      error = function(e) stop(e$message, call. = FALSE)
+      error = function(e) stop(conditionMessage(e), call. = FALSE)
     )
 
     if (!all(x %in% AMR_env$AB_lookup[, property, drop = TRUE])) {

R/amr_selectors.R

@@ -527,7 +527,7 @@ amr_selector <- function(filter,
   )
   call <- substitute(filter)
   agents <- tryCatch(AMR_env$AB_lookup[which(eval(call, envir = AMR_env$AB_lookup)), "ab", drop = TRUE],
-    error = function(e) stop_(e$message, call = -5)
+    error = function(e) stop_(conditionMessage(e), call = -5)
   )
   agents <- ab_in_data[ab_in_data %in% agents]
   message_agent_names(
@@ -640,7 +640,7 @@ not_intrinsic_resistant <- function(only_sir_columns = FALSE, col_mo = NULL, ver
         )
       }
     ),
-    error = function(e) stop_("in not_intrinsic_resistant(): ", e$message, call = FALSE)
+    error = function(e) stop_("in not_intrinsic_resistant(): ", conditionMessage(e), call = FALSE)
   )
 
   agents <- ab_in_data[ab_in_data %in% names(vars_df_R[which(vars_df_R)])]

R/antibiogram.R

@@ -576,6 +576,15 @@ antibiogram.default <- function(x,
     }
     antimicrobials <- unlist(antimicrobials)
   } else {
+    existing_ab_combined_cols <- ab_trycatch[ab_trycatch %like% "[+]" & ab_trycatch %in% colnames(x)]
+    if (length(existing_ab_combined_cols) > 0 && !is.null(ab_transform)) {
+      ab_transform <- NULL
+      warning_(
+        "Detected column name(s) containing the '+' character, which conflicts with the expected syntax in `antibiogram()`: the '+' is used to combine separate antimicrobial agent columns (e.g., \"AMP+GEN\").\n\n",
+        "To avoid incorrectly guessing which antimicrobials this represents, `ab_transform` was automatically set to `NULL`.\n\n",
+        "If this is unintended, please rename the column(s) to avoid using '+' in the name, or set `ab_transform = NULL` explicitly to suppress this message."
+      )
+    }
     antimicrobials <- ab_trycatch
   }
 

R/av_property.R

@@ -264,7 +264,7 @@ av_validate <- function(x, property, ...) {
     # try to catch an error when inputting an invalid argument
     # so the 'call.' can be set to FALSE
     tryCatch(x[1L] %in% AMR_env$AV_lookup[1, property, drop = TRUE],
-      error = function(e) stop(e$message, call. = FALSE)
+      error = function(e) stop(conditionMessage(e), call. = FALSE)
     )
 
     if (!all(x %in% AMR_env$AV_lookup[, property, drop = TRUE])) {

R/count.R

@@ -126,7 +126,7 @@ count_resistant <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -139,7 +139,7 @@ count_susceptible <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -152,7 +152,7 @@ count_S <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -165,7 +165,7 @@ count_SI <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -178,7 +178,7 @@ count_I <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -191,7 +191,7 @@ count_IR <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -204,7 +204,7 @@ count_R <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -217,7 +217,7 @@ count_all <- function(..., only_all_tested = FALSE) {
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -240,6 +240,6 @@ count_df <- function(data,
       combine_SI = combine_SI,
       confidence_level = 0.95 # doesn't matter, will be removed
     ),
-    error = function(e) stop_(gsub("in sir_calc_df(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc_df(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }

R/custom_mdro_guideline.R

@@ -175,7 +175,7 @@ custom_mdro_guideline <- function(..., as_factor = TRUE) {
 
     # Value
     val <- tryCatch(eval(dots[[i]][[3]]), error = function(e) NULL)
-    stop_if(is.null(val), "rule ", i, " must return a valid value, it now returns an error: ", tryCatch(eval(dots[[i]][[3]]), error = function(e) e$message))
+    stop_if(is.null(val), "rule ", i, " must return a valid value, it now returns an error: ", tryCatch(eval(dots[[i]][[3]]), error = function(e) conditionMessage(e)))
     stop_if(length(val) > 1, "rule ", i, " must return a value of length 1, not ", length(val))
     out[[i]]$value <- as.character(val)
   }
@@ -254,7 +254,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
   for (i in seq_len(n_dots)) {
     qry <- tryCatch(eval(parse(text = guideline[[i]]$query), envir = df, enclos = parent.frame()),
       error = function(e) {
-        AMR_env$err_msg <- e$message
+        AMR_env$err_msg <- conditionMessage(e)
         return("error")
       }
     )

R/eucast_rules.R

@@ -1178,7 +1178,7 @@ edit_sir <- function(x,
             ifelse(length(rows) > 10, "...", ""),
             " while writing value '", to,
             "' to column(s) `", paste(cols, collapse = "`, `"),
-            "`:\n", e$message
+            "`:\n", conditionMessage(e)
           ),
           call. = FALSE
         )

R/ggplot_sir.R

@@ -178,6 +178,7 @@ ggplot_sir <- function(data,
                        colours = c(
                          S = "#3CAEA3",
                          SI = "#3CAEA3",
+                         SDD = "#8FD6C4",
                          I = "#F6D55C",
                          IR = "#ED553B",
                          R = "#ED553B"

R/mean_amr_distance.R

@@ -31,7 +31,7 @@
 #'
 #' Calculates a normalised mean for antimicrobial resistance between multiple observations, to help to identify similar isolates without comparing antibiograms by hand.
 #' @param x A vector of class [sir][as.sir()], [mic][as.mic()] or [disk][as.disk()], or a [data.frame] containing columns of any of these classes.
-#' @param ... Variables to select. Supports [tidyselect language][tidyselect::language] (such as `column1:column4` and `where(is.mic)`), and can thus also be [antimicrobial selectors][amr_selector()].
+#' @param ... Variables to select. Supports [tidyselect language][tidyselect::starts_with()] such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and can thus also be [antimicrobial selectors][amr_selector()].
 #' @param combine_SI A [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is `TRUE`.
 #' @details The mean AMR distance is effectively [the Z-score](https://en.wikipedia.org/wiki/Standard_score); a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.
 #'

R/mo.R

@@ -1186,7 +1186,7 @@ parse_and_convert <- function(x) {
         parsed <- gsub('"', "", parsed, fixed = TRUE)
         parsed
       },
-      error = function(e) stop(e$message, call. = FALSE)
+      error = function(e) stop(conditionMessage(e), call. = FALSE)
     ) # this will also be thrown when running `as.mo(no_existing_object)`
   }
   out <- trimws2(out)

R/mo_property.R

@@ -974,7 +974,7 @@ mo_validate <- function(x, property, language, keep_synonyms = keep_synonyms, ..
   # try to catch an error when inputting an invalid argument
   # so the 'call.' can be set to FALSE
   tryCatch(x[1L] %in% unlist(AMR_env$MO_lookup[1, property, drop = TRUE]),
-    error = function(e) stop(e$message, call. = FALSE)
+    error = function(e) stop(conditionMessage(e), call. = FALSE)
   )
 
   dots <- list(...)

R/pca.R

@@ -99,7 +99,7 @@ pca <- function(x,
     new_list <- list(0)
     for (i in seq_len(length(dots) - 1)) {
       new_list[[i]] <- tryCatch(eval(dots[[i + 1]], envir = x),
-        error = function(e) stop(e$message, call. = FALSE)
+        error = function(e) stop(conditionMessage(e), call. = FALSE)
       )
       if (length(new_list[[i]]) == 1) {
         if (is.character(new_list[[i]]) && new_list[[i]] %in% colnames(x)) {

R/plotting.R

@@ -377,6 +377,13 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
   args <- list(...)
   args[c("value", "labels", "limits")] <- NULL
 
+  if (length(colours_SIR) == 1) {
+    colours_SIR <- rep(colours_SIR, 4)
+  } else if (length(colours_SIR) == 3) {
+    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
+  }
+  colours_SIR <- unname(colours_SIR)
+
   if (identical(aesthetics, "x")) {
     ggplot_fn <- ggplot2::scale_x_discrete
   } else {
@@ -388,8 +395,8 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
         values = c(
           S = colours_SIR[1],
           SDD = colours_SIR[2],
-          I = colours_SIR[2],
+          I = colours_SIR[3],
-          R = colours_SIR[3],
+          R = colours_SIR[4],
           NI = "grey30"
         )
       )
@@ -427,11 +434,16 @@ create_scale_sir <- function(aesthetics, colours_SIR, language, eucast_I, ...) {
 
 #' @rdname plot
 #' @export
-scale_x_sir <- function(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+scale_x_sir <- function(colours_SIR = c(
+                          S = "#3CAEA3",
+                          SDD = "#8FD6C4",
+                          I = "#F6D55C",
+                          R = "#ED553B"
+                        ),
                         language = get_AMR_locale(),
                         eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
                         ...) {
-  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
@@ -439,11 +451,16 @@ scale_x_sir <- function(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
 
 #' @rdname plot
 #' @export
-scale_colour_sir <- function(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+scale_colour_sir <- function(colours_SIR = c(
+                               S = "#3CAEA3",
+                               SDD = "#8FD6C4",
+                               I = "#F6D55C",
+                               R = "#ED553B"
+                             ),
                              language = get_AMR_locale(),
                              eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
                              ...) {
-  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
   args <- list(...)
@@ -463,11 +480,16 @@ scale_color_sir <- scale_colour_sir
 
 #' @rdname plot
 #' @export
-scale_fill_sir <- function(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+scale_fill_sir <- function(colours_SIR = c(
+                             S = "#3CAEA3",
+                             SDD = "#8FD6C4",
+                             I = "#F6D55C",
+                             R = "#ED553B"
+                           ),
                            language = get_AMR_locale(),
                            eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
                            ...) {
-  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
   args <- list(...)
@@ -491,7 +513,12 @@ plot.mic <- function(x,
                      main = deparse(substitute(x)),
                      ylab = translate_AMR("Frequency", language = language),
                      xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
-                     colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                     colours_SIR = c(
+                       S = "#3CAEA3",
+                       SDD = "#8FD6C4",
+                       I = "#F6D55C",
+                       R = "#ED553B"
+                     ),
                      language = get_AMR_locale(),
                      expand = TRUE,
                      include_PKPD = getOption("AMR_include_PKPD", TRUE),
@@ -503,15 +530,11 @@ plot.mic <- function(x,
   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))
+  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)
 
   x <- as.mic(x) # make sure that currently implemented MIC levels are used
-
-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 3)
-  }
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
   x <- plotrange_as_table(x, expand = expand)
@@ -549,13 +572,17 @@ plot.mic <- function(x,
       legend_col <- colours_SIR[1]
     }
     if (any(cols_sub$cols == colours_SIR[2] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
+      legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
       legend_col <- c(legend_col, colours_SIR[2])
     }
     if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
-      legend_txt <- c(legend_txt, "(R) Resistant")
+      legend_txt <- c(legend_txt, paste("(I)", plot_name_of_I(cols_sub$guideline)))
       legend_col <- c(legend_col, colours_SIR[3])
     }
+    if (any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
+      legend_txt <- c(legend_txt, "(R) Resistant")
+      legend_col <- c(legend_col, colours_SIR[4])
+    }
 
     legend("top",
       x.intersp = 0.5,
@@ -580,7 +607,12 @@ barplot.mic <- function(height,
                         main = deparse(substitute(height)),
                         ylab = translate_AMR("Frequency", language = language),
                         xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
-                        colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                        colours_SIR = c(
+                          S = "#3CAEA3",
+                          SDD = "#8FD6C4",
+                          I = "#F6D55C",
+                          R = "#ED553B"
+                        ),
                         language = get_AMR_locale(),
                         expand = TRUE,
                         ...) {
@@ -590,7 +622,7 @@ barplot.mic <- function(height,
   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(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
 
@@ -622,7 +654,12 @@ autoplot.mic <- function(object,
                          title = deparse(substitute(object)),
                          ylab = translate_AMR("Frequency", language = language),
                          xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language = language),
-                         colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                         colours_SIR = c(
+                           S = "#3CAEA3",
+                           SDD = "#8FD6C4",
+                           I = "#F6D55C",
+                           R = "#ED553B"
+                         ),
                          language = get_AMR_locale(),
                          expand = TRUE,
                          include_PKPD = getOption("AMR_include_PKPD", TRUE),
@@ -635,7 +672,7 @@ autoplot.mic <- function(object,
   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))
+  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)
 
@@ -731,7 +768,12 @@ plot.disk <- function(x,
                       mo = NULL,
                       ab = NULL,
                       guideline = getOption("AMR_guideline", "EUCAST"),
-                      colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                      colours_SIR = c(
+                        S = "#3CAEA3",
+                        SDD = "#8FD6C4",
+                        I = "#F6D55C",
+                        R = "#ED553B"
+                      ),
                       language = get_AMR_locale(),
                       expand = TRUE,
                       include_PKPD = getOption("AMR_include_PKPD", TRUE),
@@ -743,13 +785,10 @@ plot.disk <- function(x,
   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(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
 
-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 3)
-  }
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
   x <- plotrange_as_table(x, expand = expand)
@@ -783,12 +822,16 @@ plot.disk <- function(x,
   if (any(colours_SIR %in% cols_sub$cols)) {
     legend_txt <- character(0)
     legend_col <- character(0)
-    if (any(cols_sub$cols == colours_SIR[3] & cols_sub$count > 0)) {
+    if (any(cols_sub$cols == colours_SIR[4] & cols_sub$count > 0)) {
       legend_txt <- "(R) Resistant"
-      legend_col <- colours_SIR[3]
+      legend_col <- colours_SIR[4]
+    }
+    if (any(cols_sub$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, paste("(I)", plot_name_of_I(cols_sub$guideline)))
+      legend_txt <- c(legend_txt, "(SDD) Susceptible dose-dependent")
       legend_col <- c(legend_col, colours_SIR[2])
     }
     if (any(cols_sub$cols == colours_SIR[1] & cols_sub$count > 0)) {
@@ -818,7 +861,12 @@ barplot.disk <- function(height,
                          mo = NULL,
                          ab = NULL,
                          guideline = getOption("AMR_guideline", "EUCAST"),
-                         colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                         colours_SIR = c(
+                           S = "#3CAEA3",
+                           SDD = "#8FD6C4",
+                           I = "#F6D55C",
+                           R = "#ED553B"
+                         ),
                          language = get_AMR_locale(),
                          expand = TRUE,
                          ...) {
@@ -828,7 +876,7 @@ barplot.disk <- function(height,
   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(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
 
@@ -858,7 +906,12 @@ autoplot.disk <- function(object,
                           ylab = translate_AMR("Frequency", language = language),
                           xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
                           guideline = getOption("AMR_guideline", "EUCAST"),
-                          colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                          colours_SIR = c(
+                            S = "#3CAEA3",
+                            SDD = "#8FD6C4",
+                            I = "#F6D55C",
+                            R = "#ED553B"
+                          ),
                           language = get_AMR_locale(),
                           expand = TRUE,
                           include_PKPD = getOption("AMR_include_PKPD", TRUE),
@@ -871,7 +924,7 @@ autoplot.disk <- function(object,
   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(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
 
@@ -1024,22 +1077,31 @@ barplot.sir <- function(height,
                         main = deparse(substitute(height)),
                         xlab = translate_AMR("Antimicrobial Interpretation", language = language),
                         ylab = translate_AMR("Frequency", language = language),
-                        colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                        colours_SIR = c(
+                          S = "#3CAEA3",
+                          SDD = "#8FD6C4",
+                          I = "#F6D55C",
+                          R = "#ED553B"
+                        ),
                         language = get_AMR_locale(),
                         expand = TRUE,
                         ...) {
   meet_criteria(xlab, 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(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  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)
 
   if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 3)
+    colours_SIR <- rep(colours_SIR, 4)
+  } else if (length(colours_SIR) == 3) {
+    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
   }
+  colours_SIR <- unname(colours_SIR)
+
   # add SDD and N to colours
-  colours_SIR <- c(colours_SIR[1:2], colours_SIR[2], colours_SIR[3], "#888888")
+  colours_SIR <- c(colours_SIR, "grey30")
   main <- gsub(" +", " ", paste0(main, collapse = " "))
 
   x <- table(height)
@@ -1065,14 +1127,19 @@ autoplot.sir <- function(object,
                          title = deparse(substitute(object)),
                          xlab = translate_AMR("Antimicrobial Interpretation", language = language),
                          ylab = translate_AMR("Frequency", language = language),
-                         colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+                         colours_SIR = c(
+                           S = "#3CAEA3",
+                           SDD = "#8FD6C4",
+                           I = "#F6D55C",
+                           R = "#ED553B"
+                         ),
                          language = get_AMR_locale(),
                          ...) {
   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(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
 
   if ("main" %in% names(list(...))) {
     title <- list(...)$main
@@ -1082,8 +1149,11 @@ autoplot.sir <- function(object,
   }
 
   if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 3)
+    colours_SIR <- rep(colours_SIR, 4)
+  } else if (length(colours_SIR) == 3) {
+    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
   }
+  colours_SIR <- unname(colours_SIR)
 
   df <- as.data.frame(table(object), stringsAsFactors = TRUE)
   colnames(df) <- c("x", "n")
@@ -1095,9 +1165,9 @@ autoplot.sir <- function(object,
       values = c(
         "S" = colours_SIR[1],
         "SDD" = colours_SIR[2],
-        "I" = colours_SIR[2],
+        "I" = colours_SIR[3],
-        "R" = colours_SIR[3],
+        "R" = colours_SIR[4],
-        "NI" = "#888888"
+        "NI" = "grey30"
       ),
       limits = force
     ) +
@@ -1182,6 +1252,13 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
 
   guideline <- get_guideline(guideline, AMR::clinical_breakpoints)
 
+  if (length(colours_SIR) == 1) {
+    colours_SIR <- rep(colours_SIR, 4)
+  } else if (length(colours_SIR) == 3) {
+    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
+  }
+  colours_SIR <- unname(colours_SIR)
+
   # store previous interpretations to backup
   sir_history <- AMR_env$sir_interpretation_history
   # and clear previous interpretations
@@ -1223,9 +1300,9 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_SIR, f
     cols[is.na(sir)] <- "#BEBEBE"
     cols[sir == "S"] <- colours_SIR[1]
     cols[sir == "SDD"] <- colours_SIR[2]
-    cols[sir == "I"] <- colours_SIR[2]
+    cols[sir == "I"] <- colours_SIR[3]
-    cols[sir == "R"] <- colours_SIR[3]
+    cols[sir == "R"] <- colours_SIR[4]
-    cols[sir == "NI"] <- "#888888"
+    cols[sir == "NI"] <- "grey30"
     sub <- bquote(.(abname) ~ "-" ~ italic(.(moname)) ~ .(guideline_txt))
   } else {
     cols <- "#BEBEBE"
@@ -1284,10 +1361,15 @@ scale_y_percent <- function(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.
 #' @export
 scale_sir_colours <- function(...,
                               aesthetics,
-                              colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B")) {
+                              colours_SIR = c(
+                                S = "#3CAEA3",
+                                SDD = "#8FD6C4",
+                                I = "#F6D55C",
+                                R = "#ED553B"
+                              )) {
   stop_ifnot_installed("ggplot2")
   meet_criteria(aesthetics, allow_class = "character", is_in = c("alpha", "colour", "color", "fill", "linetype", "shape", "size"))
-  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3))
+  meet_criteria(colours_SIR, allow_class = "character", has_length = c(1, 3, 4))
 
   if ("fill" %in% aesthetics && message_not_thrown_before("scale_sir_colours", "fill", entire_session = TRUE)) {
     warning_("Using `scale_sir_colours()` for the `fill` aesthetic has been superseded by `scale_fill_sir()`, please use that instead. This warning will be shown once per session.")
@@ -1296,67 +1378,52 @@ scale_sir_colours <- function(...,
     warning_("Using `scale_sir_colours()` for the `colour` aesthetic has been superseded by `scale_colour_sir()`, please use that instead. This warning will be shown once per session.")
   }
 
-  if (length(colours_SIR) == 1) {
-    colours_SIR <- rep(colours_SIR, 3)
-  }
-  # behaviour until AMR pkg v1.5.0 and also when coming from ggplot_sir()
   if ("colours" %in% names(list(...))) {
-    original_cols <- c(
+    colours_SIR <- list(...)$colours
-      S = colours_SIR[1],
+  }
-      SI = colours_SIR[1],
+
-      I = colours_SIR[2],
+  if (length(colours_SIR) == 1) {
-      IR = colours_SIR[3],
+    colours_SIR <- rep(colours_SIR, 4)
-      R = colours_SIR[3]
+  } else if (length(colours_SIR) == 3) {
-    )
+    colours_SIR <- c(colours_SIR[1], colours_SIR[1], colours_SIR[2], colours_SIR[3])
-    colours <- replace(original_cols, names(list(...)$colours), list(...)$colours)
+  }
+
+  # behaviour when coming from ggplot_sir()
+  if ("colours" %in% names(list(...))) {
     # limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
     # https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
-    return(ggplot2::scale_fill_manual(values = colours, limits = force, aesthetics = aesthetics))
+    return(ggplot2::scale_fill_manual(values = colours_SIR, limits = force, aesthetics = aesthetics))
   }
   if (identical(unlist(list(...)), FALSE)) {
     return(invisible())
   }
 
-  names_susceptible <- c(
+  colours_SIR <- unname(colours_SIR)
-    "S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
+
-    unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
+  names_susceptible <- c("S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible")
-      "replacement",
+  names_susceptible_dose_dep <- c("SDD", "susceptible dose-dependent", "Susceptible dose-dependent")
-      drop = TRUE
-    ])
-  )
   names_incr_exposure <- c(
     "I", "intermediate", "increased exposure", "incr. exposure",
-    "Increased exposure", "Incr. exposure", "Susceptible, incr. exp.",
+    "Increased exposure", "Incr. exposure", "Susceptible, incr. exp."
-    unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
-      "replacement",
-      drop = TRUE
-    ]),
-    unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible, incr. exp."),
-      "replacement",
-      drop = TRUE
-    ])
-  )
-  names_resistant <- c(
-    "R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
-    unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
-      "replacement",
-      drop = TRUE
-    ])
   )
+  names_resistant <- c("R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant")
 
   susceptible <- rep(colours_SIR[1], length(names_susceptible))
   names(susceptible) <- names_susceptible
-  incr_exposure <- rep(colours_SIR[2], length(names_incr_exposure))
+  susceptible_dose_dep <- rep(colours_SIR[2], length(names_susceptible_dose_dep))
+  names(susceptible_dose_dep) <- names_susceptible_dose_dep
+  incr_exposure <- rep(colours_SIR[3], length(names_incr_exposure))
   names(incr_exposure) <- names_incr_exposure
-  resistant <- rep(colours_SIR[3], length(names_resistant))
+  resistant <- rep(colours_SIR[4], length(names_resistant))
   names(resistant) <- names_resistant
 
-  original_cols <- c(susceptible, incr_exposure, resistant)
+  original_cols <- c(susceptible, susceptible_dose_dep, incr_exposure, resistant)
   dots <- c(...)
-  # replace S, I, R as colours: scale_sir_colours(mydatavalue = "S")
+  # replace S, SDD, I, R as colours: scale_sir_colours(mydatavalue = "S")
   dots[dots == "S"] <- colours_SIR[1]
-  dots[dots == "I"] <- colours_SIR[2]
+  dots[dots == "SDD"] <- colours_SIR[2]
-  dots[dots == "R"] <- colours_SIR[3]
+  dots[dots == "I"] <- colours_SIR[3]
+  dots[dots == "R"] <- colours_SIR[4]
   cols <- replace(original_cols, names(dots), dots)
   # limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
   # https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530

R/proportion.R

@@ -237,7 +237,7 @@ resistance <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -255,7 +255,7 @@ susceptibility <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -283,7 +283,7 @@ sir_confidence_interval <- function(...,
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
   n <- tryCatch(
     sir_calc(...,
@@ -291,7 +291,7 @@ sir_confidence_interval <- function(...,
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 
   if (x == 0) {
@@ -347,7 +347,7 @@ proportion_R <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -365,7 +365,7 @@ proportion_IR <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -383,7 +383,7 @@ proportion_I <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -401,7 +401,7 @@ proportion_SI <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -419,7 +419,7 @@ proportion_S <- function(...,
       only_all_tested = only_all_tested,
       only_count = FALSE
     ),
-    error = function(e) stop_(gsub("in sir_calc(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }
 
@@ -443,6 +443,6 @@ proportion_df <- function(data,
       combine_SI = combine_SI,
       confidence_level = confidence_level
     ),
-    error = function(e) stop_(gsub("in sir_calc_df(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc_df(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }

R/sir.R

@@ -69,7 +69,9 @@
 #' @param reference_data A [data.frame] to be used for interpretation, which defaults to the [clinical_breakpoints] data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the [clinical_breakpoints] data set (same column names and column types). Please note that the `guideline` argument will be ignored when `reference_data` is manually set.
 #' @param threshold Maximum fraction of invalid antimicrobial interpretations of `x`, see *Examples*.
 #' @param conserve_capped_values Deprecated, use `capped_mic_handling` instead.
-#' @param ... For using on a [data.frame]: names of columns to apply [as.sir()] on (supports tidy selection such as `column1:column4`). Otherwise: arguments passed on to methods.
+#' @param ... For using on a [data.frame]: selection of columns to apply `as.sir()` to. Supports [tidyselect language][tidyselect::starts_with()] such as `where(is.mic)`, `starts_with(...)`, or `column1:column4`, and can thus also be [antimicrobial selectors][amr_selector()] such as `as.sir(df, penicillins())`.
+#'
+#' Otherwise: arguments passed on to methods.
 #' @details
 #' *Note: The clinical breakpoints in this package were validated through, and imported from, [WHONET](https://whonet.org). The public use of this `AMR` package has been endorsed by both CLSI and EUCAST. See [clinical_breakpoints] for more information.*
 #'
@@ -225,9 +227,12 @@
 #'   df_wide %>% mutate_if(is.mic, as.sir)
 #'   df_wide %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
 #'   df_wide %>% mutate(across(where(is.mic), as.sir))
+#'
 #'   df_wide %>% mutate_at(vars(amoxicillin:tobra), as.sir)
 #'   df_wide %>% mutate(across(amoxicillin:tobra, as.sir))
 #'
+#'   df_wide %>% mutate(across(aminopenicillins(), as.sir))
+#'
 #'   # approaches that all work with additional arguments:
 #'   df_long %>%
 #'     # given a certain data type, e.g. MIC values
@@ -722,8 +727,17 @@ as.sir.data.frame <- function(x,
   meet_criteria(info, allow_class = "logical", has_length = 1)
   meet_criteria(parallel, allow_class = "logical", has_length = 1)
   meet_criteria(max_cores, allow_class = c("numeric", "integer"), has_length = 1)
-
   x.bak <- x
+
+  if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
+    sel <- colnames(pm_select(x, ...))
+  } else {
+    sel <- colnames(x)
+  }
+  if (!is.null(col_mo)) {
+    sel <- sel[sel != col_mo]
+  }
+
   for (i in seq_len(ncol(x))) {
     # don't keep factors, overwriting them is hard
     if (is.factor(x[, i, drop = TRUE])) {
@@ -803,15 +817,6 @@ as.sir.data.frame <- function(x,
   }
 
   i <- 0
-  if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
-    sel <- colnames(pm_select(x, ...))
-  } else {
-    sel <- colnames(x)
-  }
-  if (!is.null(col_mo)) {
-    sel <- sel[sel != col_mo]
-  }
-
   ab_cols <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(y) {
     i <<- i + 1
     check <- is.mic(y) | is.disk(y)
@@ -863,7 +868,7 @@ as.sir.data.frame <- function(x,
     cl <- tryCatch(parallel::makeCluster(n_cores, type = "PSOCK"),
       error = function(e) {
         if (isTRUE(info)) {
-          message_("Could not create parallel cluster, using single-core computation. Error message: ", e$message, add_fn = font_red)
+          message_("Could not create parallel cluster, using single-core computation. Error message: ", conditionMessage(e), add_fn = font_red)
         }
         return(NULL)
       }
@@ -1904,11 +1909,11 @@ pillar_shaft.sir <- function(x, ...) {
     # colours will anyway not work when has_colour() == FALSE,
     # but then the indentation should also not be applied
     out[is.na(x)] <- font_grey("  NA")
-    out[x == "NI"] <- font_grey_bg(font_black("  NI "))
     out[x == "S"] <- font_green_bg("  S  ")
+    out[x == "SDD"] <- font_green_lighter_bg(" SDD ")
     out[x == "I"] <- font_orange_bg("  I  ")
-    out[x == "SDD"] <- font_orange_bg(" SDD ")
     out[x == "R"] <- font_rose_bg("  R  ")
+    out[x == "NI"] <- font_grey_bg(font_black("  NI "))
   }
   create_pillar_column(out, align = "left", width = 5)
 }

R/sir_calc.R

@@ -244,7 +244,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
   translate_ab <- get_translate_ab(translate_ab)
 
   data.bak <- data
-  # select only groups and antimicrobials
+  # select only groups and antibiotics
   if (is_null_or_grouped_tbl(data)) {
     data_has_groups <- TRUE
     groups <- get_group_names(data)
@@ -255,15 +255,14 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
   }
 
   data <- as.data.frame(data, stringsAsFactors = FALSE)
-  if (isTRUE(combine_SI)) {
+
-    for (i in seq_len(ncol(data))) {
+  for (i in seq_len(ncol(data))) {
-      if (is.sir(data[, i, drop = TRUE])) {
+    data[, i] <- as.character(as.sir(data[, i, drop = TRUE]))
-        data[, i] <- as.character(data[, i, drop = TRUE])
+    if (isTRUE(combine_SI)) {
-        if ("SDD" %in% data[, i, drop = TRUE] && message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
+      if ("SDD" %in% data[, i, drop = TRUE] && message_not_thrown_before("sir_calc_df", combine_SI, entire_session = TRUE)) {
-          message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
+        message_("Note that `sir_calc_df()` will also count dose-dependent susceptibility, 'SDD', as 'SI' when `combine_SI = TRUE`. This note will be shown once for this session.", as_note = FALSE)
-        }
-        data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
       }
+      data[, i] <- gsub("(I|S|SDD)", "SI", data[, i, drop = TRUE])
     }
   }
 
@@ -364,7 +363,7 @@ sir_calc_df <- function(type, # "proportion", "count" or "both"
   } else {
     # don't use as.sir() here, as it would add the class 'sir' and we would like
     # the same data structure as output, regardless of input
-    if (out$value[out$interpretation == "SDD"] > 0) {
+    if (any(out$value[out$interpretation == "SDD"] > 0, na.rm = TRUE)) {
       out$interpretation <- factor(out$interpretation, levels = c("S", "SDD", "I", "R"), ordered = TRUE)
     } else {
       out$interpretation <- factor(out$interpretation, levels = c("S", "I", "R"), ordered = TRUE)

R/sir_df.R

@@ -47,6 +47,6 @@ sir_df <- function(data,
       combine_SI = combine_SI,
       confidence_level = confidence_level
     ),
-    error = function(e) stop_(gsub("in sir_calc_df(): ", "", e$message, fixed = TRUE), call = -5)
+    error = function(e) stop_(gsub("in sir_calc_df(): ", "", conditionMessage(e), fixed = TRUE), call = -5)
   )
 }

R/vctrs.R

@@ -30,7 +30,6 @@
 # These are all S3 implementations for the vctrs package,
 # that is used internally by tidyverse packages such as dplyr.
 # They are to convert AMR-specific classes to bare characters and integers.
-# All of them will be exported using s3_register() in R/zzz.R when loading the package.
 
 # see https://github.com/tidyverse/dplyr/issues/5955 why this is required
 

R/zzz.R

@@ -127,7 +127,7 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
           suppressWarnings(suppressMessages(add_custom_antimicrobials(x)))
           packageStartupMessage("OK.")
         },
-        error = function(e) packageStartupMessage("Failed: ", e$message)
+        error = function(e) packageStartupMessage("Failed: ", conditionMessage(e))
       )
     }
   }
@@ -143,7 +143,7 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
           suppressWarnings(suppressMessages(add_custom_microorganisms(x)))
           packageStartupMessage("OK.")
         },
-        error = function(e) packageStartupMessage("Failed: ", e$message)
+        error = function(e) packageStartupMessage("Failed: ", conditionMessage(e))
       )
     }
   }

data-raw/_reproduction_scripts/reproduction_of_microorganisms.R

@@ -288,7 +288,7 @@ for (page in LETTERS) {
   url <- paste0("https://lpsn.dsmz.de/genus?page=", page)
   x <- tryCatch(read_html(url),
                 error = function(e) {
-                  message("Waiting 10 seconds because of error: ", e$message)
+                  message("Waiting 10 seconds because of error: ", conditionMessage(e))
                   Sys.sleep(10)
                   read_html(url)
                 })

data-raw/_reproduction_scripts/reproduction_of_poorman.R

@@ -108,3 +108,18 @@ writeLines(contents, "R/aa_helper_pm_functions.R")
 
 # note: pm_left_join() will be overwritten by aaa_helper_functions.R, which contains a faster implementation
 # replace `res <- as.data.frame(res)` with  `res <- as.data.frame(res, stringsAsFactors = FALSE)`
+
+# after running, pm_select must be altered. The line:
+# col_pos <- pm_select_positions(.data, ..., .group_pos = TRUE)
+# ... must be replaced with this to support tidyselect functionality such as `starts_with()`:
+# col_pos <- tryCatch(pm_select_positions(.data, ..., .group_pos = TRUE), error = function(e) NULL)
+# if (is.null(col_pos)) {
+#   # try with tidyverse
+#   select_dplyr <- import_fn("select", "dplyr", error_on_fail = FALSE)
+#   if (!is.null(select_dplyr)) {
+#     col_pos <- which(colnames(.data) %in% colnames(select_dplyr(.data, ...)))
+#   } else {
+#     # this will throw an error as it did, but dplyr is not available, so no other option
+#     col_pos <- pm_select_positions(.data, ..., .group_pos = TRUE)
+#   }
+# }

data-raw/read_EUCAST.R

@@ -283,7 +283,7 @@ for (i in 2:length(sheets_to_analyse)) {
         guideline_name = guideline_name
       )
     ),
-    error = function(e) message(e$message)
+    error = function(e) message(conditionMessage(e))
   )
 }
 

index.md

@@ -27,12 +27,12 @@
 
 <p style="text-align:left; width: 50%;">
 
-<small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small>
+<small><a href="https://amr-for-r.org/">amr-for-r.org</a></small>
 </p>
 
 <p style="text-align:right; width: 50%;">
 
-<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">https://doi.org/10.18637/jss.v104.i03</a></small>
+<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank">doi.org/10.18637/jss.v104.i03</a></small>
 </p>
 
 </div>
@@ -321,9 +321,9 @@ example_isolates %>%
 #> # A tibble: 3 × 5
 #>   ward       GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
 #>   <chr>            <dbl> <chr>              <dbl> <chr>       
-#> 1 Clinical     0.2289362 0.205-0.254    0.3147503 0.284-0.347 
+#> 1 Clinical         0.229 0.205-0.254        0.315 0.284-0.347 
-#> 2 ICU          0.2902655 0.253-0.33     0.4004739 0.353-0.449 
+#> 2 ICU              0.290 0.253-0.33         0.400 0.353-0.449 
-#> 3 Outpatient   0.2       0.131-0.285    0.3676471 0.254-0.493
+#> 3 Outpatient       0.2   0.131-0.285        0.368 0.254-0.493
 ```
 
 Or use [antimicrobial
@@ -351,33 +351,33 @@ out <- example_isolates %>%
 #> "Outpatient" (minimum = 30).
 out
 #> # A tibble: 3 × 6
-#>   ward             GEN       TOB       AMK   KAN       COL
+#>   ward         GEN   TOB   AMK   KAN   COL
-#>   <chr>          <dbl>     <dbl>     <dbl> <dbl>     <dbl>
+#>   <chr>      <dbl> <dbl> <dbl> <dbl> <dbl>
-#> 1 Clinical   0.2289362 0.3147503 0.6258993     1 0.7802956
+#> 1 Clinical   0.229 0.315 0.626     1 0.780
-#> 2 ICU        0.2902655 0.4004739 0.6624473     1 0.8574144
+#> 2 ICU        0.290 0.400 0.662     1 0.857
-#> 3 Outpatient 0.2       0.3676471 0.6052632    NA 0.8888889
+#> 3 Outpatient 0.2   0.368 0.605    NA 0.889
 ```
 
 ``` r
 # transform the antibiotic columns to names:
 out %>% set_ab_names()
 #> # A tibble: 3 × 6
-#>   ward       gentamicin tobramycin  amikacin kanamycin  colistin
+#>   ward       gentamicin tobramycin amikacin kanamycin colistin
-#>   <chr>           <dbl>      <dbl>     <dbl>     <dbl>     <dbl>
+#>   <chr>           <dbl>      <dbl>    <dbl>     <dbl>    <dbl>
-#> 1 Clinical    0.2289362  0.3147503 0.6258993         1 0.7802956
+#> 1 Clinical        0.229      0.315    0.626         1    0.780
-#> 2 ICU         0.2902655  0.4004739 0.6624473         1 0.8574144
+#> 2 ICU             0.290      0.400    0.662         1    0.857
-#> 3 Outpatient  0.2        0.3676471 0.6052632        NA 0.8888889
+#> 3 Outpatient      0.2        0.368    0.605        NA    0.889
 ```
 
 ``` r
 # transform the antibiotic column to ATC codes:
 out %>% set_ab_names(property = "atc")
 #> # A tibble: 3 × 6
-#>   ward         J01GB03   J01GB01   J01GB06 J01GB04   J01XB01
+#>   ward       J01GB03 J01GB01 J01GB06 J01GB04 J01XB01
-#>   <chr>          <dbl>     <dbl>     <dbl>   <dbl>     <dbl>
+#>   <chr>        <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
-#> 1 Clinical   0.2289362 0.3147503 0.6258993       1 0.7802956
+#> 1 Clinical     0.229   0.315   0.626       1   0.780
-#> 2 ICU        0.2902655 0.4004739 0.6624473       1 0.8574144
+#> 2 ICU          0.290   0.400   0.662       1   0.857
-#> 3 Outpatient 0.2       0.3676471 0.6052632      NA 0.8888889
+#> 3 Outpatient   0.2     0.368   0.605      NA   0.889
 ```
 
 ## What else can you do with this package?

man/as.sir.Rd

@@ -75,7 +75,9 @@ sir_interpretation_history(clean = FALSE)
 \arguments{
 \item{x}{Vector of values (for class \code{\link{mic}}: MIC values in mg/L, for class \code{\link{disk}}: a disk diffusion radius in millimetres).}
 
-\item{...}{For using on a \link{data.frame}: names of columns to apply \code{\link[=as.sir]{as.sir()}} on (supports tidy selection such as \code{column1:column4}). Otherwise: arguments passed on to methods.}
+\item{...}{For using on a \link{data.frame}: selection of columns to apply \code{as.sir()} to. Supports \link[tidyselect:starts_with]{tidyselect language} such as \code{where(is.mic)}, \code{starts_with(...)}, or \code{column1:column4}, and can thus also be \link[=amr_selector]{antimicrobial selectors} such as \code{as.sir(df, penicillins())}.
+
+Otherwise: arguments passed on to methods.}
 
 \item{threshold}{Maximum fraction of invalid antimicrobial interpretations of \code{x}, see \emph{Examples}.}
 
@@ -314,9 +316,12 @@ if (require("dplyr")) {
   df_wide \%>\% mutate_if(is.mic, as.sir)
   df_wide \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
   df_wide \%>\% mutate(across(where(is.mic), as.sir))
+
   df_wide \%>\% mutate_at(vars(amoxicillin:tobra), as.sir)
   df_wide \%>\% mutate(across(amoxicillin:tobra, as.sir))
 
+  df_wide \%>\% mutate(across(aminopenicillins(), as.sir))
+
   # approaches that all work with additional arguments:
   df_long \%>\%
     # given a certain data type, e.g. MIC values

man/ggplot_sir.Rd

@@ -9,10 +9,10 @@ ggplot_sir(data, position = NULL, x = "antibiotic",
   fill = "interpretation", facet = NULL, breaks = seq(0, 1, 0.1),
   limits = NULL, translate_ab = "name", combine_SI = TRUE,
   minimum = 30, language = get_AMR_locale(), nrow = NULL, colours = c(S
-  = "#3CAEA3", SI = "#3CAEA3", I = "#F6D55C", IR = "#ED553B", R = "#ED553B"),
+  = "#3CAEA3", SI = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", IR = "#ED553B",
-  datalabels = TRUE, datalabels.size = 2.5, datalabels.colour = "grey15",
+  R = "#ED553B"), datalabels = TRUE, datalabels.size = 2.5,
-  title = NULL, subtitle = NULL, caption = NULL,
+  datalabels.colour = "grey15", title = NULL, subtitle = NULL,
-  x.title = "Antimicrobial", y.title = "Proportion", ...)
+  caption = NULL, x.title = "Antimicrobial", y.title = "Proportion", ...)
 
 geom_sir(position = NULL, x = c("antibiotic", "interpretation"),
   fill = "interpretation", translate_ab = "name", minimum = 30,

man/mean_amr_distance.Rd

@@ -18,7 +18,7 @@ amr_distance_from_row(amr_distance, row)
 \arguments{
 \item{x}{A vector of class \link[=as.sir]{sir}, \link[=as.mic]{mic} or \link[=as.disk]{disk}, or a \link{data.frame} containing columns of any of these classes.}
 
-\item{...}{Variables to select. Supports \link[tidyselect:language]{tidyselect language} (such as \code{column1:column4} and \code{where(is.mic)}), and can thus also be \link[=amr_selector]{antimicrobial selectors}.}
+\item{...}{Variables to select. Supports \link[tidyselect:starts_with]{tidyselect language} such as \code{where(is.mic)}, \code{starts_with(...)}, or \code{column1:column4}, and can thus also be \link[=amr_selector]{antimicrobial selectors}.}
 
 \item{combine_SI}{A \link{logical} to indicate whether all values of S, SDD, and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant) - the default is \code{TRUE}.}
 

man/plot.Rd

@@ -33,25 +33,25 @@ scale_colour_mic(keep_operators = "edges", mic_range = NULL, ...)
 
 scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
 
-scale_x_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+scale_x_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
-  language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
+  = "#ED553B"), language = get_AMR_locale(),
-  "EUCAST") == "EUCAST", ...)
+  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
 
-scale_colour_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+scale_colour_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I =
-  language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
+  "#F6D55C", R = "#ED553B"), language = get_AMR_locale(),
-  "EUCAST") == "EUCAST", ...)
+  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
 
-scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+scale_fill_sir(colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C",
-  language = get_AMR_locale(), eucast_I = getOption("AMR_guideline",
+  R = "#ED553B"), language = get_AMR_locale(),
-  "EUCAST") == "EUCAST", ...)
+  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST", ...)
 
 \method{plot}{mic}(x, mo = NULL, ab = NULL,
   guideline = getOption("AMR_guideline", "EUCAST"),
   main = deparse(substitute(x)), ylab = translate_AMR("Frequency", language
   = language),
   xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
-  language), colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+  language), colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
-  language = get_AMR_locale(), expand = TRUE,
+  = "#ED553B"), language = get_AMR_locale(), expand = TRUE,
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
 
@@ -60,8 +60,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
   title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
   language = language),
   xlab = translate_AMR("Minimum Inhibitory Concentration (mg/L)", language =
-  language), colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+  language), colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R
-  language = get_AMR_locale(), expand = TRUE,
+  = "#ED553B"), language = get_AMR_locale(), expand = TRUE,
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
 
@@ -69,8 +69,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
   ylab = translate_AMR("Frequency", language = language),
   xlab = translate_AMR("Disk diffusion diameter (mm)", language = language),
   mo = NULL, ab = NULL, guideline = getOption("AMR_guideline", "EUCAST"),
-  colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R =
-  language = get_AMR_locale(), expand = TRUE,
+  "#ED553B"), language = get_AMR_locale(), expand = TRUE,
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
 
@@ -78,8 +78,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
   title = deparse(substitute(object)), ylab = translate_AMR("Frequency",
   language = language), xlab = translate_AMR("Disk diffusion diameter (mm)",
   language = language), guideline = getOption("AMR_guideline", "EUCAST"),
-  colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+  colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R =
-  language = get_AMR_locale(), expand = TRUE,
+  "#ED553B"), language = get_AMR_locale(), expand = TRUE,
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), ...)
 
@@ -90,8 +90,8 @@ scale_fill_sir(colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
 
 \method{autoplot}{sir}(object, title = deparse(substitute(object)),
   xlab = translate_AMR("Antimicrobial Interpretation", language = language),
-  ylab = translate_AMR("Frequency", language = language),
+  ylab = translate_AMR("Frequency", language = language), colours_SIR = c(S
-  colours_SIR = c("#3CAEA3", "#F6D55C", "#ED553B"),
+  = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
   language = get_AMR_locale(), ...)
 
 facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
@@ -99,8 +99,8 @@ facet_sir(facet = c("interpretation", "antibiotic"), nrow = NULL)
 scale_y_percent(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1),
   limits = c(0, NA))
 
-scale_sir_colours(..., aesthetics, colours_SIR = c("#3CAEA3", "#F6D55C",
+scale_sir_colours(..., aesthetics, colours_SIR = c(S = "#3CAEA3", SDD =
-  "#ED553B"))
+  "#8FD6C4", I = "#F6D55C", R = "#ED553B"))
 
 theme_sir()
 

tests/testthat/test-zzz.R

@@ -63,10 +63,12 @@ test_that("test-zzz.R", {
     "progress_bar" = "progress",
     "read_html" = "xml2",
     "right_join" = "dplyr",
+    "select" = "dplyr",
     "semi_join" = "dplyr",
     "showQuestion" = "rstudioapi",
     "symbol" = "cli",
     "tibble" = "tibble",
+    "where" = "tidyselect",
     "write.xlsx" = "openxlsx"
   )