Update _pkgdown.yml

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.0
-Date: 2025-06-01
+Version: 3.0.0.9004
+Date: 2025-06-13
 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
@@ -51,6 +51,8 @@ Suggests:
   pillar,
   progress,
   readxl,
+  recipes,
+  rlang,
   rmarkdown,
   rstudioapi,
   rvest,

NAMESPACE

@@ -106,6 +106,8 @@ S3method(print,mo_uncertainties)
 S3method(print,pca)
 S3method(print,sir)
 S3method(print,sir_log)
+S3method(print,step_mic_log2)
+S3method(print,step_sir_numeric)
 S3method(quantile,mic)
 S3method(rep,ab)
 S3method(rep,av)
@@ -159,6 +161,10 @@ export(administrable_per_os)
 export(age)
 export(age_groups)
 export(all_antimicrobials)
+export(all_mic)
+export(all_mic_predictors)
+export(all_sir)
+export(all_sir_predictors)
 export(aminoglycosides)
 export(aminopenicillins)
 export(amr_class)
@@ -352,6 +358,8 @@ export(sir_df)
 export(sir_interpretation_history)
 export(sir_predict)
 export(skewness)
+export(step_mic_log2)
+export(step_sir_numeric)
 export(streptogramins)
 export(sulfonamides)
 export(susceptibility)
@@ -388,6 +396,12 @@ if(getRversion() >= "3.0.0") S3method(pillar::type_sum, av)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mic)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, mo)
 if(getRversion() >= "3.0.0") S3method(pillar::type_sum, sir)
+if(getRversion() >= "3.0.0") S3method(recipes::bake, step_mic_log2)
+if(getRversion() >= "3.0.0") S3method(recipes::bake, step_sir_numeric)
+if(getRversion() >= "3.0.0") S3method(recipes::prep, step_mic_log2)
+if(getRversion() >= "3.0.0") S3method(recipes::prep, step_sir_numeric)
+if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
+if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, disk)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mic)
 if(getRversion() >= "3.0.0") S3method(skimr::get_skimmers, mo)

NEWS.md

@@ -1,3 +1,19 @@
+# AMR 3.0.0.9004
+
+### 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()`
+  - 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 `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 some specific Dutch translations for antimicrobials
+* Updated `random_mic()` and `random_disk()` to set skewedness of the distribution and allow multiple microorganisms
+
+
 # AMR 3.0.0
 
 This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island's Atlantic Veterinary College](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
@@ -122,7 +138,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
 
 ## Older Versions
 
-This changelog only contains changes from AMR v3.0 (March 2025) and later.
+This changelog only contains changes from AMR v3.0 (June 2025) and later.
 
 * For prior v2 versions, please see [our v2 archive](https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md).
 * For prior v1 versions, please see [our v1 archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).

R/aa_helper_functions.R

@@ -1244,7 +1244,9 @@ try_colour <- function(..., before, after, collapse = " ") {
   }
 }
 is_dark <- function() {
-  if (is.null(AMR_env$is_dark_theme)) {
+  AMR_env$current_theme <- tryCatch(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$editor, error = function(e) NULL)
+  if (!identical(AMR_env$current_theme, AMR_env$former_theme) || is.null(AMR_env$is_dark_theme)) {
+    AMR_env$former_theme <- AMR_env$current_theme
     AMR_env$is_dark_theme <- !has_colour() || tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
   }
   isTRUE(AMR_env$is_dark_theme)

R/ab.R

@@ -655,7 +655,9 @@ generalise_antibiotic_name <- function(x) {
   x <- trimws(gsub(" +", " ", x, perl = TRUE))
   # remove last couple of words if they numbers or units
   x <- gsub("( ([0-9]{3,}|U?M?C?G|L))+$", "", x, perl = TRUE)
-  # move HIGH to end
+  # remove whitespace prior to numbers if preceded by A-Z
+  x <- gsub("([A-Z]+) +([0-9]+)", "\\1\\2", x, perl = TRUE)
+  # move HIGH to the end
   x <- trimws(gsub("(.*) HIGH(.*)", "\\1\\2 HIGH", x, perl = TRUE))
   x
 }

R/age.R

@@ -208,7 +208,7 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
     split_at <- c(0, split_at)
   }
   split_at <- split_at[!is.na(split_at)]
-  stop_if(length(split_at) == 1, "invalid value for `split_at`") # only 0 is available
+  stop_if(length(split_at) == 1, "invalid value for `split_at`.") # only 0 is available
 
   # turn input values to 'split_at' indices
   y <- x

R/antibiogram.R

@@ -40,6 +40,7 @@
 #'   - A combination of the above, using `c()`, e.g.:
 #'     - `c(aminoglycosides(), "AMP", "AMC")`
 #'     - `c(aminoglycosides(), carbapenems())`
+#'   - Column indices using numbers
 #'   - Combination therapy, indicated by using `"+"`, with or without [antimicrobial selectors][antimicrobial_selectors], e.g.:
 #'     - `"cipro + genta"`
 #'     - `"TZP+TOB"`
@@ -452,7 +453,7 @@ antibiogram.default <- function(x,
     deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
     antimicrobials <- list(...)$antibiotics
   }
-  meet_criteria(antimicrobials, allow_class = "character", allow_NA = FALSE, allow_NULL = FALSE)
+  meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
   if (!is.function(mo_transform)) {
     meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE, allow_NA = TRUE)
   }
@@ -1194,12 +1195,13 @@ retrieve_wisca_parameters <- function(wisca_model, ...) {
 #' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_sum, antibiogram)
 tbl_sum.antibiogram <- function(x, ...) {
   dims <- paste(format(NROW(x), big.mark = ","), AMR_env$cross_icon, format(NCOL(x), big.mark = ","))
+  names(dims) <- "An Antibiogram"
   if (isTRUE(attributes(x)$wisca)) {
-    names(dims) <- paste0("An Antibiogram (WISCA / ", attributes(x)$conf_interval * 100, "% CI)")
+    dims <- c(dims, Type = paste0("WISCA with ", attributes(x)$conf_interval * 100, "% CI"))
   } else if (isTRUE(attributes(x)$formatting_type >= 13)) {
-    names(dims) <- paste0("An Antibiogram (non-WISCA / ", attributes(x)$conf_interval * 100, "% CI)")
+    dims <- c(dims, Type = paste0("Non-WISCA with ", attributes(x)$conf_interval * 100, "% CI"))
   } else {
-    names(dims) <- paste0("An Antibiogram (non-WISCA)")
+    dims <- c(dims, Type = paste0("Non-WISCA without CI"))
   }
   dims
 }

R/data.R

@@ -361,3 +361,15 @@
 #' @examples
 #' dosage
 "dosage"
+
+#' Data Set with `r format(nrow(esbl_isolates), big.mark = " ")` ESBL Isolates
+#'
+#' A data set containing `r format(nrow(esbl_isolates), big.mark = " ")` microbial isolates with MIC values of common antibiotics and a binary `esbl` column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with [tidymodels](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
+#' @format A [tibble][tibble::tibble] with `r format(nrow(esbl_isolates), big.mark = " ")` observations and `r ncol(esbl_isolates)` variables:
+#' - `esbl`\cr Logical indicator if the isolate is ESBL-producing
+#' - `genus`\cr Genus of the microorganism
+#' - `AMC:COL`\cr MIC values for 17 antimicrobial agents, transformed to class [`mic`] (see [as.mic()])
+#' @details See our [tidymodels integration][amr-tidymodels] for an example using this data set.
+#' @examples
+#' esbl_isolates
+"esbl_isolates"

R/eucast_rules.R

@@ -442,7 +442,7 @@ eucast_rules <- function(x,
     # big speed gain! only analyse unique rows:
     pm_distinct(`.rowid`, .keep_all = TRUE) %pm>%
     as.data.frame(stringsAsFactors = FALSE)
-  x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]), info = info)
+  x[, col_mo] <- as.mo(as.character(x[, col_mo, drop = TRUE]), info = FALSE)
   # rename col_mo to prevent interference with joined columns
   colnames(x)[colnames(x) == col_mo] <- ".col_mo"
   col_mo <- ".col_mo"
@@ -450,13 +450,20 @@ eucast_rules <- function(x,
   x <- left_join_microorganisms(x, by = col_mo, suffix = c("_oldcols", ""))
   x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
   x$genus_species <- trimws(paste(x$genus, x$species))
-  if (isTRUE(info) && NROW(x) > 10000) {
-    message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
+  if (isTRUE(info) && NROW(x.bak) > 10000) {
+    message_("OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
   }
 
   n_added <- 0
   n_changed <- 0
 
+  rule_current <- ""
+  rule_group_current <- ""
+  rule_group_previous <- ""
+  rule_next <- ""
+  rule_previous <- ""
+  rule_text <- ""
+
   # >>> Apply Other rules: enzyme inhibitors <<< ------------------------------------------
   if (any(c("all", "other") %in% rules)) {
     if (isTRUE(info)) {
@@ -617,31 +624,16 @@ eucast_rules <- function(x,
     eucast_rules_df <- eucast_rules_df %pm>%
       rbind_AMR(eucast_rules_df_total %pm>%
         subset(reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints))
-    # eucast_rules_df <- subset(
-    #   eucast_rules_df,
-    #   reference.rule_group %unlike% "breakpoint" |
-    #     (reference.rule_group %like% "breakpoint" & reference.version == version_breakpoints)
-    # )
   }
   if (any(c("all", "expected_phenotypes") %in% rules)) {
     eucast_rules_df <- eucast_rules_df %pm>%
       rbind_AMR(eucast_rules_df_total %pm>%
         subset(reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes))
-    # eucast_rules_df <- subset(
-    #   eucast_rules_df,
-    #   reference.rule_group %unlike% "expected" |
-    #     (reference.rule_group %like% "expected" & reference.version == version_expected_phenotypes)
-    # )
   }
   if (any(c("all", "expert") %in% rules)) {
     eucast_rules_df <- eucast_rules_df %pm>%
       rbind_AMR(eucast_rules_df_total %pm>%
         subset(reference.rule_group %like% "expert" & reference.version == version_expertrules))
-    # eucast_rules_df <- subset(
-    #   eucast_rules_df,
-    #   reference.rule_group %unlike% "expert" |
-    #     (reference.rule_group %like% "expert" & reference.version == version_expertrules)
-    # )
   }
   ## filter out AmpC de-repressed cephalosporin-resistant mutants ----
   # no need to filter on version number here - the rules contain these version number, so are inherently filtered
@@ -664,6 +656,9 @@ eucast_rules <- function(x,
   # we only hints on remaining rows in `eucast_rules_df`
   screening_abx <- as.character(AMR::antimicrobials$ab[which(AMR::antimicrobials$ab %like% "-S$")])
   screening_abx <- screening_abx[screening_abx %in% unique(unlist(strsplit(EUCAST_RULES_DF$and_these_antibiotics[!is.na(EUCAST_RULES_DF$and_these_antibiotics)], ", *")))]
+  if (isTRUE(info)) {
+    cat("\n")
+  }
   for (ab_s in screening_abx) {
     ab <- gsub("-S$", "", ab_s)
     if (ab %in% names(cols_ab) && !ab_s %in% names(cols_ab)) {
@@ -894,7 +889,9 @@ eucast_rules <- function(x,
     }
     for (i in seq_len(length(custom_rules))) {
       rule <- custom_rules[[i]]
-      rows <- which(eval(parse(text = rule$query), envir = x))
+      rows <- tryCatch(which(eval(parse(text = rule$query), envir = x)),
+        error = function(e) stop_(paste0(conditionMessage(e), font_red(" (check available data and compare with the custom rules set)")), call = FALSE)
+      )
       cols <- as.character(rule$result_group)
       cols <- c(
         cols[cols %in% colnames(x)], # direct column names
@@ -908,9 +905,8 @@ eucast_rules <- function(x,
         get_antibiotic_names(cols)
       )
       if (isTRUE(info)) {
-        # print rule
         cat(italicise_taxonomy(
-          word_wrap(format_custom_query_rule(rule$query, colours = FALSE),
+          word_wrap(rule_text,
             width = getOption("width") - 30,
             extra_indent = 6
           ),

R/mic.R

@@ -432,11 +432,17 @@ pillar_shaft.mic <- function(x, ...) {
   }
   crude_numbers <- as.double(x)
   operators <- gsub("[^<=>]+", "", as.character(x))
+  # colourise operators
   operators[!is.na(operators) & operators != ""] <- font_silver(operators[!is.na(operators) & operators != ""], collapse = NULL)
   out <- trimws(paste0(operators, trimws(format(crude_numbers))))
   out[is.na(x)] <- font_na(NA)
   # make trailing zeroes less visible
-  out[out %like% "[.]"] <- gsub("([.]?0+)$", font_silver("\\1"), out[out %like% "[.]"], perl = TRUE)
+  if (is_dark()) {
+    fn <- font_silver
+  } else {
+    fn <- font_white
+  }
+  out[out %like% "[.]"] <- gsub("([.]?0+)$", fn("\\1"), out[out %like% "[.]"], perl = TRUE)
   create_pillar_column(out, align = "right", width = max(nchar(font_stripstyle(out))))
 }
 

R/random.R

@@ -31,13 +31,17 @@
 #'
 #' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
 #' @param size Desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
-#' @param mo Any [character] that can be coerced to a valid microorganism code with [as.mo()].
+#' @param mo Any [character] that can be coerced to a valid microorganism code with [as.mo()]. Can be the same length as `size`.
 #' @param ab Any [character] that can be coerced to a valid antimicrobial drug code with [as.ab()].
 #' @param prob_SIR A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value).
+#' @param skew Direction of skew for MIC or disk values, either `"right"` or `"left"`. A left-skewed distribution has the majority of the data on the right.
+#' @param severity Skew severity; higher values will increase the skewedness. Default is `2`; use `0` to prevent skewedness.
 #' @param ... Ignored, only in place to allow future extensions.
-#' @details The base \R function [sample()] is used for generating values.
-#'
-#' Generated values are based on the EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` guideline as implemented in the [clinical_breakpoints] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument.
+#' @details
+#' Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the [clinical_breakpoints] data set. To create specific generated values per bug or drug, set the `mo` and/or `ab` argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the `skew` and `severity` arguments:
+#' * `skew = "right"` places more emphasis on lower MIC or higher disk values.
+#' * `skew = "left"` places more emphasis on higher MIC or lower disk values.
+#' * `severity` controls the exponential bias applied.
 #' @return class `mic` for [random_mic()] (see [as.mic()]) and class `disk` for [random_disk()] (see [as.disk()])
 #' @name random
 #' @rdname random
@@ -47,8 +51,13 @@
 #' random_disk(25)
 #' random_sir(25)
 #'
+#' # add more skewedness, make more realistic by setting a bug and/or drug:
+#' disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
+#' plot(disks)
+#' # `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
+#' plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")
+#'
 #' \donttest{
-#' # make the random generation more realistic by setting a bug and/or drug:
 #' random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
 #' random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
 #' random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4
@@ -57,26 +66,61 @@
 #' random_disk(25, "Klebsiella pneumoniae", "ampicillin") # range 11-17
 #' random_disk(25, "Streptococcus pneumoniae", "ampicillin") # range 12-27
 #' }
-random_mic <- function(size = NULL, mo = NULL, ab = NULL, ...) {
+random_mic <- function(size = NULL, mo = NULL, ab = NULL, skew = "right", severity = 1, ...) {
   meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
-  meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(mo, allow_class = "character", has_length = c(1, size), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(skew, allow_class = "character", is_in = c("right", "left"), has_length = 1)
+  meet_criteria(severity, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
+
   if (is.null(size)) {
     size <- NROW(get_current_data(arg_name = "size", call = -3))
   }
-  random_exec("MIC", size = size, mo = mo, ab = ab)
+  if (length(mo) > 1) {
+    out <- rep(NA_mic_, length(size))
+    p <- progress_ticker(n = length(unique(mo)), n_min = 10, title = "Generating random MIC values")
+    for (mo_ in unique(mo)) {
+      p$tick()
+      out[which(mo == mo_)] <- random_exec("MIC", size = sum(mo == mo_), mo = mo_, ab = ab, skew = skew, severity = severity)
+    }
+    out <- as.mic(out, keep_operators = "none")
+    if (stats::runif(1) > 0.5 && length(unique(out)) > 1) {
+      out[out == min(out)] <- paste0("<=", out[out == min(out)])
+    }
+    if (stats::runif(1) > 0.5 && length(unique(out)) > 1) {
+      out[out == max(out) & out %unlike% "<="] <- paste0(">=", out[out == max(out) & out %unlike% "<="])
+    }
+
+    return(out)
+  } else {
+    random_exec("MIC", size = size, mo = mo, ab = ab, skew = skew, severity = severity)
+  }
 }
 
 #' @rdname random
 #' @export
-random_disk <- function(size = NULL, mo = NULL, ab = NULL, ...) {
+random_disk <- function(size = NULL, mo = NULL, ab = NULL, skew = "left", severity = 1, ...) {
   meet_criteria(size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE, allow_NULL = TRUE)
-  meet_criteria(mo, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(mo, allow_class = "character", has_length = c(1, size), allow_NULL = TRUE)
   meet_criteria(ab, allow_class = "character", has_length = 1, allow_NULL = TRUE)
+  meet_criteria(skew, allow_class = "character", is_in = c("right", "left"), has_length = 1)
+  meet_criteria(severity, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
+
   if (is.null(size)) {
     size <- NROW(get_current_data(arg_name = "size", call = -3))
   }
-  random_exec("DISK", size = size, mo = mo, ab = ab)
+  if (length(mo) > 1) {
+    out <- rep(NA_mic_, length(size))
+    p <- progress_ticker(n = length(unique(mo)), n_min = 10, title = "Generating random MIC values")
+    for (mo_ in unique(mo)) {
+      p$tick()
+      out[which(mo == mo_)] <- random_exec("DISK", size = sum(mo == mo_), mo = mo_, ab = ab, skew = skew, severity = severity)
+    }
+    out <- as.disk(out)
+    return(out)
+  } else {
+    random_exec("DISK", size = size, mo = mo, ab = ab, skew = skew, severity = severity)
+  }
 }
 
 #' @rdname random
@@ -90,78 +134,60 @@ random_sir <- function(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...) {
   sample(as.sir(c("S", "I", "R")), size = size, replace = TRUE, prob = prob_SIR)
 }
 
-random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
-  df <- AMR::clinical_breakpoints %pm>%
-    pm_filter(guideline %like% "EUCAST") %pm>%
-    pm_arrange(pm_desc(guideline)) %pm>%
-    subset(guideline == max(guideline) &
-      method == method_type &
-      type == "human")
+
+random_exec <- function(method_type, size, mo = NULL, ab = NULL, skew = "right", severity = 1) {
+  df <- AMR::clinical_breakpoints %pm>% subset(method == method_type & type == "human")
 
   if (!is.null(mo)) {
-    mo_coerced <- as.mo(mo)
-    mo_include <- c(
-      mo_coerced,
-      as.mo(mo_genus(mo_coerced)),
-      as.mo(mo_family(mo_coerced)),
-      as.mo(mo_order(mo_coerced))
-    )
-    df_new <- df %pm>%
-      subset(mo %in% mo_include)
-    if (nrow(df_new) > 0) {
-      df <- df_new
-    } else {
-      warning_("in `random_", tolower(method_type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
-    }
+    mo_coerced <- as.mo(mo, info = FALSE)
+    mo_include <- c(mo_coerced, as.mo(mo_genus(mo_coerced)), as.mo(mo_family(mo_coerced)), as.mo(mo_order(mo_coerced)))
+    df_new <- df %pm>% subset(mo %in% mo_include)
+    if (nrow(df_new) > 0) df <- df_new
   }
 
   if (!is.null(ab)) {
     ab_coerced <- as.ab(ab)
-    df_new <- df %pm>%
-      subset(ab %in% ab_coerced)
-    if (nrow(df_new) > 0) {
-      df <- df_new
-    } else {
-      warning_("in `random_", tolower(method_type), "()`: no rows found that match ab '", ab, "' (", ab_name(ab_coerced, tolower = TRUE, language = NULL), "), ignoring argument `ab`")
-    }
+    df_new <- df %pm>% subset(ab %in% ab_coerced)
+    if (nrow(df_new) > 0) df <- df_new
   }
 
   if (method_type == "MIC") {
-    # set range
-    mic_range <- c(0.001, 0.002, 0.005, 0.010, 0.025, 0.0625, 0.125, 0.250, 0.5, 1, 2, 4, 8, 16, 32, 64, 128, 256)
+    lowest_mic <- min(df$breakpoint_S, na.rm = TRUE)
+    lowest_mic <- log2(lowest_mic) + sample(c(-3:2), 1)
+    lowest_mic <- 2^lowest_mic
+    highest_mic <- max(df$breakpoint_R, na.rm = TRUE)
+    highest_mic <- log2(highest_mic) + sample(c(-3:1), 1)
+    highest_mic <- max(lowest_mic * 2, 2^highest_mic)
 
-    # get highest/lowest +/- random 1 to 3 higher factors of two
-    max_range <- mic_range[min(
-      length(mic_range),
-      which(mic_range == max(df$breakpoint_R[!is.na(df$breakpoint_R)], na.rm = TRUE)) + sample(c(1:3), 1)
-    )]
-    min_range <- mic_range[max(
-      1,
-      which(mic_range == min(df$breakpoint_S, na.rm = TRUE)) - sample(c(1:3), 1)
-    )]
-
-    mic_range_new <- mic_range[mic_range <= max_range & mic_range >= min_range]
-    if (length(mic_range_new) == 0) {
-      mic_range_new <- mic_range
-    }
-    out <- as.mic(sample(mic_range_new, size = size, replace = TRUE))
-    # 50% chance that lowest will get <= and highest will get >=
+    out <- skewed_values(COMMON_MIC_VALUES, size = size, min = lowest_mic, max = highest_mic, skew = skew, severity = severity)
     if (stats::runif(1) > 0.5 && length(unique(out)) > 1) {
       out[out == min(out)] <- paste0("<=", out[out == min(out)])
     }
     if (stats::runif(1) > 0.5 && length(unique(out)) > 1) {
-      out[out == max(out)] <- paste0(">=", out[out == max(out)])
+      out[out == max(out) & out %unlike% "<="] <- paste0(">=", out[out == max(out) & out %unlike% "<="])
     }
-    return(out)
+    return(as.mic(out))
   } else if (method_type == "DISK") {
-    set_range <- seq(
-      from = as.integer(min(df$breakpoint_R[!is.na(df$breakpoint_R)], na.rm = TRUE) / 1.25),
-      to = as.integer(max(df$breakpoint_S, na.rm = TRUE) * 1.25),
+    disk_range <- seq(
+      from = floor(min(df$breakpoint_R[!is.na(df$breakpoint_R)], na.rm = TRUE) / 1.25),
+      to = ceiling(max(df$breakpoint_S[df$breakpoint_S != 50], na.rm = TRUE) * 1.25),
       by = 1
     )
-    out <- sample(set_range, size = size, replace = TRUE)
-    out[out < 6] <- sample(c(6:10), length(out[out < 6]), replace = TRUE)
-    out[out > 50] <- sample(c(40:50), length(out[out > 50]), replace = TRUE)
+    disk_range <- disk_range[disk_range >= 6 & disk_range <= 50]
+    out <- skewed_values(disk_range, size = size, min = min(disk_range), max = max(disk_range), skew = skew, severity = severity)
     return(as.disk(out))
   }
 }
+
+skewed_values <- function(values, size, min, max, skew = c("right", "left"), severity = 1) {
+  skew <- match.arg(skew)
+  range_vals <- values[values >= min & values <= max]
+  if (length(range_vals) < 2) range_vals <- values
+  ranks <- seq_along(range_vals)
+  weights <- switch(skew,
+    right = rev(ranks)^severity,
+    left = ranks^severity
+  )
+  weights <- weights / sum(weights)
+  sample(range_vals, size = size, replace = TRUE, prob = weights)
+}

R/sir.R

@@ -159,7 +159,7 @@
 #'
 #' The function [is.sir()] detects if the input contains class `sir`. If the input is a [data.frame] or [list], it iterates over all columns/items and returns a [logical] vector.
 #'
-#' The base R function [as.double()] can be used to retrieve quantitative values from a `sir` object: `"S"` = 1, `"I"`/`"SDD"` = 2, `"R"` = 3. All other values are rendered `NA` . **Note:** Do not use `as.integer()`, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.
+#' The base R function [as.double()] can be used to retrieve quantitative values from a `sir` object: `"S"` = 1, `"I"`/`"SDD"` = 2, `"R"` = 3. All other values are rendered `NA`. **Note:** Do not use `as.integer()`, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.
 #'
 #' The function [is_sir_eligible()] returns `TRUE` when a column contains at most 5% potentially invalid antimicrobial interpretations, and `FALSE` otherwise. The threshold of 5% can be set with the `threshold` argument. If the input is a [data.frame], it iterates over all columns and returns a [logical] vector.
 #' @section Interpretation of SIR:

R/tidymodels.R

@@ -0,0 +1,262 @@
+#' AMR Extensions for Tidymodels
+#'
+#' This family of functions allows using AMR-specific data types such as `<mic>` and `<sir>` inside `tidymodels` pipelines.
+#' @inheritParams recipes::step_center
+#' @details
+#' You can read more in our online [AMR with tidymodels introduction](https://amr-for-r.org/articles/AMR_with_tidymodels.html).
+#'
+#' Tidyselect helpers include:
+#' - [all_mic()] and [all_mic_predictors()] to select `<mic>` columns
+#' - [all_sir()] and [all_sir_predictors()] to select `<sir>` columns
+#'
+#' Pre-processing pipeline steps include:
+#' - [step_mic_log2()] to convert MIC columns to numeric (via `as.numeric()`) and apply a log2 transform, to be used with [all_mic_predictors()]
+#' - [step_sir_numeric()] to convert SIR columns to numeric (via `as.numeric()`), to be used with [all_sir_predictors()]: `"S"` = 1, `"I"`/`"SDD"` = 2, `"R"` = 3. All other values are rendered `NA`. Keep this in mind for further processing, especially if the model does not allow for `NA` values.
+#'
+#' These steps integrate with `recipes::recipe()` and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
+#' @seealso [recipes::recipe()], [as.mic()], [as.sir()]
+#' @name amr-tidymodels
+#' @keywords internal
+#' @export
+#' @examples
+#' library(tidymodels)
+#'
+#' # The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703
+#' # Presence of ESBL genes was predicted based on raw MIC values.
+#'
+#'
+#' # example data set in the AMR package
+#' esbl_isolates
+#'
+#' # Prepare a binary outcome and convert to ordered factor
+#' data <- esbl_isolates %>%
+#'   mutate(esbl = factor(esbl, levels = c(FALSE, TRUE), ordered = TRUE))
+#'
+#' # Split into training and testing sets
+#' split <- initial_split(data)
+#' training_data <- training(split)
+#' testing_data <- testing(split)
+#'
+#' # Create and prep a recipe with MIC log2 transformation
+#' mic_recipe <- recipe(esbl ~ ., data = training_data) %>%
+#'   # Optionally remove non-predictive variables
+#'   remove_role(genus, old_role = "predictor") %>%
+#'   # Apply the log2 transformation to all MIC predictors
+#'   step_mic_log2(all_mic_predictors()) %>%
+#'   prep()
+#'
+#' # View prepped recipe
+#' mic_recipe
+#'
+#' # Apply the recipe to training and testing data
+#' out_training <- bake(mic_recipe, new_data = NULL)
+#' out_testing <- bake(mic_recipe, new_data = testing_data)
+#'
+#' # Fit a logistic regression model
+#' fitted <- logistic_reg(mode = "classification") %>%
+#'   set_engine("glm") %>%
+#'   fit(esbl ~ ., data = out_training)
+#'
+#' # Generate predictions on the test set
+#' predictions <- predict(fitted, out_testing) %>%
+#'   bind_cols(out_testing)
+#'
+#' # Evaluate predictions using standard classification metrics
+#' our_metrics <- metric_set(accuracy, kap, ppv, npv)
+#' metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
+#'
+#' # Show performance:
+#' # - negative predictive value (NPV) of ~98%
+#' # - positive predictive value (PPV) of ~94%
+#' metrics
+all_mic <- function() {
+  x <- tidymodels_amr_select(levels(NA_mic_))
+  names(x)
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_mic_predictors <- function() {
+  x <- tidymodels_amr_select(levels(NA_mic_))
+  intersect(x, recipes::has_role("predictor"))
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_sir <- function() {
+  x <- tidymodels_amr_select(levels(NA_sir_))
+  names(x)
+}
+
+#' @rdname amr-tidymodels
+#' @export
+all_sir_predictors <- function() {
+  x <- tidymodels_amr_select(levels(NA_sir_))
+  intersect(x, recipes::has_role("predictor"))
+}
+
+#' @rdname amr-tidymodels
+#' @export
+step_mic_log2 <- function(
+    recipe,
+    ...,
+    role = NA,
+    trained = FALSE,
+    columns = NULL,
+    skip = FALSE,
+    id = recipes::rand_id("mic_log2")) {
+  recipes::add_step(
+    recipe,
+    step_mic_log2_new(
+      terms = rlang::enquos(...),
+      role = role,
+      trained = trained,
+      columns = columns,
+      skip = skip,
+      id = id
+    )
+  )
+}
+
+step_mic_log2_new <- function(terms, role, trained, columns, skip, id) {
+  recipes::step(
+    subclass = "mic_log2",
+    terms = terms,
+    role = role,
+    trained = trained,
+    columns = columns,
+    skip = skip,
+    id = id
+  )
+}
+
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::prep, step_mic_log2)
+prep.step_mic_log2 <- function(x, training, info = NULL, ...) {
+  col_names <- recipes::recipes_eval_select(x$terms, training, info)
+  recipes::check_type(training[, col_names], types = "ordered")
+  step_mic_log2_new(
+    terms = x$terms,
+    role = x$role,
+    trained = TRUE,
+    columns = col_names,
+    skip = x$skip,
+    id = x$id
+  )
+}
+
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::bake, step_mic_log2)
+bake.step_mic_log2 <- function(object, new_data, ...) {
+  recipes::check_new_data(object$columns, object, new_data)
+  for (col in object$columns) {
+    new_data[[col]] <- log2(as.numeric(as.mic(new_data[[col]])))
+  }
+  new_data
+}
+
+#' @export
+print.step_mic_log2 <- function(x, width = max(20, options()$width - 35), ...) {
+  title <- "Log2 transformation of MIC columns"
+  recipes::print_step(x$columns, x$terms, x$trained, title, width)
+  invisible(x)
+}
+
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_mic_log2)
+tidy.step_mic_log2 <- function(x, ...) {
+  if (recipes::is_trained(x)) {
+    res <- tibble::tibble(terms = x$columns)
+  } else {
+    res <- tibble::tibble(terms = recipes::sel2char(x$terms))
+  }
+  res$id <- x$id
+  res
+}
+
+#' @rdname amr-tidymodels
+#' @export
+step_sir_numeric <- function(
+    recipe,
+    ...,
+    role = NA,
+    trained = FALSE,
+    columns = NULL,
+    skip = FALSE,
+    id = recipes::rand_id("sir_numeric")) {
+  recipes::add_step(
+    recipe,
+    step_sir_numeric_new(
+      terms = rlang::enquos(...),
+      role = role,
+      trained = trained,
+      columns = columns,
+      skip = skip,
+      id = id
+    )
+  )
+}
+
+step_sir_numeric_new <- function(terms, role, trained, columns, skip, id) {
+  recipes::step(
+    subclass = "sir_numeric",
+    terms = terms,
+    role = role,
+    trained = trained,
+    columns = columns,
+    skip = skip,
+    id = id
+  )
+}
+
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::prep, step_sir_numeric)
+prep.step_sir_numeric <- function(x, training, info = NULL, ...) {
+  col_names <- recipes::recipes_eval_select(x$terms, training, info)
+  recipes::check_type(training[, col_names], types = "ordered")
+  step_sir_numeric_new(
+    terms = x$terms,
+    role = x$role,
+    trained = TRUE,
+    columns = col_names,
+    skip = x$skip,
+    id = x$id
+  )
+}
+
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::bake, step_sir_numeric)
+bake.step_sir_numeric <- function(object, new_data, ...) {
+  recipes::check_new_data(object$columns, object, new_data)
+  for (col in object$columns) {
+    new_data[[col]] <- as.numeric(as.sir(new_data[[col]]))
+  }
+  new_data
+}
+
+#' @export
+print.step_sir_numeric <- function(x, width = max(20, options()$width - 35), ...) {
+  title <- "Numeric transformation of SIR columns"
+  recipes::print_step(x$columns, x$terms, x$trained, title, width)
+  invisible(x)
+}
+
+#' @rawNamespace if(getRversion() >= "3.0.0") S3method(recipes::tidy, step_sir_numeric)
+tidy.step_sir_numeric <- function(x, ...) {
+  if (recipes::is_trained(x)) {
+    res <- tibble::tibble(terms = x$columns)
+  } else {
+    res <- tibble::tibble(terms = recipes::sel2char(x$terms))
+  }
+  res$id <- x$id
+  res
+}
+
+tidymodels_amr_select <- function(check_vector) {
+  df <- get_current_data()
+  ind <- which(
+    vapply(
+      FUN.VALUE = logical(1),
+      df,
+      function(x) all(x %in% c(check_vector, NA), na.rm = TRUE) & any(x %in% check_vector),
+      USE.NAMES = TRUE
+    ),
+    useNames = TRUE
+  )
+  ind
+}

R/translate.R

@@ -258,6 +258,11 @@ translate_into_language <- function(from,
     return(from)
   }
 
+  if (only_affect_ab_names == TRUE) {
+    df_trans$pattern[df_trans$regular_expr == TRUE] <- paste0(df_trans$pattern[df_trans$regular_expr == TRUE], "$")
+    df_trans$pattern[df_trans$regular_expr == TRUE] <- gsub("$$", "$", df_trans$pattern[df_trans$regular_expr == TRUE], fixed = TRUE)
+  }
+
   lapply(
     # starting with longest pattern, since more general translations are shorter, such as 'Group'
     order(nchar(df_trans$pattern), decreasing = TRUE),

_pkgdown.yml

@@ -234,6 +234,7 @@ reference:
     - "`antimicrobials`"
     - "`clinical_breakpoints`"
     - "`example_isolates`"
+    - "`esbl_isolates`"
     - "`microorganisms.codes`"
     - "`microorganisms.groups`"
     - "`intrinsic_resistant`"

data-raw/_pre_commit_checks.R

@@ -663,7 +663,9 @@ if (files_changed()) {
 }
 
 # Update index.md and README.md -------------------------------------------
-if (files_changed("man/microorganisms.Rd") ||
+if (files_changed("README.Rmd") ||
+    files_changed("index.Rmd") ||
+    files_changed("man/microorganisms.Rd") ||
     files_changed("man/antimicrobials.Rd") ||
     files_changed("man/clinical_breakpoints.Rd") ||
     files_changed("man/antibiogram.Rd") ||

index.Rmd

@@ -28,8 +28,8 @@ AMR:::reset_all_thrown_messages()
 > Now available for Python too! [Click here](./articles/AMR_for_Python.html) to read more.
 
 <div style="display: flex; font-size: 0.8em;">
-  <p style="text-align:left; width: 50%;"><small><a href="https://amr-for-r.org/">https://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></p>
+  <p style="text-align:left; width: 50%;"><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">doi.org/10.18637/jss.v104.i03</a></small></p>
 </div>
 
 <a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120" /></a>

man/amr-tidymodels.Rd

@@ -0,0 +1,122 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tidymodels.R
+\name{amr-tidymodels}
+\alias{amr-tidymodels}
+\alias{all_mic}
+\alias{all_mic_predictors}
+\alias{all_sir}
+\alias{all_sir_predictors}
+\alias{step_mic_log2}
+\alias{step_sir_numeric}
+\title{AMR Extensions for Tidymodels}
+\usage{
+all_mic()
+
+all_mic_predictors()
+
+all_sir()
+
+all_sir_predictors()
+
+step_mic_log2(recipe, ..., role = NA, trained = FALSE, columns = NULL,
+  skip = FALSE, id = recipes::rand_id("mic_log2"))
+
+step_sir_numeric(recipe, ..., role = NA, trained = FALSE, columns = NULL,
+  skip = FALSE, id = recipes::rand_id("sir_numeric"))
+}
+\arguments{
+\item{recipe}{A recipe object. The step will be added to the sequence of
+operations for this recipe.}
+
+\item{...}{One or more selector functions to choose variables for this step.
+See \code{\link[recipes:selections]{selections()}} for more details.}
+
+\item{role}{Not used by this step since no new variables are created.}
+
+\item{trained}{A logical to indicate if the quantities for preprocessing have
+been estimated.}
+
+\item{skip}{A logical. Should the step be skipped when the recipe is baked by
+\code{\link[recipes:bake]{bake()}}? While all operations are baked when \code{\link[recipes:prep]{prep()}} is run, some
+operations may not be able to be conducted on new data (e.g. processing the
+outcome variable(s)). Care should be taken when using \code{skip = TRUE} as it
+may affect the computations for subsequent operations.}
+
+\item{id}{A character string that is unique to this step to identify it.}
+}
+\description{
+This family of functions allows using AMR-specific data types such as \verb{<mic>} and \verb{<sir>} inside \code{tidymodels} pipelines.
+}
+\details{
+You can read more in our online \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{AMR with tidymodels introduction}.
+
+Tidyselect helpers include:
+\itemize{
+\item \code{\link[=all_mic]{all_mic()}} and \code{\link[=all_mic_predictors]{all_mic_predictors()}} to select \verb{<mic>} columns
+\item \code{\link[=all_sir]{all_sir()}} and \code{\link[=all_sir_predictors]{all_sir_predictors()}} to select \verb{<sir>} columns
+}
+
+Pre-processing pipeline steps include:
+\itemize{
+\item \code{\link[=step_mic_log2]{step_mic_log2()}} to convert MIC columns to numeric (via \code{as.numeric()}) and apply a log2 transform, to be used with \code{\link[=all_mic_predictors]{all_mic_predictors()}}
+\item \code{\link[=step_sir_numeric]{step_sir_numeric()}} to convert SIR columns to numeric (via \code{as.numeric()}), to be used with \code{\link[=all_sir_predictors]{all_sir_predictors()}}: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. Keep this in mind for further processing, especially if the model does not allow for \code{NA} values.
+}
+
+These steps integrate with \code{recipes::recipe()} and work like standard preprocessing steps. They are useful for preparing data for modelling, especially with classification models.
+}
+\examples{
+library(tidymodels)
+
+# The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703
+# Presence of ESBL genes was predicted based on raw MIC values.
+
+
+# example data set in the AMR package
+esbl_isolates
+
+# Prepare a binary outcome and convert to ordered factor
+data <- esbl_isolates \%>\%
+  mutate(esbl = factor(esbl, levels = c(FALSE, TRUE), ordered = TRUE))
+
+# Split into training and testing sets
+split <- initial_split(data)
+training_data <- training(split)
+testing_data <- testing(split)
+
+# Create and prep a recipe with MIC log2 transformation
+mic_recipe <- recipe(esbl ~ ., data = training_data) \%>\%
+  # Optionally remove non-predictive variables
+  remove_role(genus, old_role = "predictor") \%>\%
+  # Apply the log2 transformation to all MIC predictors
+  step_mic_log2(all_mic_predictors()) \%>\%
+  prep()
+
+# View prepped recipe
+mic_recipe
+
+# Apply the recipe to training and testing data
+out_training <- bake(mic_recipe, new_data = NULL)
+out_testing <- bake(mic_recipe, new_data = testing_data)
+
+# Fit a logistic regression model
+fitted <- logistic_reg(mode = "classification") \%>\%
+  set_engine("glm") \%>\%
+  fit(esbl ~ ., data = out_training)
+
+# Generate predictions on the test set
+predictions <- predict(fitted, out_testing) \%>\%
+  bind_cols(out_testing)
+
+# Evaluate predictions using standard classification metrics
+our_metrics <- metric_set(accuracy, kap, ppv, npv)
+metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
+
+# Show performance:
+# - negative predictive value (NPV) of ~98\%
+# - positive predictive value (PPV) of ~94\%
+metrics
+}
+\seealso{
+\code{\link[recipes:recipe]{recipes::recipe()}}, \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.sir]{as.sir()}}
+}
+\keyword{internal}

man/antibiogram.Rd

@@ -56,6 +56,7 @@ retrieve_wisca_parameters(wisca_model, ...)
 \item \code{c(aminoglycosides(), "AMP", "AMC")}
 \item \code{c(aminoglycosides(), carbapenems())}
 }
+\item Column indices using numbers
 \item Combination therapy, indicated by using \code{"+"}, with or without \link[=antimicrobial_selectors]{antimicrobial selectors}, e.g.:
 \itemize{
 \item \code{"cipro + genta"}

man/as.sir.Rd

@@ -247,7 +247,7 @@ To determine which isolates are multi-drug resistant, be sure to run \code{\link
 
 The function \code{\link[=is.sir]{is.sir()}} detects if the input contains class \code{sir}. If the input is a \link{data.frame} or \link{list}, it iterates over all columns/items and returns a \link{logical} vector.
 
-The base R function \code{\link[=as.double]{as.double()}} can be used to retrieve quantitative values from a \code{sir} object: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA} . \strong{Note:} Do not use \code{as.integer()}, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.
+The base R function \code{\link[=as.double]{as.double()}} can be used to retrieve quantitative values from a \code{sir} object: \code{"S"} = 1, \code{"I"}/\code{"SDD"} = 2, \code{"R"} = 3. All other values are rendered \code{NA}. \strong{Note:} Do not use \code{as.integer()}, since that (because of how R works internally) will return the factor level indices, and not these aforementioned quantitative values.
 
 The function \code{\link[=is_sir_eligible]{is_sir_eligible()}} returns \code{TRUE} when a column contains at most 5\% potentially invalid antimicrobial interpretations, and \code{FALSE} otherwise. The threshold of 5\% can be set with the \code{threshold} argument. If the input is a \link{data.frame}, it iterates over all columns and returns a \link{logical} vector.
 }

man/esbl_isolates.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{esbl_isolates}
+\alias{esbl_isolates}
+\title{Data Set with 500 ESBL Isolates}
+\format{
+A \link[tibble:tibble]{tibble} with 500 observations and 19 variables:
+\itemize{
+\item \code{esbl}\cr Logical indicator if the isolate is ESBL-producing
+\item \code{genus}\cr Genus of the microorganism
+\item \code{AMC:COL}\cr MIC values for 17 antimicrobial agents, transformed to class \code{\link{mic}} (see \code{\link[=as.mic]{as.mic()}})
+}
+}
+\usage{
+esbl_isolates
+}
+\description{
+A data set containing 500 microbial isolates with MIC values of common antibiotics and a binary \code{esbl} column for extended-spectrum beta-lactamase (ESBL) production. This data set contains randomised fictitious data but reflects reality and can be used to practise AMR-related machine learning, e.g., classification modelling with \href{https://amr-for-r.org/articles/AMR_with_tidymodels.html}{tidymodels}.
+}
+\details{
+See our \link[=amr-tidymodels]{tidymodels integration} for an example using this data set.
+}
+\examples{
+esbl_isolates
+}
+\keyword{datasets}

man/random.Rd

@@ -7,19 +7,25 @@
 \alias{random_sir}
 \title{Random MIC Values/Disk Zones/SIR Generation}
 \usage{
-random_mic(size = NULL, mo = NULL, ab = NULL, ...)
+random_mic(size = NULL, mo = NULL, ab = NULL, skew = "right",
+  severity = 1, ...)
 
-random_disk(size = NULL, mo = NULL, ab = NULL, ...)
+random_disk(size = NULL, mo = NULL, ab = NULL, skew = "left",
+  severity = 1, ...)
 
 random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)
 }
 \arguments{
 \item{size}{Desired size of the returned vector. If used in a \link{data.frame} call or \code{dplyr} verb, will get the current (group) size if left blank.}
 
-\item{mo}{Any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}.}
+\item{mo}{Any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}. Can be the same length as \code{size}.}
 
 \item{ab}{Any \link{character} that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}.}
 
+\item{skew}{Direction of skew for MIC or disk values, either \code{"right"} or \code{"left"}. A left-skewed distribution has the majority of the data on the right.}
+
+\item{severity}{Skew severity; higher values will increase the skewedness. Default is \code{2}; use \code{0} to prevent skewedness.}
+
 \item{...}{Ignored, only in place to allow future extensions.}
 
 \item{prob_SIR}{A vector of length 3: the probabilities for "S" (1st value), "I" (2nd value) and "R" (3rd value).}
@@ -31,17 +37,25 @@ class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=a
 These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
 }
 \details{
-The base \R function \code{\link[=sample]{sample()}} is used for generating values.
-
-Generated values are based on the EUCAST 2025 guideline as implemented in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument.
+Internally, MIC and disk zone values are sampled based on clinical breakpoints defined in the \link{clinical_breakpoints} data set. To create specific generated values per bug or drug, set the \code{mo} and/or \code{ab} argument. The MICs are sampled on a log2 scale and disks linearly, using weighted probabilities. The weights are based on the \code{skew} and \code{severity} arguments:
+\itemize{
+\item \code{skew = "right"} places more emphasis on lower MIC or higher disk values.
+\item \code{skew = "left"} places more emphasis on higher MIC or lower disk values.
+\item \code{severity} controls the exponential bias applied.
+}
 }
 \examples{
 random_mic(25)
 random_disk(25)
 random_sir(25)
 
+# add more skewedness, make more realistic by setting a bug and/or drug:
+disks <- random_disk(100, severity = 2, mo = "Escherichia coli", ab = "CIP")
+plot(disks)
+# `plot()` and `ggplot2::autoplot()` allow for coloured bars if `mo` and `ab` are set
+plot(disks, mo = "Escherichia coli", ab = "CIP", guideline = "CLSI 2025")
+
 \donttest{
-# make the random generation more realistic by setting a bug and/or drug:
 random_mic(25, "Klebsiella pneumoniae") # range 0.0625-64
 random_mic(25, "Klebsiella pneumoniae", "meropenem") # range 0.0625-16
 random_mic(25, "Streptococcus pneumoniae", "meropenem") # range 0.0625-4

pkgdown/extra.css

@@ -41,7 +41,7 @@
 
   --bs-success: var(--amr-green-dark) !important;
   --bs-light: var(--amr-green-light) !important;
-  /* --bs-light was this: #128f76a6; that's success with 60% alpha */
+  /* --bs-light was this: #128f76a6; that's bs-success with 60% alpha */
   --bs-info: var(--amr-green-middle) !important;
   --bs-link-color: var(--amr-green-dark) !important;
   --bs-link-color-rgb: var(--amr-green-dark-rgb) !important;
@@ -104,6 +104,16 @@ body.amr-for-python * {
 .navbar .algolia-autocomplete .aa-dropdown-menu {
   background-color: var(--amr-green-dark) !important;
 }
+
+.version-main {
+  font-weight: bold;
+  color: var(--bs-navbar-brand-color);
+}
+.version-build {
+  font-weight: normal;
+  opacity: 0.75;
+  font-size: 0.85em;
+}
 input[type="search"] {
   color: var(--bs-tertiary-bg) !important;
   background-color: var(--amr-green-light) !important;
@@ -149,6 +159,7 @@ this shows on top of every sidebar to the right
   margin-top: 10px;
   border: 2px dashed var(--amr-green-dark);
   text-align: center;
+  background: var(--bs-body-bg);
 }
 .amr-gpt-assistant * {
   width: 90%;

pkgdown/extra.js

@@ -29,10 +29,22 @@
 # ==================================================================== #
 */
 
-$(document).ready(function() {
+$(function () {
   // add GPT assistant info
   $('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chat.amr-for-r.org"><img src="https://amr-for-r.org/AMRforRGPT.svg"></a></div>');
 
+  // split version number in navbar into main version and build number
+  $('.nav-text').each(function () {
+    const $el = $(this);
+    const text = $.trim($el.text());
+    const lastDotIndex = text.lastIndexOf('.');
+    if (lastDotIndex > -1) {
+      const main = text.substring(0, lastDotIndex);
+      const build = text.substring(lastDotIndex);
+      $el.html(`<span class="version-main">${main}</span><span class="version-build">${build}</span>`);
+    }
+  });
+
   // replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
   $(".developers h2").text("Maintainers");
   $(".template-citation-authors h1:nth(0)").text("Contributors and Citation");

tests/testthat/test-zzz.R

@@ -127,6 +127,24 @@ test_that("test-zzz.R", {
     "type_sum" = "pillar",
     # readxl
     "read_excel" = "readxl",
+    # recipes
+    "add_step" = "recipes",
+    "bake" = "recipes",
+    "check_new_data" = "recipes",
+    "check_type" = "recipes",
+    "has_role" = "recipes",
+    "is_trained" = "recipes",
+    "prep" = "recipes",
+    "print_step" = "recipes",
+    "rand_id" = "recipes",
+    "recipe" = "recipes",
+    "recipes_eval_select" = "recipes",
+    "sel2char" = "recipes",
+    "step" = "recipes",
+    "step_center" = "recipes",
+    "tidy" = "recipes",
+    # rlang
+    "enquos" = "rlang",
     # rmarkdown
     "html_vignette" = "rmarkdown",
     # skimr

vignettes/AMR_with_tidymodels.Rmd

@@ -28,6 +28,13 @@ Antimicrobial resistance (AMR) is a global health crisis, and understanding resi
 
 In this post, we will explore how to use the `tidymodels` framework to predict resistance patterns in the `example_isolates` dataset in two examples.
 
+This post contains the following examples:
+
+1. Using Antimicrobial Selectors
+2. Predicting ESBL Presence Using Raw MICs
+3. Predicting AMR Over Time
+
+
 ## Example 1: Using Antimicrobial Selectors
 
 By leveraging the power of `tidymodels` and the `AMR` package, we’ll build a reproducible machine learning workflow to predict the Gramstain of the microorganism to two important antibiotic classes: aminoglycosides and beta-lactams.
@@ -208,10 +215,150 @@ This workflow is extensible to other antimicrobial classes and resistance patter
 
 ---
 
+## Example 2: Predicting ESBL Presence Using Raw MICs
 
-## Example 2: Predicting AMR Over Time
+In this second example, we demonstrate how to use `<mic>` columns directly in `tidymodels` workflows using AMR-specific recipe steps. This includes a transformation to `log2` scale using `step_mic_log2()`, which prepares MIC values for use in classification models.
 
-In this second example, we aim to predict antimicrobial resistance (AMR) trends over time using `tidymodels`. We will model resistance to three antibiotics (amoxicillin `AMX`, amoxicillin-clavulanic acid `AMC`, and ciprofloxacin `CIP`), based on historical data grouped by year and hospital ward.
+This approach and idea formed the basis for the publication [DOI: 10.3389/fmicb.2025.1582703](https://doi.org/10.3389/fmicb.2025.1582703) to model the presence of extended-spectrum beta-lactamases (ESBL).
+
+### **Objective**
+
+Our goal is to:
+
+1. Use raw MIC values to predict whether a bacterial isolate produces ESBL.
+2. Apply AMR-aware preprocessing in a `tidymodels` recipe.
+3. Train a classification model and evaluate its predictive performance.
+
+### **Data Preparation**
+
+We use the `esbl_isolates` dataset that comes with the AMR package.
+
+```{r}
+# Load required libraries
+library(AMR)
+library(tidymodels)
+
+# View the esbl_isolates data set
+esbl_isolates
+
+# Prepare a binary outcome and convert to ordered factor
+data <- esbl_isolates %>%
+  mutate(esbl = factor(esbl, levels = c(FALSE, TRUE), ordered = TRUE))
+```
+
+**Explanation:**
+
+- `esbl_isolates`: Contains MIC test results and ESBL status for each isolate.
+- `mutate(esbl = ...)`: Converts the target column to an ordered factor for classification.
+
+### **Defining the Workflow**
+
+#### 1. Preprocessing with a Recipe
+
+We use our `step_mic_log2()` function to log2-transform MIC values, ensuring that MICs are numeric and properly scaled. All MIC predictors can easily and agnostically selected using the new `all_mic_predictors()`:
+
+```{r}
+# Split into training and testing sets
+set.seed(123)
+split <- initial_split(data)
+training_data <- training(split)
+testing_data <- testing(split)
+
+# Define the recipe
+mic_recipe <- recipe(esbl ~ ., data = training_data) %>%
+  remove_role(genus, old_role = "predictor") %>%  # Remove non-informative variable
+  step_mic_log2(all_mic_predictors()) #%>%         # Log2 transform all MIC predictors
+ # prep()
+
+mic_recipe
+```
+
+**Explanation:**
+
+- `remove_role()`: Removes irrelevant variables like genus.
+- `step_mic_log2()`: Applies `log2(as.numeric(...))` to all MIC predictors in one go.
+- `prep()`: Finalises the recipe based on training data.
+
+#### 2. Specifying the Model
+
+We use a simple logistic regression to model ESBL presence, though recent models such as xgboost ([link to `parsnip` manual](https://parsnip.tidymodels.org/reference/details_boost_tree_xgboost.html)) could be much more precise.
+
+```{r}
+# Define the model
+model <- logistic_reg(mode = "classification") %>%
+  set_engine("glm")
+
+model
+```
+
+**Explanation:**
+
+- `logistic_reg()`: Specifies a binary classification model.
+- `set_engine("glm")`: Uses the base R GLM engine.
+
+#### 3. Building the Workflow
+
+```{r}
+# Create workflow
+workflow_model <- workflow() %>%
+  add_recipe(mic_recipe) %>%
+  add_model(model)
+
+workflow_model
+```
+
+### **Training and Evaluating the Model**
+
+```{r}
+# Fit the model
+fitted <- fit(workflow_model, training_data)
+
+# Generate predictions
+predictions <- predict(fitted, testing_data) %>%
+  bind_cols(testing_data)
+
+# Evaluate model performance
+our_metrics <- metric_set(accuracy, kap, ppv, npv)
+metrics <- our_metrics(predictions, truth = esbl, estimate = .pred_class)
+
+metrics
+```
+
+**Explanation:**
+
+- `fit()`: Trains the model on the processed training data.
+- `predict()`: Produces predictions for unseen test data.
+- `metric_set()`: Allows evaluating multiple classification metrics.
+
+It appears we can predict ESBL gene presence with a positive predictive value (PPV) of `r round(metrics$.estimate[3], 3) * 100`% and a negative predictive value (NPV) of `r round(metrics$.estimate[4], 3) * 100` using a simplistic logistic regression model.
+
+### **Visualising Predictions**
+
+We can visualise predictions by comparing predicted and actual ESBL status.
+
+```{r}
+library(ggplot2)
+
+ggplot(predictions, aes(x = esbl, fill = .pred_class)) +
+  geom_bar(position = "stack") +
+  labs(title = "Predicted vs Actual ESBL Status",
+       x = "Actual ESBL",
+       y = "Count") +
+  theme_minimal()
+```
+
+### **Conclusion**
+
+In this example, we showcased how the new `AMR`-specific recipe steps simplify working with `<mic>` columns in `tidymodels`. The `step_mic_log2()` transformation converts ordered MICs to log2-transformed numerics, improving compatibility with classification models.
+
+This pipeline enables realistic, reproducible, and interpretable modelling of antimicrobial resistance data.
+
+---
+
+
+## Example 3: Predicting AMR Over Time
+
+In this third example, we aim to predict antimicrobial resistance (AMR) trends over time using `tidymodels`. We will model resistance to three antibiotics (amoxicillin `AMX`, amoxicillin-clavulanic acid `AMC`, and ciprofloxacin `CIP`), based on historical data grouped by year and hospital ward.
 
 ### **Objective**
 

vignettes/welcome_to_AMR.Rmd

@@ -28,7 +28,7 @@ Note: to keep the package size as small as possible, we only include this vignet
 
 The `AMR` package is a peer-reviewed, [free and open-source](https://amr-for-r.org/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. **Our aim is to provide a standard** for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of [many different researchers](https://amr-for-r.org/authors.html) from around the globe to make this a successful and durable project!
 
-This work was published in the Journal of Statistical Software (Volume 104(3); \doi{10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\doi{10.33612/diss.177417131} and \doi{10.33612/diss.192486375}).
+This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
 
 After installing this package, R knows [**`r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species**](https://amr-for-r.org/reference/microorganisms.html) (updated June 2024) and all [**`r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial and antiviral drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))` and EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))` are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). **It was designed to work in any setting, including those with very limited resources**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl) and the [University Medical Center Groningen](https://www.umcg.nl).