(v3.0.1.9021) add guideline to resistance() and susceptibility()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1.9020
+Version: 3.0.1.9021
-Date: 2026-02-09
+Date: 2026-02-12
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
   data analysis and to work with microbial and antimicrobial properties by

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9020
+# AMR 3.0.1.9021
 
 ### New
 * Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`
@@ -18,13 +18,14 @@
 
 ### Fixes
 * Fixed a bug in `antibiogram()` for when no antimicrobials are set
-* Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `i`,  and `R` would not be considered (#244)
+* Fixed a bug in `as.sir()` where for numeric input the arguments `S`,  `I`,  and `R` would not be considered (#244)
 * Fixed some foreign translations of antimicrobial drugs
 * Fixed a bug for printing column names to the console when using `mutate_at(vars(...), as.mic)` (#249)
 * Fixed a bug to disregard `NI` for susceptibility proportion functions
 * Fixed Italian translation of CoNS to Stafilococco coagulasi-negativo and CoPS to Stafilococco coagulasi-positivo (#256)
 
 ### Updates
+* `susceptibility()` and `resistance()` gained the argument `guideline`, which defaults to EUCAST, for interpreting the 'I' category correctly.
 * `as.mic()` and `rescale_mic()` gained the argument `round_to_next_log2`, which can be set to `TRUE` to round all values up to the nearest next log2 level (#255)
 * `antimicrobials$group` is now a `list` instead of a `character`, to contain any group the drug is in (#246)
 * `ab_group()` gained an argument `all_groups` to return all groups the antimicrobial drug is in (#246)

R/aa_options.R

@@ -29,8 +29,11 @@
 
 #' Options for the AMR package
 #'
-#' This is an overview of all the package-specific [options()] you can set in the `AMR` package.
+#' @description
-#' @section Options:
+#' This is an overview of all the package-specific options you can set in the `AMR` package. Set them using the [options()] function, e.g.:
+#'
+#' `options(AMR_guideline = "CLSI")`
+#' @section Options (alphabetical order):
 #' * `AMR_antibiogram_formatting_type` \cr A [numeric] (1-22) to use in [antibiogram()], to indicate which formatting type to use.
 #' * `AMR_breakpoint_type` \cr A [character] to use in [as.sir()], to indicate which breakpoint type to use. This must be either `r vector_or(clinical_breakpoints$type)`.
 #' * `AMR_capped_mic_handling` \cr A [character] to use in [as.sir()], to indicate how capped MIC values (`<`, `<=`, `>`, `>=`) should be interpreted. Must be one of `"none"`, `"conservative"`, `"standard"`, or `"lenient"` - the default is `"conservative"`.
@@ -38,6 +41,15 @@
 #' * `AMR_custom_ab` \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in [add_custom_antimicrobials()].
 #' * `AMR_custom_mo` \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in [add_custom_microorganisms()].
 #' * `AMR_eucastrules` \cr A [character] to set the default types of rules for [eucast_rules()] function, must be one or more of: `"breakpoints"`, `"expert"`, `"other"`, `"custom"`, `"all"`, and defaults to `c("breakpoints", "expert")`.
+#' * `AMR_guideline` \cr A [character] to set the default guideline used throughout the `AMR` package wherever a `guideline` argument is available. This option is used as the default in e.g. [as.sir()], [resistance()], [susceptibility()], [interpretive_rules()] and many plotting functions. **While unset**, the AMR package uses the latest implemented EUCAST guideline (currently `r AMR::clinical_breakpoints$guideline[1]`).
+#'
+#'   - For [as.sir()], this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`, and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))` to `r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`.
+#'
+#'   - For [resistance()] and [susceptibility()], this setting determines how the `"I"` (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, `"I"` is considered *resistant* in susceptibility calculations; under EUCAST, `"I"` is considered *susceptible* in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
+#'
+#'   - For [interpretive_rules()], this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
+#'
+#'   - For many plotting functions (e.g., for MIC or disk diffusion values), supplying `mo` and `ab` enables automatic SIR-based interpretative colouring. These colours are derived from [as.sir()] in the background and therefore depend on the active `guideline` setting, which again uses `r AMR::clinical_breakpoints$guideline[1]` if not set explicitly.
 #' * `AMR_guideline` \cr A [character] to set the default guideline for interpreting MIC values and disk diffusion diameters with [as.sir()]. Can be only the guideline name (e.g., `"CLSI"`) or the name with a year (e.g. `"CLSI 2019"`). The default to the latest implemented EUCAST guideline, currently \code{"`r clinical_breakpoints$guideline[1]`"}. Supported guideline are currently EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(clinical_breakpoints, guideline %like% "CLSI")$guideline)))`).
 #' * `AMR_ignore_pattern` \cr A [regular expression][base::regex] to ignore (i.e., make `NA`) any match given in [as.mo()] and all [`mo_*`][mo_property()] functions.
 #' * `AMR_include_PKPD` \cr A [logical] to use in [as.sir()], to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`.
@@ -63,9 +75,9 @@
 #'
 #' ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with [as.sir()].
 #'
-#' ### Share Options Within Team
+#' ## Share Options Within Team
 #'
-#' For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
+#' For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
 #'
 #' 1. Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
 #'

R/count.R

@@ -33,13 +33,16 @@
 #'
 #' [count_resistant()] should be used to count resistant isolates, [count_susceptible()] should be used to count susceptible isolates.
 #' @param ... One or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with [as.sir()] if needed.
+#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
+#'   * EUCAST: [count_susceptible()] \eqn{= N_{S} + N_{I}}, [count_resistant()] \eqn{= N_{R}}
+#'   * CLSI: [count_susceptible()] \eqn{= N_{S} + N_{SDD}}, [count_resistant()] \eqn{= N_{I} + N_{R}}
+#'
+#' You can also use e.g. [count_R()] or [count_S()] instead, to be explicit.
 #' @inheritParams proportion
 #' @inheritSection as.sir Interpretation of SIR
 #' @details These functions are meant to count isolates. Use the [resistance()]/[susceptibility()] functions to calculate microbial resistance/susceptibility.
 #'
-#' The function [count_resistant()] is equal to the function [count_R()]. The function [count_susceptible()] is equal to the function [count_SI()].
+#' The function [n_sir()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to `dplyr`'s `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
-#'
-#' The function [n_sir()] is an alias of [count_all()]. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to `n_distinct()`. Their function is equal to `count_susceptible(...) + count_resistant(...)`.
 #'
 #' The function [count_df()] takes any variable from `data` that has an [`sir`] class (created with [as.sir()]) and counts the number of S's, I's and R's. It also supports grouped variables. The function [sir_df()] works exactly like [count_df()], but adds the percentage of S, I and R.
 #' @inheritSection proportion Combination Therapy
@@ -119,10 +122,21 @@
 #'     count_df(translate = FALSE)
 #' }
 #' }
-count_resistant <- function(..., only_all_tested = FALSE) {
+count_resistant <- function(...,
+                            only_all_tested = FALSE,
+                            guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_resistant", "eucast_default", entire_session = TRUE)) {
+    message_("`count_resistant()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("R", "NWT", "NS"),
+      ab_result = c(
+        "R", "NWT", "NS",
+        if (identical(guideline, "CLSI")) "I"
+      ),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),
@@ -132,10 +146,21 @@ count_resistant <- function(..., only_all_tested = FALSE) {
 
 #' @rdname count
 #' @export
-count_susceptible <- function(..., only_all_tested = FALSE) {
+count_susceptible <- function(...,
+                              only_all_tested = FALSE,
+                              guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("count_susceptible", "eucast_default", entire_session = TRUE)) {
+    message_("`count_susceptible()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I", "WT"),
+      ab_result = c(
+        "S", "SDD", "WT",
+        if (identical(guideline, "EUCAST")) "I"
+      ),
       only_all_tested = only_all_tested,
       only_count = TRUE
     ),

R/mean_amr_distance.R

@@ -118,7 +118,7 @@ mean_amr_distance.disk <- function(x, ...) {
 mean_amr_distance.sir <- function(x, ..., combine_SI = TRUE) {
   meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = -1)
   if (isTRUE(combine_SI)) {
-    x[x %in% c("I", "SDD")] <- "S"
+    x[x %in% c("I", "SDD")] <- "S" # do not acknowledge CLSI/EUCAST guideline here to keep the numeric mean_amr_distance consistent between systems
   }
   mean_amr_distance(as.double(x))
 }

R/proportion.R

@@ -38,6 +38,11 @@
 #' @param only_all_tested (for combination therapies, i.e. using more than one variable for `...`): a [logical] to indicate that isolates must be tested for all antimicrobials, see section *Combination Therapy* below.
 #' @param data A [data.frame] containing columns with class [`sir`] (see [as.sir()]).
 #' @param translate_ab A column name of the [antimicrobials] data set to translate the antibiotic abbreviations to, using [ab_property()].
+#' @param guideline Either `"EUCAST"` (default) or `"CLSI"`. With EUCAST, the 'I' category will be considered as susceptible (see [EUCAST website](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/)), but with with CLSI, it will be considered resistant. Therefore:
+#'   * EUCAST: [susceptibility()] \eqn{= \%S + \%I}, [resistance()] \eqn{= \%R}
+#'   * CLSI: [susceptibility()] \eqn{= \%S + \%SDD}, [resistance()] \eqn{= \%I + \%R}
+#'
+#' You can also use e.g. [proportion_R()] or [proportion_S()] instead, to be explicit.
 #' @inheritParams ab_property
 #' @param combine_SI A [logical] to indicate whether all values of S, SDD, and I must be merged into one, so the output only consists of S+SDD+I vs. R (susceptible vs. resistant) - the default is `TRUE`.
 #' @param ab_result Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".
@@ -228,10 +233,20 @@
 resistance <- function(...,
                        minimum = 30,
                        as_percent = FALSE,
-                       only_all_tested = FALSE) {
+                       only_all_tested = FALSE,
+                       guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("resistance", "eucast_default", entire_session = TRUE)) {
+    message_("`resistance()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("R", "NWT", "NS"),
+      ab_result = c(
+        "R", "NWT", "NS",
+        if (identical(guideline, "CLSI")) "I"
+      ),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,
@@ -246,10 +261,20 @@ resistance <- function(...,
 susceptibility <- function(...,
                            minimum = 30,
                            as_percent = FALSE,
-                           only_all_tested = FALSE) {
+                           only_all_tested = FALSE,
+                           guideline = getOption("AMR_guideline", "EUCAST")) {
+  # other arguments for meet_criteria are handled by sir_calc()
+  meet_criteria(guideline, allow_class = "character", is_in = c("EUCAST", "CLSI"), has_length = 1)
+  if (is.null(getOption("AMR_guideline")) && missing(guideline) && message_not_thrown_before("susceptibility", "eucast_default", entire_session = TRUE)) {
+    message_("`susceptibility()` assumes the EUCAST guideline and thus considers the 'I' category susceptible. Set the `guideline` argument or the `AMR_guideline` option to either \"CLSI\" or \"EUCAST\", see `?AMR-options`.")
+    message_("This message will be shown once per session.")
+  }
   tryCatch(
     sir_calc(...,
-      ab_result = c("S", "SDD", "I", "WT"),
+      ab_result = c(
+        "S", "SDD", "WT",
+        if (identical(guideline, "EUCAST")) "I"
+      ),
       minimum = minimum,
       as_percent = as_percent,
       only_all_tested = only_all_tested,

R/sir.R

@@ -156,9 +156,9 @@ VALID_SIR_LEVELS <- c("S", "SDD", "I", "R", "NI", "WT", "NWT", "NS")
 #'
 #' ### After Interpretation
 #'
-#' After using [as.sir()], you can use the [eucast_rules()] defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
+#' After using [as.sir()], you can use the [interpretive_rules()] to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 #'
-#' To determine which isolates are multi-drug resistant, be sure to run [mdro()] (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about [interpreting multidrug-resistant organisms here][mdro()].
+#' To determine which isolates are multi-drug resistant, be sure to run [mdro()] (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about [detecting multidrug-resistant organisms here][mdro()].
 #'
 #' ### Other
 #'

R/zzz.R

@@ -115,6 +115,21 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
 }
 
 .onAttach <- function(libname, pkgname) {
+  if (interactive() && is.null(getOption("AMR_guideline"))) {
+    packageStartupMessage(
+      word_wrap(
+        "Welcome to AMR v", format(utils::packageVersion("AMR")), ". ",
+        "You have not set the 'AMR_guideline' option to either \"CLSI\" or \"EUCAST\". ",
+        "You can set it using either:\n",
+        "  options(AMR_guideline = \"CLSI\")\n",
+        "  options(AMR_guideline = \"EUCAST\")\n",
+        "See `?AMR-options`. While unset, the AMR package uses the current default guideline: ", AMR::clinical_breakpoints$guideline[1], ".",
+        add_fn = NULL
+      )
+    )
+  }
+
+
   # if custom ab option is available, load it
   if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
     if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {

man/AMR-options.Rd

@@ -4,9 +4,11 @@
 \alias{AMR-options}
 \title{Options for the AMR package}
 \description{
-This is an overview of all the package-specific \code{\link[=options]{options()}} you can set in the \code{AMR} package.
+This is an overview of all the package-specific options you can set in the \code{AMR} package. Set them using the \code{\link[=options]{options()}} function, e.g.:
+
+\code{options(AMR_guideline = "CLSI")}
 }
-\section{Options}{
+\section{Options (alphabetical order)}{
 
 \itemize{
 \item \code{AMR_antibiogram_formatting_type} \cr A \link{numeric} (1-22) to use in \code{\link[=antibiogram]{antibiogram()}}, to indicate which formatting type to use.
@@ -16,6 +18,13 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
 \item \code{AMR_custom_ab} \cr A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
 \item \code{AMR_custom_mo} \cr A file location to an RDS file, to use custom microorganisms with this package. This is explained in \code{\link[=add_custom_microorganisms]{add_custom_microorganisms()}}.
 \item \code{AMR_eucastrules} \cr A \link{character} to set the default types of rules for \code{\link[=eucast_rules]{eucast_rules()}} function, must be one or more of: \code{"breakpoints"}, \code{"expert"}, \code{"other"}, \code{"custom"}, \code{"all"}, and defaults to \code{c("breakpoints", "expert")}.
+\item \code{AMR_guideline} \cr A \link{character} to set the default guideline used throughout the \code{AMR} package wherever a \code{guideline} argument is available. This option is used as the default in e.g. \code{\link[=as.sir]{as.sir()}}, \code{\link[=resistance]{resistance()}}, \code{\link[=susceptibility]{susceptibility()}}, \code{\link[=interpretive_rules]{interpretive_rules()}} and many plotting functions. \strong{While unset}, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).
+\itemize{
+\item For \code{\link[=as.sir]{as.sir()}}, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., \code{"CLSI"} or \code{"EUCAST"}) or the name including a year (e.g., \code{"CLSI 2019"}). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.
+\item For \code{\link[=resistance]{resistance()}} and \code{\link[=susceptibility]{susceptibility()}}, this setting determines how the \code{"I"} (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, \code{"I"} is considered \emph{resistant} in susceptibility calculations; under EUCAST, \code{"I"} is considered \emph{susceptible} in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.
+\item For \code{\link[=interpretive_rules]{interpretive_rules()}}, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.
+\item For many plotting functions (e.g., for MIC or disk diffusion values), supplying \code{mo} and \code{ab} enables automatic SIR-based interpretative colouring. These colours are derived from \code{\link[=as.sir]{as.sir()}} in the background and therefore depend on the active \code{guideline} setting, which again uses EUCAST 2025 if not set explicitly.
+}
 \item \code{AMR_guideline} \cr A \link{character} to set the default guideline for interpreting MIC values and disk diffusion diameters with \code{\link[=as.sir]{as.sir()}}. Can be only the guideline name (e.g., \code{"CLSI"}) or the name with a year (e.g. \code{"CLSI 2019"}). The default to the latest implemented EUCAST guideline, currently \code{"EUCAST 2025"}. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).
 \item \code{AMR_ignore_pattern} \cr A \link[base:regex]{regular expression} to ignore (i.e., make \code{NA}) any match given in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions.
 \item \code{AMR_include_PKPD} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}.
@@ -43,7 +52,7 @@ In this file, you can set options such as...
 ...to add Portuguese language support of antimicrobials, and allow PK/PD rules when interpreting MIC values with \code{\link[=as.sir]{as.sir()}}.
 \subsection{Share Options Within Team}{
 
-For a more global approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
+For a more collaborative approach, e.g. within a (data) team, save an options file to a remote file location, such as a shared network drive, and have each user read in this file automatically at start-up. This would work in this way:
 \enumerate{
 \item Save a plain text file to e.g. "X:/team_folder/R_options.R" and fill it with preferred settings.
 \item For each user, open the \code{.Rprofile} file using \code{utils::file.edit("~/.Rprofile")} and put in there:

man/as.sir.Rd

@@ -247,9 +247,9 @@ Regarding choice of veterinary guidelines, these might be the best options to se
 
 \subsection{After Interpretation}{
 
-After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=eucast_rules]{eucast_rules()}} defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
+After using \code{\link[=as.sir]{as.sir()}}, you can use the \code{\link[=interpretive_rules]{interpretive_rules()}} to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.
 
-To determine which isolates are multi-drug resistant, be sure to run \code{\link[=mdro]{mdro()}} (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about \link[=mdro]{interpreting multidrug-resistant organisms here}.
+To determine which isolates are multi-drug resistant, be sure to run \code{\link[=mdro]{mdro()}} (which applies the MDR/PDR/XDR guideline from 2012 at default) on a data set that contains S/I/R values. Read more about \link[=mdro]{detecting multidrug-resistant organisms here}.
 }
 
 \subsection{Other}{

man/count.Rd

@@ -14,9 +14,11 @@
 \alias{count_df}
 \title{Count Available Isolates}
 \usage{
-count_resistant(..., only_all_tested = FALSE)
+count_resistant(..., only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST"))
 
-count_susceptible(..., only_all_tested = FALSE)
+count_susceptible(..., only_all_tested = FALSE,
+  guideline = getOption("AMR_guideline", "EUCAST"))
 
 count_S(..., only_all_tested = FALSE)
 
@@ -40,6 +42,14 @@ count_df(data, translate_ab = "name", language = get_AMR_locale(),
 
 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below.}
 
+\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
+\itemize{
+\item EUCAST: \code{\link[=count_susceptible]{count_susceptible()}} \eqn{= N_{S} + N_{I}}, \code{\link[=count_resistant]{count_resistant()}} \eqn{= N_{R}}
+\item CLSI: \code{\link[=count_susceptible]{count_susceptible()}} \eqn{= N_{S} + N_{SDD}}, \code{\link[=count_resistant]{count_resistant()}} \eqn{= N_{I} + N_{R}}
+}
+
+You can also use e.g. \code{\link[=count_R]{count_R()}} or \code{\link[=count_S]{count_S()}} instead, to be explicit.}
+
 \item{data}{A \link{data.frame} containing columns with class \code{\link{sir}} (see \code{\link[=as.sir]{as.sir()}}).}
 
 \item{translate_ab}{A column name of the \link{antimicrobials} data set to translate the antibiotic abbreviations to, using \code{\link[=ab_property]{ab_property()}}.}
@@ -59,9 +69,7 @@ These functions can be used to count resistant/susceptible microbial isolates. A
 \details{
 These functions are meant to count isolates. Use the \code{\link[=resistance]{resistance()}}/\code{\link[=susceptibility]{susceptibility()}} functions to calculate microbial resistance/susceptibility.
 
-The function \code{\link[=count_resistant]{count_resistant()}} is equal to the function \code{\link[=count_R]{count_R()}}. The function \code{\link[=count_susceptible]{count_susceptible()}} is equal to the function \code{\link[=count_SI]{count_SI()}}.
+The function \code{\link[=n_sir]{n_sir()}} is an alias of \code{\link[=count_all]{count_all()}}. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to \code{dplyr}'s \code{n_distinct()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
-
-The function \code{\link[=n_sir]{n_sir()}} is an alias of \code{\link[=count_all]{count_all()}}. They can be used to count all available isolates, i.e. where all input antimicrobials have an available result (S, I or R). Their use is equal to \code{n_distinct()}. Their function is equal to \code{count_susceptible(...) + count_resistant(...)}.
 
 The function \code{\link[=count_df]{count_df()}} takes any variable from \code{data} that has an \code{\link{sir}} class (created with \code{\link[=as.sir]{as.sir()}}) and counts the number of S's, I's and R's. It also supports grouped variables. The function \code{\link[=sir_df]{sir_df()}} works exactly like \code{\link[=count_df]{count_df()}}, but adds the percentage of S, I and R.
 }

man/proportion.Rd

@@ -19,10 +19,12 @@
 }
 \usage{
 resistance(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+  only_all_tested = FALSE, guideline = getOption("AMR_guideline",
+  "EUCAST"))
 
 susceptibility(..., minimum = 30, as_percent = FALSE,
-  only_all_tested = FALSE)
+  only_all_tested = FALSE, guideline = getOption("AMR_guideline",
+  "EUCAST"))
 
 sir_confidence_interval(..., ab_result = "R", minimum = 30,
   as_percent = FALSE, only_all_tested = FALSE, confidence_level = 0.95,
@@ -60,6 +62,14 @@ sir_df(data, translate_ab = "name", language = get_AMR_locale(),
 
 \item{only_all_tested}{(for combination therapies, i.e. using more than one variable for \code{...}): a \link{logical} to indicate that isolates must be tested for all antimicrobials, see section \emph{Combination Therapy} below.}
 
+\item{guideline}{Either \code{"EUCAST"} (default) or \code{"CLSI"}. With EUCAST, the 'I' category will be considered as susceptible (see \href{https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/definition-of-s-i-and-r/}{EUCAST website}), but with with CLSI, it will be considered resistant. Therefore:
+\itemize{
+\item EUCAST: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%I}, \code{\link[=resistance]{resistance()}} \eqn{= \%R}
+\item CLSI: \code{\link[=susceptibility]{susceptibility()}} \eqn{= \%S + \%SDD}, \code{\link[=resistance]{resistance()}} \eqn{= \%I + \%R}
+}
+
+You can also use e.g. \code{\link[=proportion_R]{proportion_R()}} or \code{\link[=proportion_S]{proportion_S()}} instead, to be explicit.}
+
 \item{ab_result}{Antibiotic results to test against, must be one or more values of "S", "SDD", "I", or "R".}
 
 \item{confidence_level}{The confidence level for the returned confidence interval. For the calculation, the number of S or SI isolates, and R isolates are compared with the total number of available isolates with R, S, or I by using \code{\link[=binom.test]{binom.test()}}, i.e., the Clopper-Pearson method.}

tests/testthat/test-count.R

@@ -30,8 +30,10 @@
 test_that("test-count.R", {
   skip_on_cran()
 
-  expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))
+  expect_equal(count_R(example_isolates$AMX), count_resistant(example_isolates$AMX))
-  expect_equal(count_susceptible(example_isolates$AMX), count_SI(example_isolates$AMX))
+  expect_equal(count_SI(example_isolates$AMX), count_susceptible(example_isolates$AMX))
+  expect_equal(count_IR(example_isolates$AMX), count_resistant(example_isolates$AMX, guideline = "CLSI"))
+  expect_equal(count_S(example_isolates$AMX), count_susceptible(example_isolates$AMX, guideline = "CLSI"))
   expect_equal(count_all(example_isolates$AMX), n_sir(example_isolates$AMX))
 
   # AMX resistance in `example_isolates`

tests/testthat/test-proportion.R

@@ -32,6 +32,8 @@ test_that("test-proportion.R", {
 
   expect_equal(proportion_R(example_isolates$AMX), resistance(example_isolates$AMX))
   expect_equal(proportion_SI(example_isolates$AMX), susceptibility(example_isolates$AMX))
+  expect_equal(proportion_IR(example_isolates$AMX), resistance(example_isolates$AMX, guideline = "CLSI"))
+  expect_equal(proportion_S(example_isolates$AMX), susceptibility(example_isolates$AMX, guideline = "CLSI"))
   # AMX resistance in `example_isolates`
   expect_equal(proportion_R(example_isolates$AMX), 0.5955556, tolerance = 0.0001)
   expect_equal(proportion_I(example_isolates$AMX), 0.002222222, tolerance = 0.0001)