(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9193
+Version: 2.1.1.9194
 Date: 2025-03-12
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9193
+# AMR 2.1.1.9194
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 
@@ -28,6 +28,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
 * **Updated clinical breakpoints**
   * EUCAST 2024 and CLSI 2024 are now supported, by adding all of their over 4,000 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2024 is now the new default guideline for all MIC and disk diffusion interpretations.
   * `as.sir()` now brings additional factor levels: "NI" for non-interpretable and "SDD" for susceptible dose-dependent. Currently, the `clinical_breakpoints` data set contains 24 breakpoints that can return the value "SDD" instead of "I".
+  * EUCAST interpretive rules (using `eucast_rules()`) are now available for EUCAST 12 (2022), 13 (2023), and 14 (2024).
 * **New advanced ggplot2 extensions for MIC and SIR plotting and transforming**
   * New function group `scale_*_mic()`, namely: `scale_x_mic()`, `scale_y_mic()`, `scale_colour_mic()` and `scale_fill_mic()`. They allow easy plotting of MIC values. They allow for manual range definition and plotting missing intermediate log2 levels.
   * New function group `scale_*_sir()`, namely: `scale_x_sir()`, `scale_colour_sir()` and `scale_fill_sir()`. They allow to plot the `sir` class, and translates into the system language at default. They also set colourblind-safe colours to the plots.

PythonPackage/AMR/AMR.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: AMR
-Version: 2.1.1.9193
+Version: 2.1.1.9194
 Summary: A Python wrapper for the AMR R package
 Home-page: https://github.com/msberends/AMR
 Author: Matthijs Berends

PythonPackage/AMR/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='AMR',
-    version='2.1.1.9193',
+    version='2.1.1.9194',
     packages=find_packages(),
     install_requires=[
         'rpy2',

R/aa_options.R

@@ -40,6 +40,7 @@
 #' * `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`.
+#' * `AMR_substitute_missing_r_breakpoint` \cr A [logical] to use in [as.sir()], to indicate that missing R breakpoints must be substituted with `"R"` - the default is `FALSE`.
 #' * `AMR_include_screening` \cr A [logical] to use in [as.sir()], to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`.
 #' * `AMR_keep_synonyms` \cr A [logical] to use in [as.mo()] and all [`mo_*`][mo_property()] functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is `FALSE`.
 #' * `AMR_locale` \cr A [character] to set the language for the `AMR` package, can be one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. The default is the current system language (if supported, English otherwise).

R/data.R

@@ -294,7 +294,7 @@
 #' - `ref_tbl`\cr Info about where the guideline rule can be found
 #' - `disk_dose`\cr Dose of the used disk diffusion method
 #' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
-#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
+#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R", can be `NA`
 #' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
 #' - `is_SDD`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to `r sum(clinical_breakpoints$is_SDD)` breakpoints.
 #' @details

R/mic.R

@@ -191,6 +191,10 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
   if (is.null(x.bak)) {
     x.bak <- x
   }
+  # remove NAs on beforehand to not count them
+  x.bak <- gsub("(NA)+", "", x.bak)
+  # and trim
+  x.bak <- trimws2(x.bak)
 
   # comma to period
   x <- gsub(",", ".", x, fixed = TRUE)

R/random.R

@@ -133,7 +133,7 @@ random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
     # get highest/lowest +/- random 1 to 3 higher factors of two
     max_range <- mic_range[min(
       length(mic_range),
-      which(mic_range == max(df$breakpoint_R, na.rm = TRUE)) + sample(c(1:3), 1)
+      which(mic_range == max(df$breakpoint_R[!is.na(df$breakpoint_R)], na.rm = TRUE)) + sample(c(1:3), 1)
     )]
     min_range <- mic_range[max(
       1,
@@ -155,7 +155,7 @@ random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
     return(out)
   } else if (method_type == "DISK") {
     set_range <- seq(
-      from = as.integer(min(df$breakpoint_R, na.rm = TRUE) / 1.25),
+      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),
       by = 1
     )

R/sir.R

@@ -46,6 +46,7 @@
 #' @param guideline defaults to `r AMR::clinical_breakpoints$guideline[1]` (the latest implemented EUCAST guideline in the [AMR::clinical_breakpoints] data set), but can be set with the package option [`AMR_guideline`][AMR-options]. Currently supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*.
 #' @param conserve_capped_values a [logical] to indicate that MIC values starting with `">"` (but not `">="`) must always return "R" , and that MIC values starting with `"<"` (but not `"<="`) must always return "S"
 #' @param add_intrinsic_resistance *(only useful when using a EUCAST guideline)* a [logical] to indicate whether intrinsic antibiotic resistance must also be considered for applicable bug-drug combinations, meaning that e.g. ampicillin will always return "R" in *Klebsiella* species. Determination is based on the [intrinsic_resistant] data set, that itself is based on `r format_eucast_version_nr(3.3)`.
+#' @param substitute_missing_r_breakpoint a [logical] to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is `FALSE`. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be `"S"` or `NA`. Setting this to `TRUE` will convert the `NA`s to `"R"` only if the R breakpoint is missing. Can also be set with the package option [`AMR_substitute_missing_r_breakpoint`][AMR-options].
 #' @param include_screening a [logical] to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`. Can also be set with the package option [`AMR_include_screening`][AMR-options].
 #' @param include_PKPD a [logical] to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is `TRUE`. Can also be set with the package option [`AMR_include_PKPD`][AMR-options].
 #' @param breakpoint_type the type of breakpoints to use, either `r vector_or(clinical_breakpoints$type)`. ECOFF stands for Epidemiological Cut-Off values. The default is `"human"`, which can also be set with the package option [`AMR_breakpoint_type`][AMR-options]. If `host` is set to values of veterinary species, this will automatically be set to `"animal"`.
@@ -563,6 +564,7 @@ as.sir.mic <- function(x,
                        conserve_capped_values = FALSE,
                        add_intrinsic_resistance = FALSE,
                        reference_data = AMR::clinical_breakpoints,
+                       substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
                        include_screening = getOption("AMR_include_screening", FALSE),
                        include_PKPD = getOption("AMR_include_PKPD", TRUE),
                        breakpoint_type = getOption("AMR_breakpoint_type", "human"),
@@ -580,6 +582,7 @@ as.sir.mic <- function(x,
     conserve_capped_values = conserve_capped_values,
     add_intrinsic_resistance = add_intrinsic_resistance,
     reference_data = reference_data,
+    substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
     include_screening = include_screening,
     include_PKPD = include_PKPD,
     breakpoint_type = breakpoint_type,
@@ -598,6 +601,7 @@ as.sir.disk <- function(x,
                         uti = NULL,
                         add_intrinsic_resistance = FALSE,
                         reference_data = AMR::clinical_breakpoints,
+                        substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
                         include_screening = getOption("AMR_include_screening", FALSE),
                         include_PKPD = getOption("AMR_include_PKPD", TRUE),
                         breakpoint_type = getOption("AMR_breakpoint_type", "human"),
@@ -615,10 +619,11 @@ as.sir.disk <- function(x,
     conserve_capped_values = FALSE,
     add_intrinsic_resistance = add_intrinsic_resistance,
     reference_data = reference_data,
+    substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
     include_screening = include_screening,
     include_PKPD = include_PKPD,
     breakpoint_type = breakpoint_type,
-    host = NULL,
+    host = host,
     verbose = verbose,
     ...
   )
@@ -634,6 +639,7 @@ as.sir.data.frame <- function(x,
                               conserve_capped_values = FALSE,
                               add_intrinsic_resistance = FALSE,
                               reference_data = AMR::clinical_breakpoints,
+                              substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
                               include_screening = getOption("AMR_include_screening", FALSE),
                               include_PKPD = getOption("AMR_include_PKPD", TRUE),
                               breakpoint_type = getOption("AMR_breakpoint_type", "human"),
@@ -646,6 +652,7 @@ as.sir.data.frame <- function(x,
   meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
   meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
   meet_criteria(reference_data, allow_class = "data.frame")
+  meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1)
   meet_criteria(include_screening, allow_class = "logical", has_length = 1)
   meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
   meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1)
@@ -797,6 +804,7 @@ as.sir.data.frame <- function(x,
           conserve_capped_values = conserve_capped_values,
           add_intrinsic_resistance = add_intrinsic_resistance,
           reference_data = reference_data,
+          substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
           include_screening = include_screening,
           include_PKPD = include_PKPD,
           breakpoint_type = breakpoint_type,
@@ -817,6 +825,7 @@ as.sir.data.frame <- function(x,
           uti = uti,
           add_intrinsic_resistance = add_intrinsic_resistance,
           reference_data = reference_data,
+          substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
           include_screening = include_screening,
           include_PKPD = include_PKPD,
           breakpoint_type = breakpoint_type,
@@ -925,6 +934,7 @@ as_sir_method <- function(method_short,
                           conserve_capped_values,
                           add_intrinsic_resistance,
                           reference_data,
+                          substitute_missing_r_breakpoint,
                           include_screening,
                           include_PKPD,
                           breakpoint_type,
@@ -939,6 +949,7 @@ as_sir_method <- function(method_short,
   meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(reference_data, allow_class = "data.frame", .call_depth = -2)
+  meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(include_screening, allow_class = "logical", has_length = 1, .call_depth = -2)
   meet_criteria(include_PKPD, allow_class = "logical", has_length = 1, .call_depth = -2)
   check_reference_data(reference_data, .call_depth = -2)
@@ -1321,7 +1332,9 @@ as_sir_method <- function(method_short,
     # This seems to not work well: as.sir(as.mic(c(4, ">4", ">=4", 8, ">8", ">=8")), ab = "AMC", mo = "E. coli", breakpoint_type = "animal", host = "dogs", guideline = "CLSI 2024")
 
     ## fall-back methods for veterinary guidelines ----
-    if (breakpoint_type == "animal" && !host_current %in% breakpoints_current$host) {
+    ## TODO actually implement this well
+    if (FALSE) {
+      # if (breakpoint_type == "animal" && !host_current %in% breakpoints_current$host) {
       if (guideline_coerced %like% "CLSI") {
         # VET09 says that staph/strep/enterococcus BP can be extrapolated to all Gr+ cocci except for intrinsic resistance, so take all Gr+ cocci:
         gram_plus_cocci_vet09 <- microorganisms$mo[microorganisms$genus %in% c("Staphylococcus", "Streptococcus", "Peptostreptococcus", "Aerococcus", "Micrococcus") & microorganisms$rank == "genus"] # TODO should probably include genera that were either of these before
@@ -1475,6 +1488,10 @@ as_sir_method <- function(method_short,
       if (method == "mic" && conserve_capped_values == TRUE && any(as.character(values) %like% "^[>][0-9]")) {
         notes_current <- c(notes_current, "MIC values 'greater than' are all considered 'R' since conserve_capped_values = TRUE")
       }
+      if (isTRUE(substitute_missing_r_breakpoint) && !is.na(breakpoints_current$breakpoint_S) && is.na(breakpoints_current$breakpoint_R)) {
+        breakpoints_current$breakpoint_R <- breakpoints_current$breakpoint_S # breakpoints_current only has 1 row at this moment
+        notes_current <- c(notes_current, "NAs because of missing R breakpoints were substituted with R since substitute_missing_r_breakpoint = TRUE")
+      }
 
       if (method == "mic") {
         new_sir <- case_when_AMR(

data-raw/clin_break.md5

@@ -1 +1 @@
-10fd88018ca098a76a8b1e9c86d2e40c
+dbf340329f7547aba18ecaa09e990b79

data-raw/gpt_training_text_v2.1.1.9194.txt

@@ -1,6 +1,6 @@
 This knowledge base contains all context you must know about the AMR package for R. You are a GPT trained to be an assistant for the AMR package in R. You are an incredible R specialist, especially trained in this package and in the tidyverse.
 
-First and foremost, you are trained on version 2.1.1.9193. Remember this whenever someone asks which AMR package version you’re at.
+First and foremost, you are trained on version 2.1.1.9194. Remember this whenever someone asks which AMR package version you’re at.
 
 Below are the contents of the  file, the  file, and all the  files (documentation) in the package. Every file content is split using 100 hypens.
 ----------------------------------------------------------------------------------------------------
@@ -771,6 +771,7 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
 \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 2024"}. Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).
 \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}.
+\item \code{AMR_substitute_missing_r_breakpoint} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that missing R breakpoints must be substituted with \code{"R"} - the default is \code{FALSE}.
 \item \code{AMR_include_screening} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}.
 \item \code{AMR_keep_synonyms} \cr A \link{logical} to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}.
 \item \code{AMR_locale} \cr A \link{character} to set the language for the \code{AMR} package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).
@@ -3336,7 +3337,8 @@ is_sir_eligible(x, threshold = 0.05)
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   conserve_capped_values = FALSE, add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
-  include_screening = getOption("AMR_include_screening", FALSE),
+  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
+  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
   verbose = FALSE, ...)
@@ -3345,7 +3347,8 @@ is_sir_eligible(x, threshold = 0.05)
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
-  include_screening = getOption("AMR_include_screening", FALSE),
+  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
+  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
   verbose = FALSE, ...)
@@ -3354,7 +3357,8 @@ is_sir_eligible(x, threshold = 0.05)
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   conserve_capped_values = FALSE, add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
-  include_screening = getOption("AMR_include_screening", FALSE),
+  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
+  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
   verbose = FALSE)
@@ -3384,6 +3388,8 @@ sir_interpretation_history(clean = FALSE)
 
 \item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
 
+\item{substitute_missing_r_breakpoint}{a \link{logical} to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is \code{FALSE}. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be \code{"S"} or \code{NA}. Setting this to \code{TRUE} will convert the \code{NA}s to \code{"R"} only if the R breakpoint is missing. Can also be set with the package option \code{\link[=AMR-options]{AMR_substitute_missing_r_breakpoint}}.}
+
 \item{include_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_screening}}.}
 
 \item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
@@ -3486,7 +3492,7 @@ To determine which isolates are multi-drug resistant, be sure to run \code{\link
 
 \subsection{Machine-Readable Clinical Breakpoints}{
 
-The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 063 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
+The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 382 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
 }
 
 \subsection{Other}{
@@ -4128,7 +4134,7 @@ THE PART HEREAFTER CONTAINS CONTENTS FROM FILE 'man/clinical_breakpoints.Rd':
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
+A \link[tibble:tibble]{tibble} with 34 382 observations and 14 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
@@ -4141,7 +4147,7 @@ A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
 \item \code{ref_tbl}\cr Info about where the guideline rule can be found
 \item \code{disk_dose}\cr Dose of the used disk diffusion method
 \item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
-\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
+\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA}
 \item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
 \item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 24 breakpoints.
 }

data-raw/reproduction_of_clinical_breakpoints.R

@@ -271,7 +271,8 @@ breakpoints_new <- breakpoints %>%
   mutate(disk_dose = disk_dose %>%
     gsub("μ", "mc", ., fixed = TRUE) %>% # this is 'mu', \u03bc
     gsub("µ", "mc", ., fixed = TRUE) %>% # this is 'micro', \u00b5 (yes, they look the same)
-    gsub("–", "-", ., fixed = TRUE)) %>%
+    gsub("–", "-", ., fixed = TRUE) %>%
+    gsub("(?<=\\d)(?=[a-zA-Z])", " ", ., perl = TRUE)) %>% # make sure we keep a space after a number, e.g. "1mcg" to "1 mcg"
   arrange(desc(guideline), mo, ab, type, method) %>%
   filter(!(is.na(breakpoint_S) & is.na(breakpoint_R)) & !is.na(mo) & !is.na(ab)) %>%
   distinct(guideline, type, host, ab, mo, method, site, breakpoint_S, .keep_all = TRUE)
@@ -299,7 +300,7 @@ breakpoints_new <- breakpoints_new %>%
 m <- unique(as.double(as.mic(levels(as.mic(1)))))
 
 # WHONET has no >1024 but instead uses 1025, 513, etc, so as.mic() cannot be used to clean.
-# instead, clean based on MIC factor levels
+# instead, raise these one higher valid MIC factor level:
 breakpoints_new[which(breakpoints_new$breakpoint_R == 129), "breakpoint_R"] <- m[which(m == 128) + 1]
 breakpoints_new[which(breakpoints_new$breakpoint_R == 257), "breakpoint_R"] <- m[which(m == 256) + 1]
 breakpoints_new[which(breakpoints_new$breakpoint_R == 513), "breakpoint_R"] <- m[which(m == 512) + 1]
@@ -316,9 +317,9 @@ breakpoints_new %>%
               values_fill = list(n = 0)) |>
   View()
 
-breakpoints_new[which(breakpoints_new$method == "MIC" &
-                        is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
-# raise these one higher valid MIC factor level:
+# 2025-03-12 don't do this anymore - we now use as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
+# breakpoints_new[which(breakpoints_new$method == "MIC" &
+#                         is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- max(m)
 
 
 # fix streptococci in WHONET table of EUCAST: Strep A, B, C and G must only include these groups and not all streptococci:
@@ -373,7 +374,8 @@ breakpoints_new <- breakpoints_new %>%
     breakpoint_R
   ))
 # fill missing R breakpoint where there is an S breakpoint
-breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
+# 2025-03-12 don't do this anymore - we now use as.sir(..., substitute_missing_r_breakpoint = TRUE/FALSE, ...)
+# breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_R"] <- breakpoints_new[which(is.na(breakpoints_new$breakpoint_R)), "breakpoint_S"]
 
 
 # check the strange duplicates
@@ -392,7 +394,7 @@ breakpoints_new <- breakpoints_new %>%
 # check again
 breakpoints_new %>% filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 # compare with current version
-clinical_breakpoints %>% filter(guideline == "EUCAST 2023", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
+clinical_breakpoints %>% filter(guideline == "EUCAST 2024", ab == "AMC", mo == "B_[ORD]_ENTRBCTR", method == "MIC")
 
 # must have "human" and "ECOFF"
 breakpoints_new %>% filter(mo == "B_STRPT_PNMN", ab == "AMP", guideline == "EUCAST 2020", method == "MIC")

man/AMR-options.Rd

@@ -18,6 +18,7 @@ This is an overview of all the package-specific \code{\link[=options]{options()}
 \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 2024"}. Supported guideline are currently EUCAST (2011-2024) and CLSI (2011-2024).
 \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}.
+\item \code{AMR_substitute_missing_r_breakpoint} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that missing R breakpoints must be substituted with \code{"R"} - the default is \code{FALSE}.
 \item \code{AMR_include_screening} \cr A \link{logical} to use in \code{\link[=as.sir]{as.sir()}}, to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}.
 \item \code{AMR_keep_synonyms} \cr A \link{logical} to use in \code{\link[=as.mo]{as.mo()}} and all \code{\link[=mo_property]{mo_*}} functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is \code{FALSE}.
 \item \code{AMR_locale} \cr A \link{character} to set the language for the \code{AMR} package, can be one of these supported language names or ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Norwegian (no), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), or Ukrainian (uk). The default is the current system language (if supported, English otherwise).

man/as.sir.Rd

@@ -40,7 +40,8 @@ is_sir_eligible(x, threshold = 0.05)
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   conserve_capped_values = FALSE, add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
-  include_screening = getOption("AMR_include_screening", FALSE),
+  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
+  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
   verbose = FALSE, ...)
@@ -49,7 +50,8 @@ is_sir_eligible(x, threshold = 0.05)
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
-  include_screening = getOption("AMR_include_screening", FALSE),
+  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
+  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
   verbose = FALSE, ...)
@@ -58,7 +60,8 @@ is_sir_eligible(x, threshold = 0.05)
   guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
   conserve_capped_values = FALSE, add_intrinsic_resistance = FALSE,
   reference_data = AMR::clinical_breakpoints,
-  include_screening = getOption("AMR_include_screening", FALSE),
+  substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint",
+  FALSE), include_screening = getOption("AMR_include_screening", FALSE),
   include_PKPD = getOption("AMR_include_PKPD", TRUE),
   breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
   verbose = FALSE)
@@ -88,6 +91,8 @@ sir_interpretation_history(clean = FALSE)
 
 \item{reference_data}{a \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.}
 
+\item{substitute_missing_r_breakpoint}{a \link{logical} to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is \code{FALSE}. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning the outcome can only be \code{"S"} or \code{NA}. Setting this to \code{TRUE} will convert the \code{NA}s to \code{"R"} only if the R breakpoint is missing. Can also be set with the package option \code{\link[=AMR-options]{AMR_substitute_missing_r_breakpoint}}.}
+
 \item{include_screening}{a \link{logical} to indicate that clinical breakpoints for screening are allowed - the default is \code{FALSE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_screening}}.}
 
 \item{include_PKPD}{a \link{logical} to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is \code{TRUE}. Can also be set with the package option \code{\link[=AMR-options]{AMR_include_PKPD}}.}
@@ -190,7 +195,7 @@ To determine which isolates are multi-drug resistant, be sure to run \code{\link
 
 \subsection{Machine-Readable Clinical Breakpoints}{
 
-The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 063 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
+The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 34 382 rows and 14 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
 }
 
 \subsection{Other}{

man/clinical_breakpoints.Rd

@@ -5,7 +5,7 @@
 \alias{clinical_breakpoints}
 \title{Data Set with Clinical Breakpoints for SIR Interpretation}
 \format{
-A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
+A \link[tibble:tibble]{tibble} with 34 382 observations and 14 variables:
 \itemize{
 \item \code{guideline}\cr Name of the guideline
 \item \code{type}\cr Breakpoint type, either "ECOFF", "animal", or "human"
@@ -18,7 +18,7 @@ A \link[tibble:tibble]{tibble} with 34 063 observations and 14 variables:
 \item \code{ref_tbl}\cr Info about where the guideline rule can be found
 \item \code{disk_dose}\cr Dose of the used disk diffusion method
 \item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S"
-\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R"
+\item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA}
 \item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI)
 \item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 24 breakpoints.
 }

tests/testthat/test-data.R

@@ -45,15 +45,15 @@ test_that("data works", {
   expect_true(all(clinical_breakpoints$ab %in% AMR::antimicrobials$ab))
   expect_true(all(intrinsic_resistant$mo %in% microorganisms$mo))
   expect_true(all(intrinsic_resistant$ab %in% AMR::antimicrobials$ab))
-  expect_false(any(is.na(microorganisms.codes$code)))
-  expect_false(any(is.na(microorganisms.codes$mo)))
+  expect_false(anyNA(microorganisms.codes$code))
+  expect_false(anyNA(microorganisms.codes$mo))
   expect_true(all(dosage$ab %in% AMR::antimicrobials$ab))
   expect_true(all(dosage$name %in% AMR::antimicrobials$name))
   # check valid disks/MICs
-  expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE]))))
-  expect_false(any(is.na(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE]))))
-  expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE]))))
-  expect_false(any(is.na(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE]))))
+  expect_false(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE])))
+  expect_true(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE])))
+  expect_false(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE])))
+  expect_true(anyNA(as.disk(clinical_breakpoints[which(clinical_breakpoints$method == "DISK" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE])))
 
   # antibiotic names must always be coercible to their original AB code
   expect_identical(as.ab(AMR::antimicrobials$name), AMR::antimicrobials$ab)