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(v3.0.1.9084) Fix breakpoint infer rules

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dr. M.S. (Matthijs) Berends committed 2026-07-09 17:14:59 +02:00
1 parent ea996c8361
commit 9237bfbc19
24 files changed
+545 -318
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R/interpretive_rules.R
+2 -7
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@@ -110,13 +110,8 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @references
#' - EUCAST Expert Rules. Version 2.0, 2012.\cr
#' Leclercq et al. **EUCAST expert rules in antimicrobial susceptibility testing.** *Clin Microbiol Infect.* 2013;19(2):141-60; \doi{https://doi.org/10.1111/j.1469-0691.2011.03703.x}
#' - EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
#' - EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
#' - EUCAST Expected Phenotypes. [(link)](https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/)
#' - EUCAST Breakpoint tables for interpretation of MICs and zone diameters. [(link)](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/)
#' @inheritSection AMR Download Our Reference Data
#' @examples
#' \donttest{
R/sysdata.rda
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R/tidymodels.R
+14 -16
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@@ -120,14 +120,13 @@ all_disk_predictors <- function() {
#' @rdname amr-tidymodels
#' @export
step_mic_log2 <- function(
recipe,
...,
role = NA,
trained = FALSE,
columns = NULL,
skip = FALSE,
id = recipes::rand_id("mic_log2")
) {
recipe,
...,
role = NA,
trained = FALSE,
columns = NULL,
skip = FALSE,
id = recipes::rand_id("mic_log2")) {
recipes::add_step(
recipe,
step_mic_log2_new(
@@ -196,14 +195,13 @@ tidy.step_mic_log2 <- function(x, ...) {
#' @rdname amr-tidymodels
#' @export
step_sir_numeric <- function(
recipe,
...,
role = NA,
trained = FALSE,
columns = NULL,
skip = FALSE,
id = recipes::rand_id("sir_numeric")
) {
recipe,
...,
role = NA,
trained = FALSE,
columns = NULL,
skip = FALSE,
id = recipes::rand_id("sir_numeric")) {
recipes::add_step(
recipe,
step_sir_numeric_new(