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(v.1.5.0.9000) implementation of EUCAST rules v11 (2021)
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@ -23,12 +23,16 @@
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# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv"
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# (running "data-raw/internals.R" will process that TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list("10.0" = list(version_txt = "v10.0",
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# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and rsi_translation
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# (running "data-raw/internals.R" will process the TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
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year = 2021,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/clinical_breakpoints/"),
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"10.0" = list(version_txt = "v10.0",
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year = 2020,
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title = "'EUCAST Clinical Breakpoints'",
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url = "https://www.eucast.org/clinical_breakpoints/"))
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"))
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EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(version_txt = "v3.1",
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year = 2016,
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title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
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@ -44,17 +48,17 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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version <- format(version, nsmall = 1)
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if (markdown == TRUE) {
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paste0("[", lst[[version]]$title, " ", lst[[version]]$version_txt, "](", lst[[version]]$url, ")",
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" from ", lst[[version]]$year)
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" (", lst[[version]]$year, ")")
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} else {
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paste0(lst[[version]]$title, " ", lst[[version]]$version_txt,
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" from ", lst[[version]]$year)
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" (", lst[[version]]$year, ")")
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}
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}
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#' Apply EUCAST rules
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#'
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#' @description
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#' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://eucast.org>), see *Source*.
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#' Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <https://eucast.org>), see *Source*. Use [eucast_dosage()] to get advised dosages of a certain bug-drug combination, which is based on the [dosage] data set.
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#'
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#' To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details.
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#' @inheritSection lifecycle Stable lifecycle
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@ -62,11 +66,12 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' @param info a logical to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions
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#' @param rules a character vector that specifies which rules should be applied. Must be one or more of `"breakpoints"`, `"expert"`, `"other"`, `"all"`, and defaults to `c("breakpoints", "expert")`. The default value can be set to another value, e.g. using `options(AMR_eucastrules = "all")`.
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#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
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#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Currently supported: `r paste0(names(EUCAST_VERSION_BREAKPOINTS), collapse = ", ")`.
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#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Currently supported: `r paste0(names(EUCAST_VERSION_EXPERT_RULES), collapse = ", ")`.
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#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
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#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
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#' @param ampc_cephalosporin_resistance a character value that should be applied for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2`; '*EUCAST Expert Rules v3.2 on Enterobacterales*' states that susceptible (S) results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these agents. A value of `NA` for this argument will remove results for these agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` to not alter the results for AmpC de-repressed cephalosporin-resistant mutants. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: *`r gsub("[)(^]", "", gsub("|", ", ", eucast_rules_file[which(eucast_rules_file$reference.version == 3.2 & eucast_rules_file$reference.rule %like% "ampc"), "this_value"][1], fixed = TRUE))`*.
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#'
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#' @param ... column name of an antibiotic, please see section *Antibiotics* below
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#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()]
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#' @param administration route of administration, either `r vector_or(dosage$administration)`
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#' @inheritParams first_isolate
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#' @details
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#' **Note:** This function does not translate MIC values to RSI values. Use [as.rsi()] for that. \cr
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@ -101,6 +106,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' - 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)
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#' - 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)
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#' - 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)
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#' - 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)
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#' @inheritSection AMR Reference data publicly available
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#' @inheritSection AMR Read more on our website!
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#' @examples
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@ -144,12 +150,14 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
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#' # containing all details about the transformations:
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#' c <- eucast_rules(a, verbose = TRUE)
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#' }
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#'
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#' eucast_dosage(c("tobra", "genta", "cipro"), "iv")
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eucast_rules <- function(x,
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col_mo = NULL,
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info = interactive(),
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rules = getOption("AMR_eucastrules", default = c("breakpoints", "expert")),
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verbose = FALSE,
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version_breakpoints = 10.0,
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version_breakpoints = 11.0,
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version_expertrules = 3.2,
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ampc_cephalosporin_resistance = NA,
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...) {
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@ -1168,3 +1176,26 @@ edit_rsi <- function(x,
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}
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return(track_changes)
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}
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#' @rdname eucast_rules
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#' @export
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eucast_dosage <- function(ab, administration = "iv", version_breakpoints = 11.0) {
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# show used version_breakpoints number once per session (pkg_env will reload every session)
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if (message_not_thrown_before(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)) {
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message_("Dosages for antimicrobial drugs, as meant for ",
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format_eucast_version_nr(version_breakpoints, markdown = FALSE), ". ",
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font_red("This note will be shown once per session."))
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remember_thrown_message(paste0("eucast_dosage_v", gsub("[^0-9]", "", version_breakpoints)), entire_session = TRUE)
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}
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ab <- as.ab(ab)
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out <- character(length(ab))
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for (i in seq_len(length(ab))) {
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df <- data.frame(ab = ab[i], stringsAsFactors = FALSE, administration = administration) %pm>%
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pm_inner_join(AMR::dosage, by = c("ab", "administration")) %pm>%
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pm_mutate(txt = paste0(gsub("_", " ", type), ": ", dose_times, "x ", dose, " ", administration), perl = TRUE)
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out[i] <- paste(df$txt, collapse = ", ")
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}
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names(out) <- ab_name(ab, language = NULL)
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out[out == ""] <- NA_character_
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out
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}
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