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(v2.1.1.9194) new argument for missing R breakpoints - updated from WHONET
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@ -40,6 +40,7 @@
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#' * `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)))`).
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#' * `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.
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#' * `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`.
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#' * `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`.
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#' * `AMR_include_screening` \cr A [logical] to use in [as.sir()], to indicate that clinical breakpoints for screening are allowed - the default is `FALSE`.
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#' * `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`.
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#' * `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).
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2
R/data.R
2
R/data.R
@ -294,7 +294,7 @@
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#' - `ref_tbl`\cr Info about where the guideline rule can be found
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#' - `disk_dose`\cr Dose of the used disk diffusion method
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#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S"
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#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R"
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#' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R", can be `NA`
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#' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI)
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#' - `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.
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#' @details
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4
R/mic.R
4
R/mic.R
@ -191,6 +191,10 @@ as.mic <- function(x, na.rm = FALSE, keep_operators = "all") {
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if (is.null(x.bak)) {
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x.bak <- x
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}
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# remove NAs on beforehand to not count them
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x.bak <- gsub("(NA)+", "", x.bak)
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# and trim
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x.bak <- trimws2(x.bak)
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# comma to period
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x <- gsub(",", ".", x, fixed = TRUE)
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@ -133,7 +133,7 @@ random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
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# get highest/lowest +/- random 1 to 3 higher factors of two
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max_range <- mic_range[min(
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length(mic_range),
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which(mic_range == max(df$breakpoint_R, na.rm = TRUE)) + sample(c(1:3), 1)
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which(mic_range == max(df$breakpoint_R[!is.na(df$breakpoint_R)], na.rm = TRUE)) + sample(c(1:3), 1)
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)]
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min_range <- mic_range[max(
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1,
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@ -155,7 +155,7 @@ random_exec <- function(method_type, size, mo = NULL, ab = NULL) {
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return(out)
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} else if (method_type == "DISK") {
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set_range <- seq(
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from = as.integer(min(df$breakpoint_R, na.rm = TRUE) / 1.25),
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from = as.integer(min(df$breakpoint_R[!is.na(df$breakpoint_R)], na.rm = TRUE) / 1.25),
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to = as.integer(max(df$breakpoint_S, na.rm = TRUE) * 1.25),
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by = 1
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)
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21
R/sir.R
21
R/sir.R
@ -46,6 +46,7 @@
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#' @param guideline defaults to `r AMR::clinical_breakpoints$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*.
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#' @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"
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#' @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)`.
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#' @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].
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#' @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].
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#' @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].
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#' @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"`.
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@ -563,6 +564,7 @@ as.sir.mic <- function(x,
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conserve_capped_values = FALSE,
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add_intrinsic_resistance = FALSE,
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reference_data = AMR::clinical_breakpoints,
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substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
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include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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@ -580,6 +582,7 @@ as.sir.mic <- function(x,
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conserve_capped_values = conserve_capped_values,
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add_intrinsic_resistance = add_intrinsic_resistance,
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reference_data = reference_data,
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substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
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include_screening = include_screening,
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include_PKPD = include_PKPD,
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breakpoint_type = breakpoint_type,
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@ -598,6 +601,7 @@ as.sir.disk <- function(x,
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uti = NULL,
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add_intrinsic_resistance = FALSE,
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reference_data = AMR::clinical_breakpoints,
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substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
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include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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@ -615,10 +619,11 @@ as.sir.disk <- function(x,
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conserve_capped_values = FALSE,
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add_intrinsic_resistance = add_intrinsic_resistance,
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reference_data = reference_data,
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substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
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include_screening = include_screening,
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include_PKPD = include_PKPD,
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breakpoint_type = breakpoint_type,
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host = NULL,
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host = host,
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verbose = verbose,
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...
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)
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@ -634,6 +639,7 @@ as.sir.data.frame <- function(x,
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conserve_capped_values = FALSE,
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add_intrinsic_resistance = FALSE,
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reference_data = AMR::clinical_breakpoints,
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substitute_missing_r_breakpoint = getOption("AMR_substitute_missing_r_breakpoint", FALSE),
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include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"),
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@ -646,6 +652,7 @@ as.sir.data.frame <- function(x,
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meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
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meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
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meet_criteria(reference_data, allow_class = "data.frame")
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meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1)
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meet_criteria(include_screening, allow_class = "logical", has_length = 1)
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meet_criteria(include_PKPD, allow_class = "logical", has_length = 1)
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meet_criteria(breakpoint_type, allow_class = "character", is_in = reference_data$type, has_length = 1)
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@ -797,6 +804,7 @@ as.sir.data.frame <- function(x,
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conserve_capped_values = conserve_capped_values,
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add_intrinsic_resistance = add_intrinsic_resistance,
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reference_data = reference_data,
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substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
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include_screening = include_screening,
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include_PKPD = include_PKPD,
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breakpoint_type = breakpoint_type,
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@ -817,6 +825,7 @@ as.sir.data.frame <- function(x,
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uti = uti,
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add_intrinsic_resistance = add_intrinsic_resistance,
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reference_data = reference_data,
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substitute_missing_r_breakpoint = substitute_missing_r_breakpoint,
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include_screening = include_screening,
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include_PKPD = include_PKPD,
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breakpoint_type = breakpoint_type,
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@ -925,6 +934,7 @@ as_sir_method <- function(method_short,
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conserve_capped_values,
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add_intrinsic_resistance,
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reference_data,
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substitute_missing_r_breakpoint,
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include_screening,
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include_PKPD,
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breakpoint_type,
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@ -939,6 +949,7 @@ as_sir_method <- function(method_short,
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meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1, .call_depth = -2)
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meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1, .call_depth = -2)
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meet_criteria(reference_data, allow_class = "data.frame", .call_depth = -2)
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meet_criteria(substitute_missing_r_breakpoint, allow_class = "logical", has_length = 1, .call_depth = -2)
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meet_criteria(include_screening, allow_class = "logical", has_length = 1, .call_depth = -2)
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meet_criteria(include_PKPD, allow_class = "logical", has_length = 1, .call_depth = -2)
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check_reference_data(reference_data, .call_depth = -2)
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@ -1321,7 +1332,9 @@ as_sir_method <- function(method_short,
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# 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")
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## fall-back methods for veterinary guidelines ----
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if (breakpoint_type == "animal" && !host_current %in% breakpoints_current$host) {
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## TODO actually implement this well
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if (FALSE) {
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# if (breakpoint_type == "animal" && !host_current %in% breakpoints_current$host) {
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if (guideline_coerced %like% "CLSI") {
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# VET09 says that staph/strep/enterococcus BP can be extrapolated to all Gr+ cocci except for intrinsic resistance, so take all Gr+ cocci:
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gram_plus_cocci_vet09 <- microorganisms$mo[microorganisms$genus %in% c("Staphylococcus", "Streptococcus", "Peptostreptococcus", "Aerococcus", "Micrococcus") & microorganisms$rank == "genus"] # TODO should probably include genera that were either of these before
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@ -1475,6 +1488,10 @@ as_sir_method <- function(method_short,
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if (method == "mic" && conserve_capped_values == TRUE && any(as.character(values) %like% "^[>][0-9]")) {
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notes_current <- c(notes_current, "MIC values 'greater than' are all considered 'R' since conserve_capped_values = TRUE")
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}
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if (isTRUE(substitute_missing_r_breakpoint) && !is.na(breakpoints_current$breakpoint_S) && is.na(breakpoints_current$breakpoint_R)) {
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breakpoints_current$breakpoint_R <- breakpoints_current$breakpoint_S # breakpoints_current only has 1 row at this moment
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notes_current <- c(notes_current, "NAs because of missing R breakpoints were substituted with R since substitute_missing_r_breakpoint = TRUE")
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}
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if (method == "mic") {
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new_sir <- case_when_AMR(
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