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(v2.1.1.9277) mdro fix

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dr. M.S. (Matthijs) Berends
2025-05-15 13:07:47 +02:00
parent 4b171745de
commit b8d7c8af7f
4 changed files with 25 additions and 22 deletions
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31
R/mdro.R
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@ -56,19 +56,19 @@
#'
#' Currently supported guidelines are (case-insensitive):
#'
#' * `guideline = "CMI2012"` (default)
#' * `guideline = "CMI 2012"` (default)
#'
#' Magiorakos AP, Srinivasan A *et al.* "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\doi{10.1111/j.1469-0691.2011.03570.x})
#'
#' * `guideline = "EUCAST3.3"` (or simply `guideline = "EUCAST"`)
#' * `guideline = "EUCAST 3.3"` (or simply `guideline = "EUCAST"`)
#'
#' The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf))
#'
#' * `guideline = "EUCAST3.2"`
#' * `guideline = "EUCAST 3.2"`
#'
#' The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf))
#'
#' * `guideline = "EUCAST3.1"`
#' * `guideline = "EUCAST 3.1"`
#'
#' The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" ([link](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf))
#'
@ -80,7 +80,7 @@
#'
#' The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}
#'
#' * `guideline = "BRMO"`
#' * `guideline = "BRMO 2024"` (or simply `guideline = "BRMO"`)
#'
#' The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" ([link](https://www.sri-richtlijnen.nl/brmo))
#'
@ -183,7 +183,7 @@
#' }
#' }
mdro <- function(x = NULL,
guideline = "CMI2012",
guideline = "CMI 2012",
col_mo = NULL,
esbl = NA,
carbapenemase = NA,
@ -220,8 +220,10 @@ mdro <- function(x = NULL,
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
if (!isTRUE(only_sir_columns) && (!any(is.sir(x)) || !any(is_sir_eligible(x)))) {
stop_("There were no possible SIR columns found in the data set. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
stop_("There were no SIR columns found in the data set, despite `only_sir_columns` being `TRUE`. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
} else if (!isTRUE(only_sir_columns) && !any(is.sir(x)) && !any(is_sir_eligible(x))) {
stop_("There were no eligible SIR columns found in the data set. Transform columns with `as.sir()` for valid antimicrobial interpretations.")
}
# get gene values as TRUE/FALSE
@ -382,14 +384,15 @@ mdro <- function(x = NULL,
# turn into latest EUCAST guideline
guideline <- "eucast3.3"
}
if (guideline == "nl") {
guideline <- "brmo"
if (guideline %in% c("nl", "brmo")) {
# turn into latest BRMO guideline
guideline <- "brmo2024"
}
if (guideline == "de") {
guideline <- "mrgn"
}
stop_ifnot(
guideline %in% c("brmo", "mrgn", "eucast3.1", "eucast3.2", "eucast3.3", "tb", "cmi2012"),
guideline %in% c("brmo2017", "brmo2024", "mrgn", "eucast3.1", "eucast3.2", "eucast3.3", "tb", "cmi2012"),
"invalid guideline: ", guideline.bak
)
guideline <- list(code = guideline)
@ -447,7 +450,7 @@ mdro <- function(x = NULL,
guideline$version <- NA_character_
guideline$source_url <- paste0("Antimicrobial Resistance and Infection Control 4:7, 2015; ", font_url("https://doi.org/10.1186/s13756-015-0047-6", "doi: 10.1186/s13756-015-0047-6"))
guideline$type <- "MRGNs"
} else if (guideline$code == "brmo") {
} else if (guideline$code == "brmo2024") {
combine_SI <- TRUE # I must not be considered resistant
guideline$name <- "Bijzonder Resistente Micro-organismen (BRMO)"
guideline$author <- "Samenwerkingsverband Richtlijnen Infectiepreventie (SRI)"
@ -1520,7 +1523,7 @@ mdro <- function(x = NULL,
x[which(x$MDRO == 3), "reason"] <- "4MRGN"
}
if (guideline$code == "brmo") {
if (guideline$code == "brmo2024") {
# Netherlands 2024 --------------------------------------------------------
aminoglycosides <- c(GEN, TOB, AMK) # note 4: gentamicin or tobramycin or amikacin
aminoglycosides_serratia_marcescens <- GEN # note 4: TOB and AMK do not count towards S. marcescens
@ -2189,7 +2192,7 @@ mdr_cmi2012 <- function(x = NULL, only_sir_columns = any(is.sir(x)), verbose = F
"guideline" %in% names(list(...)),
"argument `guideline` must not be set since this is a guideline-specific function"
)
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "CMI2012", ...)
mdro(x = x, only_sir_columns = only_sir_columns, verbose = verbose, guideline = "CMI 2012", ...)
}
#' @rdname mdro