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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
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 2.1.1.9276 Version: 2.1.1.9277
Date: 2025-05-15 Date: 2025-05-15
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9276 # AMR 2.1.1.9277
*(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://amr-for-r.org/#get-this-package).)* *(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://amr-for-r.org/#get-this-package).)*

31
R/mdro.R
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@ -56,19 +56,19 @@
#' #'
#' Currently supported guidelines are (case-insensitive): #' 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}) #' 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)) #' 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)) #' 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)) #' 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} #' 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)) #' 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, mdro <- function(x = NULL,
guideline = "CMI2012", guideline = "CMI 2012",
col_mo = NULL, col_mo = NULL,
esbl = NA, esbl = NA,
carbapenemase = NA, carbapenemase = NA,
@ -220,8 +220,10 @@ mdro <- function(x = NULL,
meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1) 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)))) { if (isTRUE(only_sir_columns) && !any(is.sir(x))) {
stop_("There were no possible SIR columns found in the data set. Transform columns with `as.sir()` for valid antimicrobial interpretations.") 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 # get gene values as TRUE/FALSE
@ -382,14 +384,15 @@ mdro <- function(x = NULL,
# turn into latest EUCAST guideline # turn into latest EUCAST guideline
guideline <- "eucast3.3" guideline <- "eucast3.3"
} }
if (guideline == "nl") { if (guideline %in% c("nl", "brmo")) {
guideline <- "brmo" # turn into latest BRMO guideline
guideline <- "brmo2024"
} }
if (guideline == "de") { if (guideline == "de") {
guideline <- "mrgn" guideline <- "mrgn"
} }
stop_ifnot( 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 "invalid guideline: ", guideline.bak
) )
guideline <- list(code = guideline) guideline <- list(code = guideline)
@ -447,7 +450,7 @@ mdro <- function(x = NULL,
guideline$version <- NA_character_ guideline$version <- NA_character_
guideline$source_url <- paste0("Antimicrobial Resistance and Infection Control 4:7, 2015; ", font_url("https://doi.org/10.1186/s13756-015-0047-6", "doi: 10.1186/s13756-015-0047-6")) guideline$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$type <- "MRGNs" guideline$type <- "MRGNs"
} else if (guideline$code == "brmo") { } else if (guideline$code == "brmo2024") {
combine_SI <- TRUE # I must not be considered resistant combine_SI <- TRUE # I must not be considered resistant
guideline$name <- "Bijzonder Resistente Micro-organismen (BRMO)" guideline$name <- "Bijzonder Resistente Micro-organismen (BRMO)"
guideline$author <- "Samenwerkingsverband Richtlijnen Infectiepreventie (SRI)" guideline$author <- "Samenwerkingsverband Richtlijnen Infectiepreventie (SRI)"
@ -1520,7 +1523,7 @@ mdro <- function(x = NULL,
x[which(x$MDRO == 3), "reason"] <- "4MRGN" x[which(x$MDRO == 3), "reason"] <- "4MRGN"
} }
if (guideline$code == "brmo") { if (guideline$code == "brmo2024") {
# Netherlands 2024 -------------------------------------------------------- # Netherlands 2024 --------------------------------------------------------
aminoglycosides <- c(GEN, TOB, AMK) # note 4: gentamicin or tobramycin or amikacin 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 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(...)), "guideline" %in% names(list(...)),
"argument `guideline` must not be set since this is a guideline-specific function" "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 #' @rdname mdro

12
man/mdro.Rd
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@ -19,7 +19,7 @@
See the supported guidelines above for the \link{list} of publications used for this function. See the supported guidelines above for the \link{list} of publications used for this function.
} }
\usage{ \usage{
mdro(x = NULL, guideline = "CMI2012", col_mo = NULL, esbl = NA, mdro(x = NULL, guideline = "CMI 2012", col_mo = NULL, esbl = NA,
carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA, carbapenemase = NA, mecA = NA, mecC = NA, vanA = NA, vanB = NA,
info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE, info = interactive(), pct_required_classes = 0.5, combine_SI = TRUE,
verbose = FALSE, only_sir_columns = any(is.sir(x)), ...) verbose = FALSE, only_sir_columns = any(is.sir(x)), ...)
@ -100,16 +100,16 @@ For the \code{pct_required_classes} argument, values above 1 will be divided by
Currently supported guidelines are (case-insensitive): Currently supported guidelines are (case-insensitive):
\itemize{ \itemize{
\item \code{guideline = "CMI2012"} (default) \item \code{guideline = "CMI 2012"} (default)
Magiorakos AP, Srinivasan A \emph{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}) Magiorakos AP, Srinivasan A \emph{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})
\item \code{guideline = "EUCAST3.3"} (or simply \code{guideline = "EUCAST"}) \item \code{guideline = "EUCAST 3.3"} (or simply \code{guideline = "EUCAST"})
The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{link}) The European international guideline - EUCAST Expert Rules Version 3.3 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf}{link})
\item \code{guideline = "EUCAST3.2"} \item \code{guideline = "EUCAST 3.2"}
The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link}) The European international guideline - EUCAST Expert Rules Version 3.2 "Intrinsic Resistance and Unusual Phenotypes" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf}{link})
\item \code{guideline = "EUCAST3.1"} \item \code{guideline = "EUCAST 3.1"}
The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link}) The European international guideline - EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (\href{https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf}{link})
\item \code{guideline = "TB"} \item \code{guideline = "TB"}
@ -118,7 +118,7 @@ The international guideline for multi-drug resistant tuberculosis - World Health
\item \code{guideline = "MRGN"} \item \code{guideline = "MRGN"}
The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6} The German national guideline - Mueller et al. (2015) Antimicrobial Resistance and Infection Control 4:7; \doi{10.1186/s13756-015-0047-6}
\item \code{guideline = "BRMO"} \item \code{guideline = "BRMO 2024"} (or simply \code{guideline = "BRMO"})
The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (\href{https://www.sri-richtlijnen.nl/brmo}{link}) The Dutch national guideline - Samenwerkingverband Richtlijnen Infectiepreventie (SRI) (2024) "Bijzonder Resistente Micro-Organismen (BRMO)" (\href{https://www.sri-richtlijnen.nl/brmo}{link})