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(v3.0.0.9018) keep all reasons in mdro(), fixed #227

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dr. M.S. (Matthijs) Berends
2025-08-07 16:23:47 +02:00
parent fc72cf9324
commit 9b07a8573a
4 changed files with 9 additions and 7 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 3.0.0.9017 Version: 3.0.0.9018
Date: 2025-07-28 Date: 2025-08-07
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)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

3
NEWS.md
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# AMR 3.0.0.9017 # AMR 3.0.0.9018
This is primarily a bugfix release, though we added one nice feature too. This is primarily a bugfix release, though we added one nice feature too.
@ -15,6 +15,7 @@ This is primarily a bugfix release, though we added one nice feature too.
* Fixed a bug in `as.sir()` to allow any tidyselect language (#220) * Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
* Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216) * Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
* Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213) * Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
* Fixed `mdro()` to contain all reasons in verbose output (#227)
* Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223) * Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (#223)
* Fixed some specific Dutch translations for antimicrobials * Fixed some specific Dutch translations for antimicrobials
* Added `names` to `age_groups()` so that custom names can be given (#215) * Added `names` to `age_groups()` so that custom names can be given (#215)

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R/mdro.R
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@ -41,7 +41,7 @@
#' @inheritParams eucast_rules #' @inheritParams eucast_rules
#' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate. #' @param pct_required_classes Minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for *S. aureus*. Setting this `pct_required_classes` argument to `0.5` (default) means that for every *S. aureus* isolate at least 8 different classes must be available. Any lower number of available classes will return `NA` for that isolate.
#' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I. #' @param combine_SI A [logical] to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the [mdro()] function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using `combine_SI = FALSE`, resistance is considered when isolates are R or I.
#' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not. #' @param verbose A [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
#' @details #' @details
#' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*. #' These functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#' #'
@ -772,7 +772,7 @@ mdro <- function(x = NULL,
) )
} }
x[rows_to_change, "MDRO"] <<- to x[rows_to_change, "MDRO"] <<- to
x[rows_to_change, "reason"] <<- reason x[rows_to_change, "reason"] <<- paste0(x[rows_to_change, "reason", drop = TRUE], "; ", reason)
x[rows_not_to_change, "reason"] <<- "guideline criteria not met" x[rows_not_to_change, "reason"] <<- "guideline criteria not met"
} }
} }
@ -854,7 +854,7 @@ mdro <- function(x = NULL,
x <- left_join_microorganisms(x, by = col_mo) x <- left_join_microorganisms(x, by = col_mo)
x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_) x$MDRO <- ifelse(!is.na(x$genus), 1, NA_integer_)
x$row_number <- seq_len(nrow(x)) x$row_number <- seq_len(nrow(x))
x$reason <- NA_character_ x$reason <- ""
x$all_nonsusceptible_columns <- "" x$all_nonsusceptible_columns <- ""
if (guideline$code == "cmi2012") { if (guideline$code == "cmi2012") {
@ -1899,6 +1899,7 @@ mdro <- function(x = NULL,
# fill in empty reasons # fill in empty reasons
x$reason[is.na(x$reason)] <- "not covered by guideline" x$reason[is.na(x$reason)] <- "not covered by guideline"
x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)") x[rows_empty, "reason"] <- paste(x[rows_empty, "reason"], "(note: no available test results)")
x$reason <- trimws(gsub("^;", "", x$reason))
# format data set # format data set
colnames(x)[colnames(x) == col_mo] <- "microorganism" colnames(x)[colnames(x) == col_mo] <- "microorganism"
x$microorganism <- mo_name(x$microorganism, language = NULL) x$microorganism <- mo_name(x$microorganism, language = NULL)

2
man/mdro.Rd
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@ -57,7 +57,7 @@ eucast_exceptional_phenotypes(x = NULL, only_sir_columns = any(is.sir(x)),
\item{combine_SI}{A \link{logical} to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{\link[=mdro]{mdro()}} function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.} \item{combine_SI}{A \link{logical} to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{\link[=mdro]{mdro()}} function, it follows the redefinition by EUCAST about the interpretation of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.}
\item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.} \item{verbose}{A \link{logical} to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.}
\item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.} \item{only_sir_columns}{A \link{logical} to indicate whether only antimicrobial columns must be included that were transformed to class \link[=as.sir]{sir} on beforehand. Defaults to \code{FALSE} if no columns of \code{x} have a class \link[=as.sir]{sir}.}