From 38ae865a07b47089c9b01ff26f9a8472913b8407 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Thu, 15 Oct 2026 10:37:40 +0200 Subject: [PATCH] Document all values of rank_index in the clinical_breakpoints data set, including species groups, and the stored value of EUCAST's off-scale S breakpoint --- R/data.R | 4 ++-- man/clinical_breakpoints.Rd | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/R/data.R b/R/data.R index 10d589337..5dc7880c1 100755 --- a/R/data.R +++ b/R/data.R @@ -297,11 +297,11 @@ #' - `method`\cr Testing method, either `r vector_or(clinical_breakpoints$method, documentation = TRUE)` #' - `site`\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory" #' - `mo`\cr Microbial ID, see [as.mo()] -#' - `rank_index`\cr Taxonomic rank index of `mo` from 1 (subspecies/infraspecies) to 7 (non-species related breakpoints), used to choose the most specific breakpoint; blocking rows (see *Details*) have the rank index of their organism + 0.1 +#' - `rank_index`\cr Taxonomic rank index of `mo`, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., *Streptococcus* group A), 3 for genus, 4 for family, 5 for order, 6 for other groups (e.g., Gram-negative or anaerobic bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see *Details*) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence. #' - `ab`\cr Antimicrobial code as used by this package, EARS-Net and WHONET, see [as.ab()] #' - `ref_tbl`\cr Info about where the guideline rule can be found #' - `disk_dose`\cr Dose of the used disk diffusion method -#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S", is `NA` for blocking rows (see *Details*) +#' - `breakpoint_S`\cr Lowest MIC value or highest number of millimetres that leads to "S", is `NA` for blocking rows (see *Details*). EUCAST's off-scale MIC breakpoint of 0.001 mg/L, which indicates that there is no S category, is stored as 0.0001 to keep all isolates out of "S". #' - `breakpoint_R`\cr Highest MIC value or lowest number of millimetres that leads to "R", can be `NA` #' - `uti`\cr A [logical] value (`TRUE`/`FALSE`) to indicate whether the rule applies to a urinary tract infection (UTI) #' - `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. diff --git a/man/clinical_breakpoints.Rd b/man/clinical_breakpoints.Rd index 5fb9370f3..4dfa2f66a 100644 --- a/man/clinical_breakpoints.Rd +++ b/man/clinical_breakpoints.Rd @@ -13,11 +13,11 @@ A \link[tibble:tibble]{tibble} with 60 237 observations and 15 variables: \item \code{method}\cr Testing method, either \code{"DISK"} or \code{"MIC"} \item \code{site}\cr Body site for which the breakpoint must be applied, e.g. "Oral" or "Respiratory" \item \code{mo}\cr Microbial ID, see \code{\link[=as.mo]{as.mo()}} -\item \code{rank_index}\cr Taxonomic rank index of \code{mo} from 1 (subspecies/infraspecies) to 7 (non-species related breakpoints), used to choose the most specific breakpoint; blocking rows (see \emph{Details}) have the rank index of their organism + 0.1 +\item \code{rank_index}\cr Taxonomic rank index of \code{mo}, used to choose the most specific breakpoint (the lowest index): 1 for subspecies and infraspecies, 2 for species, 2.5 for species groups (e.g., \emph{Streptococcus} group A), 3 for genus, 4 for family, 5 for order, 6 for other groups (e.g., Gram-negative or anaerobic bacteria), and 7 for non-species related (PK-PD) breakpoints. Blocking rows (see \emph{Details}) have the rank index of their organism + 0.1, e.g., 2.6 for a species group, so that a breakpoint for the same organism always takes precedence. \item \code{ab}\cr Antimicrobial code as used by this package, EARS-Net and WHONET, see \code{\link[=as.ab]{as.ab()}} \item \code{ref_tbl}\cr Info about where the guideline rule can be found \item \code{disk_dose}\cr Dose of the used disk diffusion method -\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S", is \code{NA} for blocking rows (see \emph{Details}) +\item \code{breakpoint_S}\cr Lowest MIC value or highest number of millimetres that leads to "S", is \code{NA} for blocking rows (see \emph{Details}). EUCAST's off-scale MIC breakpoint of 0.001 mg/L, which indicates that there is no S category, is stored as 0.0001 to keep all isolates out of "S". \item \code{breakpoint_R}\cr Highest MIC value or lowest number of millimetres that leads to "R", can be \code{NA} \item \code{uti}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the rule applies to a urinary tract infection (UTI) \item \code{is_SDD}\cr A \link{logical} value (\code{TRUE}/\code{FALSE}) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 72 breakpoints.