diff --git a/DESCRIPTION b/DESCRIPTION index dfe70862a..d737e261c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 3.0.1.9051 +Version: 3.0.1.9052 Date: 2026-04-25 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index b7496f805..42ca28b1e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9051 +# AMR 3.0.1.9052 ### New * Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations. diff --git a/man/as.sir.Rd b/man/as.sir.Rd index 88e5bfa1e..1121f8ff9 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -130,7 +130,7 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain \item{add_intrinsic_resistance}{\emph{(only useful when using a EUCAST guideline)} a \link{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 \emph{Klebsiella} species. Determination is based on the \link{intrinsic_resistant} data set, that itself is based on \href{https://www.eucast.org/bacteria/important-additional-information/expert-rules/}{'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3} (2021).} -\item{reference_data}{A \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the \link{clinical_breakpoints} data set (same column names and column types). Please note that the \code{guideline} argument will be ignored when \code{reference_data} is manually set.} +\item{reference_data}{A \link{data.frame} to be used for interpretation, which defaults to the \link{clinical_breakpoints} data set. Changing this argument allows for using own interpretation guidelines. This argument must have the same column names as the \link{clinical_breakpoints} data set. Column types are coerced automatically where possible: the \code{mo} column is passed through \code{\link[=as.mo]{as.mo()}}, the \code{ab} column through \code{\link[=as.ab]{as.ab()}}, and plain character, numeric, or logical columns are cast to the expected type. When \code{reference_data} is manually set, the \code{guideline} argument is optional: if omitted (or if its value does not match any row in the custom data), all rows in \code{reference_data} are considered. If \code{guideline} is set to a value that exists in the \code{guideline} column of the custom data, only matching rows are used — useful when a single custom table contains multiple guidelines. For the R classification, the EUCAST convention is used by default: MIC values \verb{> breakpoint_R} and disk diffusion values \verb{< breakpoint_R} are classified as R, with values between \code{breakpoint_S} and \code{breakpoint_R} classified as I (or SDD). Only when using the standard \link{clinical_breakpoints} with a CLSI guideline are the closed-interval rules (\verb{>= breakpoint_R} for MIC, \verb{<= breakpoint_R} for disk) applied; custom \code{reference_data} always uses the open-interval (EUCAST) convention regardless of the guideline name.} \item{substitute_missing_r_breakpoint}{A \link{logical} to indicate that a missing clinical breakpoints for R (resistant) must be substituted with R - the default is \code{FALSE}. Some (especially CLSI) breakpoints only have a breakpoint for S, meaning that the outcome can only be \code{"S"} or \code{NA}. Setting this to \code{TRUE} will convert the \code{NA}s in these cases to \code{"R"}. Can also be set with the package option \code{\link[=AMR-options]{AMR_substitute_missing_r_breakpoint}}.} @@ -150,7 +150,7 @@ The default \code{"conservative"} setting ensures cautious handling of uncertain \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} -\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. This requires no additional packages, as the used \code{parallel} package is part of base \R. On Windows and on \R < 4.0.0 \code{\link[parallel:clusterApply]{parallel::parLapply()}} will be used, in all other cases the more efficient \code{\link[parallel:mclapply]{parallel::mclapply()}} will be used.} +\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. The \code{parallel} package is part of base \R and no additional packages are required. On Unix/macOS with \R >= 4.0.0, \code{\link[parallel:mclapply]{parallel::mclapply()}} (fork-based) is used; on Windows and \R < 4.0.0, \code{\link[parallel:clusterApply]{parallel::parLapply()}} with a PSOCK cluster is used (requires the AMR package to be installed, not just loaded via \code{devtools::load_all()}). Parallelism distributes columns across cores; it is most beneficial when there are many antibiotic columns and a large number of rows.} \item{max_cores}{Maximum number of cores to use if \code{parallel = TRUE}. Use a negative value to subtract that number from the available number of cores, e.g. a value of \code{-2} on an 8-core machine means that at most 6 cores will be used. Defaults to \code{-1}. There will never be used more cores than variables to analyse. The available number of cores are detected using \code{\link[parallelly:availableCores]{parallelly::availableCores()}} if that package is installed, and base \R's \code{\link[parallel:detectCores]{parallel::detectCores()}} otherwise.}