diff --git a/DESCRIPTION b/DESCRIPTION index b7ce75421..62a3a0a3f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9248 +Version: 2.1.1.9249 Date: 2025-04-20 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 000032ca6..8d8a2a35e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9248 +# AMR 2.1.1.9249 *(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).)* diff --git a/R/sir.R b/R/sir.R index ad53151c9..c80a9b161 100755 --- a/R/sir.R +++ b/R/sir.R @@ -31,7 +31,7 @@ #' #' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] containing the levels `S`, `SDD`, `I`, `R`, `NI`. #' -#' Breakpoints are currently implemented from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*. All breakpoints used for interpretation are available in our [clinical_breakpoints] data set. +#' Breakpoints are currently implemented from EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`, see *Details*. All breakpoints used for interpretation are available in our [clinical_breakpoints] data set. #' @rdname as.sir #' @param x Vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres). #' @param mo A vector (or column name) with [character]s that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically. diff --git a/man/as.sir.Rd b/man/as.sir.Rd index 337ca60f5..40c560056 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -144,7 +144,7 @@ Ordered \link{factor} with new class \code{sir} \description{ Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. \code{\link[=as.sir]{as.sir()}} transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} containing the levels \code{S}, \code{SDD}, \code{I}, \code{R}, \code{NI}. -Breakpoints are currently implemented from EUCAST (2011-2025) and CLSI (2011-2025), see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set. +Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set. } \details{ \emph{Note: The clinical breakpoints in this package were validated through, and imported from, \href{https://whonet.org}{WHONET}. The public use of this \code{AMR} package has been endorsed by both CLSI and EUCAST. See \link{clinical_breakpoints} for more information.} diff --git a/tests/testthat/test-sir.R b/tests/testthat/test-sir.R index 28c7b2f29..e80431685 100644 --- a/tests/testthat/test-sir.R +++ b/tests/testthat/test-sir.R @@ -129,7 +129,7 @@ test_that("test-sir.R", { # allow for guideline length > 1 expect_equal( AMR:::get_guideline(c("CLSI", "CLSI", "CLSI2023", "EUCAST", "EUCAST2020"), AMR::clinical_breakpoints), - c("CLSI 2024", "CLSI 2024", "CLSI 2023", "EUCAST 2024", "EUCAST 2020") + c("CLSI 2025", "CLSI 2025", "CLSI 2023", "EUCAST 2025", "EUCAST 2020") ) # these are used in the script