(v2.1.1.9248) unit test fix

.github/workflows/check-current-testthat.yaml

@@ -53,7 +53,7 @@ jobs:
       matrix:
         config:
           # current development version, check all major OSes:
-          - {os: macOS-latest,   r: 'devel', allowfail: true}
+          # - {os: macOS-latest,   r: 'devel', allowfail: true}
           - {os: windows-latest, r: 'devel', allowfail: false}
           - {os: ubuntu-latest,  r: 'devel', allowfail: false, http-user-agent: 'release'}
 

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9247
+Version: 2.1.1.9248
 Date: 2025-04-20
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 2.1.1.9247
+# AMR 2.1.1.9248
 
 *(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).)*
 

R/sir.R

@@ -31,12 +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`.
 #'
-#' These breakpoints are currently implemented:
-#' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
-#' - For **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`;
-#' - For **ECOFFs** (Epidemiological Cut-off Values): EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`.
-#'
-#' 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.

data-raw/datasets/microorganisms.codes.txt

@@ -4944,7 +4944,7 @@
 "VFL"	"B_VIBRI_FLVL"
 "VFU"	"B_VIBRI_FRNS"
 "VGC"	"B_VGCCC"
-"VGS"	"B_VGCCC_SLMN"
+"VGS"	"B_STRPT_VIRI"
 "VHI"	"B_VIBRI_CHLR"
 "VHO"	"B_GRMNT_HLLS"
 "VI-"	"B_VIBRI"

data-raw/microorganisms.codes.md5

@@ -1 +1 @@
-4862699a91a23f2fe6a790ac277697d0
+85b172c713e3e5aed32dc760c337ec34

man/as.sir.Rd

@@ -144,14 +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}.
 
-These breakpoints are currently implemented:
-\itemize{
-\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
-\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
-\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
-}
-
-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.}