diff --git a/.github/workflows/check-current-testthat.yaml b/.github/workflows/check-current-testthat.yaml index 961b79e9d..d59035888 100644 --- a/.github/workflows/check-current-testthat.yaml +++ b/.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'} diff --git a/DESCRIPTION b/DESCRIPTION index ff9a90a06..b7ce75421 100644 --- a/DESCRIPTION +++ b/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) diff --git a/NEWS.md b/NEWS.md index c649b1809..000032ca6 100644 --- a/NEWS.md +++ b/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).)* diff --git a/R/sir.R b/R/sir.R index 96136cea1..ad53151c9 100755 --- a/R/sir.R +++ b/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. diff --git a/data-raw/datasets/microorganisms.codes.dta b/data-raw/datasets/microorganisms.codes.dta index c10d4be5b..12838b122 100644 Binary files a/data-raw/datasets/microorganisms.codes.dta and b/data-raw/datasets/microorganisms.codes.dta differ diff --git a/data-raw/datasets/microorganisms.codes.feather b/data-raw/datasets/microorganisms.codes.feather index ee5dfd6ef..6d0427cda 100644 Binary files a/data-raw/datasets/microorganisms.codes.feather and b/data-raw/datasets/microorganisms.codes.feather differ diff --git a/data-raw/datasets/microorganisms.codes.parquet b/data-raw/datasets/microorganisms.codes.parquet index c082c3cfb..b11391142 100644 Binary files a/data-raw/datasets/microorganisms.codes.parquet and b/data-raw/datasets/microorganisms.codes.parquet differ diff --git a/data-raw/datasets/microorganisms.codes.rds b/data-raw/datasets/microorganisms.codes.rds index f89de6fdc..269f37ce2 100644 Binary files a/data-raw/datasets/microorganisms.codes.rds and b/data-raw/datasets/microorganisms.codes.rds differ diff --git a/data-raw/datasets/microorganisms.codes.sav b/data-raw/datasets/microorganisms.codes.sav index 0af49e517..4bbe35c79 100644 Binary files a/data-raw/datasets/microorganisms.codes.sav and b/data-raw/datasets/microorganisms.codes.sav differ diff --git a/data-raw/datasets/microorganisms.codes.txt b/data-raw/datasets/microorganisms.codes.txt index 1bafd8a27..68cb37cab 100644 --- a/data-raw/datasets/microorganisms.codes.txt +++ b/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" diff --git a/data-raw/datasets/microorganisms.codes.xlsx b/data-raw/datasets/microorganisms.codes.xlsx index 6d64da999..f9dd97e3a 100644 Binary files a/data-raw/datasets/microorganisms.codes.xlsx and b/data-raw/datasets/microorganisms.codes.xlsx differ diff --git a/data-raw/microorganisms.codes.md5 b/data-raw/microorganisms.codes.md5 index e3fe15bdd..7a5e1fddb 100644 --- a/data-raw/microorganisms.codes.md5 +++ b/data-raw/microorganisms.codes.md5 @@ -1 +1 @@ -4862699a91a23f2fe6a790ac277697d0 +85b172c713e3e5aed32dc760c337ec34 diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda index 8d2c1e577..41242ae3a 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/man/as.sir.Rd b/man/as.sir.Rd index dc1806752..337ca60f5 100644 --- a/man/as.sir.Rd +++ b/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.}