diff --git a/DESCRIPTION b/DESCRIPTION index a7c4d6f33..782182cf9 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 3.0.1.9090 -Date: 2026-09-04 +Version: 3.0.1.9091 +Date: 2026-09-08 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index 578281a34..1f19cae7e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 3.0.1.9090 +# AMR 3.0.1.9091 Planned as v3.1.0, end of September 2026. diff --git a/R/interpretive_rules.R b/R/interpretive_rules.R index 0ae0cca86..f17094621 100755 --- a/R/interpretive_rules.R +++ b/R/interpretive_rules.R @@ -80,7 +80,7 @@ format_eucast_version_nr <- function(version, markdown = TRUE) { #' **Note:** This function does not translate MIC or disk values to SIR values. Use [as.sir()] for that. \cr #' **Note:** When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr #' -#' The file containing all interpretive rules is located here: . **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms]. +#' The file containing all interpretive rules is located here: . **Note:** Old taxonomic names are replaced with the current taxonomy where applicable. For example, *Ochrobactrum anthropi* was renamed to *Brucella anthropi* in 2020; older interpretive rules may not yet contain this new taxonomic name. The `AMR` package contains the full microbial taxonomy updated until `r documentation_date(max(TAXONOMY_VERSION$GBIF$accessed_date, TAXONOMY_VERSION$LPSN$accessed_date))`, see [microorganisms]. #' #' ### Custom Rules #' diff --git a/man/interpretive_rules.Rd b/man/interpretive_rules.Rd index 59142be70..66a6e1d70 100644 --- a/man/interpretive_rules.Rd +++ b/man/interpretive_rules.Rd @@ -94,7 +94,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive \strong{Note:} This function does not translate MIC or disk values to SIR values. Use \code{\link[=as.sir]{as.sir()}} for that. \cr \strong{Note:} When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. \cr -The file containing all interpretive rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until 7th of May, 2026, see \link{microorganisms}. +The file containing all interpretive rules is located here: \url{https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv}. \strong{Note:} Old taxonomic names are replaced with the current taxonomy where applicable. For example, \emph{Ochrobactrum anthropi} was renamed to \emph{Brucella anthropi} in 2020; older interpretive rules may not yet contain this new taxonomic name. The \code{AMR} package contains the full microbial taxonomy updated until 7th of May, 2026, see \link{microorganisms}. \subsection{Custom Rules}{ Custom rules can be created using \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}, e.g.: diff --git a/tests/testthat/test-interpretive_rules.R b/tests/testthat/test-interpretive_rules.R index 2b9971bdf..d2fd10856 100755 --- a/tests/testthat/test-interpretive_rules.R +++ b/tests/testthat/test-interpretive_rules.R @@ -136,7 +136,7 @@ test_that("test-interpretive_rules.R", { CLR = factor("R"), stringsAsFactors = FALSE ), - version_expertrules = 3.1, + version_expertrules = 3.3, rules = "expert", overwrite = TRUE, only_sir_columns = FALSE