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(v3.0.1.9091) unit test

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dr. M.S. (Matthijs) Berends
2026-09-08 15:02:07 +02:00
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DESCRIPTION
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Package: AMR Package: AMR
Version: 3.0.1.9090 Version: 3.0.1.9091
Date: 2026-09-04 Date: 2026-09-08
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

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NEWS.md
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# AMR 3.0.1.9090 # AMR 3.0.1.9091
Planned as v3.1.0, end of September 2026. Planned as v3.1.0, end of September 2026.

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R/interpretive_rules.R
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@@ -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:** 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 #' **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: <https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv>. **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: <https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv>. **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 #' ### Custom Rules
#' #'

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man/interpretive_rules.Rd
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@@ -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:} 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 \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}{ \subsection{Custom Rules}{
Custom rules can be created using \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}, e.g.: Custom rules can be created using \code{\link[=custom_interpretive_rules]{custom_interpretive_rules()}}, e.g.:

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tests/testthat/test-interpretive_rules.R
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@@ -136,7 +136,7 @@ test_that("test-interpretive_rules.R", {
CLR = factor("R"), CLR = factor("R"),
stringsAsFactors = FALSE stringsAsFactors = FALSE
), ),
version_expertrules = 3.1, version_expertrules = 3.3,
rules = "expert", rules = "expert",
overwrite = TRUE, overwrite = TRUE,
only_sir_columns = FALSE only_sir_columns = FALSE