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(v3.0.0.9001) the first fixes

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dr. M.S. (Matthijs) Berends 2025-06-04 13:10:20 +02:00
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5 changed files with 23 additions and 7 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 3.0.0
Date: 2025-06-01
Version: 3.0.0.9001
Date: 2025-06-04
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

10
NEWS.md
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@ -1,3 +1,11 @@
# AMR 3.0.0.9001
# Changed
* Fix for `antibiogram()` for when no antimicrobials are set
* Fixed some specific Dutch translations antimicrobials
# AMR 3.0.0
This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the [University of Prince Edward Island's Atlantic Veterinary College](https://www.upei.ca/avc), Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.
@ -122,7 +130,7 @@ This package now supports not only tools for AMR data analysis in clinical setti
## Older Versions
This changelog only contains changes from AMR v3.0 (March 2025) and later.
This changelog only contains changes from AMR v3.0 (June 2025) and later.
* For prior v2 versions, please see [our v2 archive](https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md).
* For prior v1 versions, please see [our v1 archive](https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md).

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R/antibiogram.R
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@ -40,6 +40,7 @@
#' - A combination of the above, using `c()`, e.g.:
#' - `c(aminoglycosides(), "AMP", "AMC")`
#' - `c(aminoglycosides(), carbapenems())`
#' - Column indices using numbers
#' - Combination therapy, indicated by using `"+"`, with or without [antimicrobial selectors][antimicrobial_selectors], e.g.:
#' - `"cipro + genta"`
#' - `"TZP+TOB"`
@ -452,7 +453,7 @@ antibiogram.default <- function(x,
deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
antimicrobials <- list(...)$antibiotics
}
meet_criteria(antimicrobials, allow_class = "character", allow_NA = FALSE, allow_NULL = FALSE)
meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
if (!is.function(mo_transform)) {
meet_criteria(mo_transform, allow_class = "character", has_length = 1, is_in = c("name", "shortname", "gramstain", colnames(AMR::microorganisms)), allow_NULL = TRUE, allow_NA = TRUE)
}
@ -1194,12 +1195,13 @@ retrieve_wisca_parameters <- function(wisca_model, ...) {
#' @rawNamespace if(getRversion() >= "3.0.0") S3method(pillar::tbl_sum, antibiogram)
tbl_sum.antibiogram <- function(x, ...) {
dims <- paste(format(NROW(x), big.mark = ","), AMR_env$cross_icon, format(NCOL(x), big.mark = ","))
names(dims) <- "An Antibiogram"
if (isTRUE(attributes(x)$wisca)) {
names(dims) <- paste0("An Antibiogram (WISCA / ", attributes(x)$conf_interval * 100, "% CI)")
dims <- c(dims, Type = paste0("WISCA with ", attributes(x)$conf_interval * 100, "% CI"))
} else if (isTRUE(attributes(x)$formatting_type >= 13)) {
names(dims) <- paste0("An Antibiogram (non-WISCA / ", attributes(x)$conf_interval * 100, "% CI)")
dims <- c(dims, Type = paste0("Non-WISCA with ", attributes(x)$conf_interval * 100, "% CI"))
} else {
names(dims) <- paste0("An Antibiogram (non-WISCA)")
dims <- c(dims, Type = paste0("Non-WISCA without CI"))
}
dims
}

5
R/translate.R
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@ -258,6 +258,11 @@ translate_into_language <- function(from,
return(from)
}
if (only_affect_ab_names == TRUE) {
df_trans$pattern[df_trans$regular_expr == TRUE] <- paste0(df_trans$pattern[df_trans$regular_expr == TRUE], "$")
df_trans$pattern[df_trans$regular_expr == TRUE] <- gsub("$$", "$", df_trans$pattern[df_trans$regular_expr == TRUE], fixed = TRUE)
}
lapply(
# starting with longest pattern, since more general translations are shorter, such as 'Group'
order(nchar(df_trans$pattern), decreasing = TRUE),

1
man/antibiogram.Rd
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@ -56,6 +56,7 @@ retrieve_wisca_parameters(wisca_model, ...)
\item \code{c(aminoglycosides(), "AMP", "AMC")}
\item \code{c(aminoglycosides(), carbapenems())}
}
\item Column indices using numbers
\item Combination therapy, indicated by using \code{"+"}, with or without \link[=antimicrobial_selectors]{antimicrobial selectors}, e.g.:
\itemize{
\item \code{"cipro + genta"}