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(v3.0.1.9017) fix documentation

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dr. M.S. (Matthijs) Berends
2026-01-08 14:03:02 +01:00
parent cfd1922dd9
commit fd50c51543
5 changed files with 7 additions and 5 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR
Version: 3.0.1.9016
Version: 3.0.1.9017
Date: 2026-01-08
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 3.0.1.9016
# AMR 3.0.1.9017
### New
* Integration with the **tidymodels** framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via `recipes`

5
R/ab_property.R
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@@ -163,6 +163,7 @@ ab_tradenames <- function(x, ...) {
}
#' @rdname ab_property
#' @param all_groups A [logical] to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting `all_groups = TRUE` would return all three for such an antibiotic, while `all_groups = FALSE` (default) only returns the most distinctive group name.
#' @export
ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
meet_criteria(x, allow_NA = TRUE)
@@ -171,11 +172,9 @@ ab_group <- function(x, language = get_AMR_locale(), all_groups = FALSE, ...) {
grps <- ab_validate(x = x, property = "group", ...)
for (i in seq_along(grps)) {
# take the first match based on ABX_PRIORITY_LIST
if (all_groups == FALSE) {
# take the first match based on ABX_PRIORITY_LIST
grps[[i]] <- grps[[i]][1]
} else if (length(grps[[i]]) > 1) {
grps[[i]] <- grps[[i]][grps[[i]] != "Beta-lactamase inhibitors"] # leave these out if there are other groups
}
if (language != "en") {
grps[[i]] <- translate_into_language(grps[[i]], language = language, only_affect_ab_names = TRUE)

2
man/ab_property.Rd
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@@ -59,6 +59,8 @@ set_ab_names(data, ..., property = "name", language = get_AMR_locale(),
\item{...}{In case of \code{\link[=set_ab_names]{set_ab_names()}} and \code{data} is a \link{data.frame}: columns to select (supports tidy selection such as \code{column1:column4}), otherwise other arguments passed on to \code{\link[=as.ab]{as.ab()}}.}
\item{all_groups}{A \link{logical} to indicate whether all antimicrobial groups must be return as a vector for each input value. For example, an antibiotic in the "aminopenicillins" group, is also in the "penicillins" and "beta-lactams" groups. Setting \code{all_groups = TRUE} would return all three for such an antibiotic, while \code{all_groups = FALSE} (default) only returns the most distinctive group name.}
\item{only_first}{A \link{logical} to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group).}
\item{administration}{Way of administration, either \code{"oral"} or \code{"iv"}.}

1
tests/testthat/test-ab_property.R
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@@ -40,6 +40,7 @@ test_that("test-ab_property.R", {
expect_inherits(ab_tradenames(c("AMX", "AMX")), "list")
expect_identical(ab_group("AMX", language = NULL), "Aminopenicillins")
expect_identical(ab_group("AMX", language = NULL, all_groups = TRUE), c("Aminopenicillins", "Penicillins", "Beta-lactams"))
expect_identical(ab_atc_group1("AMX", language = NULL), "Beta-lactam antibacterials, penicillins")
expect_identical(ab_atc_group2("AMX", language = NULL), "Penicillins with extended spectrum")