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(v3.0.1.9079) docs: rename remaining 'antibiotic selectors'/'AB selectors' to 'antimicrobial selectors'/'AMR selectors'

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* docs: rename remaining 'antibiotic selectors'/'AB selectors' to 'antimicrobial selectors'/'AMR selectors'

Five leftover occurrences of the old terminology updated in the AMR
vignette (section heading + code comment), the amr_selectors test file,
and two roxygen example comments in amr_selectors.R. The auto-generated
man/antimicrobial_selectors.Rd will update on the next devtools::document() run.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_0169LucQ7SHDLHdTnDs1ENhd

* fix

---------

Co-authored-by: Claude <noreply@anthropic.com>
This commit is contained in:
Matthijs Berends
2026-06-27 14:31:58 +02:00
committed by GitHub
parent 12cabca29d
commit 03be4b87fc
10 changed files with 13 additions and 13 deletions
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2
DESCRIPTION
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@@ -1,5 +1,5 @@
Package: AMR
Version: 3.0.1.9078
Version: 3.0.1.9079
Date: 2026-06-27
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 3.0.1.9078
# AMR 3.0.1.9079
Planned as v3.1.0, end of June 2026.

4
R/amr_selectors.R
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@@ -202,7 +202,7 @@
#' # data.table --------------------------------------------------------------
#'
#' # data.table is supported as well, just use it in the same way as with
#' # base R, but add `with = FALSE` if using a single AB selector.
#' # base R, but add `with = FALSE` if using a single AMR selector.
#'
#' if (require("data.table")) {
#' dt <- as.data.table(example_isolates)
@@ -215,7 +215,7 @@
#' dt[, carbapenems(), with = FALSE]
#' }
#'
#' # for multiple selections or AB selectors, `with = FALSE` is not needed:
#' # for multiple selections or AMR selectors, `with = FALSE` is not needed:
#' if (require("data.table")) {
#' dt[, c("mo", aminoglycosides())]
#' }

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R/sysdata.rda
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data/antibiotics.rda
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data/antimicrobials.rda
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4
man/antimicrobial_selectors.Rd
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@@ -437,7 +437,7 @@ example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]
# data.table --------------------------------------------------------------
# data.table is supported as well, just use it in the same way as with
# base R, but add `with = FALSE` if using a single AB selector.
# base R, but add `with = FALSE` if using a single AMR selector.
if (require("data.table")) {
dt <- as.data.table(example_isolates)
@@ -450,7 +450,7 @@ if (require("data.table")) {
dt[, carbapenems(), with = FALSE]
}
# for multiple selections or AB selectors, `with = FALSE` is not needed:
# for multiple selections or AMR selectors, `with = FALSE` is not needed:
if (require("data.table")) {
dt[, c("mo", aminoglycosides())]
}

6
man/plot.Rd
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@@ -36,21 +36,21 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
scale_x_sir(
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
...
)
scale_colour_sir(
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
...
)
scale_fill_sir(
colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
language = get_AMR_locale(),
eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
eucast_I = getOption("AMR_guideline", "EUCAST") \%like\% "EUCAST",
...
)

2
tests/testthat/test-amr_selectors.R
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@@ -88,7 +88,7 @@ test_that("test-amr selectors.R", {
expect_equal(nrow(example_isolates[any(carbapenems() != "R"), ]), 910, tolerance = 0.5)
expect_equal(nrow(example_isolates[carbapenems() != "R", ]), 704, tolerance = 0.5)
# filter with multiple antibiotic selectors using c()
# filter with multiple antimicrobial selectors using c()
expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
# filter + select in one go: get penicillins in carbapenems-resistant strains

6
vignettes/AMR.Rmd
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@@ -220,9 +220,9 @@ our_data_1st %>%
count(mo_name(bacteria), sort = TRUE)
```
## Select and filter with antibiotic selectors
## Select and filter with antimicrobial selectors
Using so-called antibiotic class selectors, you can select or filter columns based on the antibiotic class that your antibiotic results are in:
Using so-called antimicrobial class selectors, you can select or filter columns based on the antimicrobial class that your antimicrobial results are in:
```{r bug_drg 2a}
our_data_1st %>%
@@ -234,7 +234,7 @@ our_data_1st %>%
our_data_1st %>%
select(bacteria, where(is.sir))
# filtering using AB selectors is also possible:
# filtering using antimicrobial selectors is also possible:
our_data_1st %>%
filter(any(aminoglycosides() == "R"))