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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
Download Patch File Download Diff File Expand all files Collapse all files

4
man/antimicrobial_selectors.Rd
View File

@@ -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
View File

@@ -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",
...
)