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

* 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>

DESCRIPTION

@@ -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)

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 3.0.1.9078
+# AMR 3.0.1.9079
 
 Planned as v3.1.0, end of June 2026.
 

R/amr_selectors.R

@@ -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())]
 #' }

man/antimicrobial_selectors.Rd

@@ -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())]
 }

man/plot.Rd

@@ -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",
   ...
 )
 

tests/testthat/test-amr_selectors.R

@@ -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

vignettes/AMR.Rmd

@@ -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"))