(v3.0.1.9001) fix antibiogram

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 3.0.1
+Version: 3.0.1.9001
-Date: 2025-09-20
+Date: 2025-09-30
 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
@@ -27,10 +27,10 @@ Authors@R: c(
   person(given = c("Judith", "M."),                 family = "Fonville",    role = "ctb"),
   person(given = c("Kathryn"),                      family = "Holt",        role = "ctb", comment = c(ORCID = "0000-0003-3949-2471")),
   person(given = c("Larisse"),                      family = "Bolton",      role = "ctb", comment = c(ORCID = "0000-0001-7879-2173")),
-  person(given = c("Matthew"),                      family = "Saab",        role = "ctb"),
+  person(given = c("Matthew"),                      family = "Saab",        role = "ctb", comment = c(ORCID = "0009-0008-6626-7919")),
   person(given = c("Natacha"),                      family = "Couto",       role = "ctb", comment = c(ORCID = "0000-0002-9152-5464")),
   person(given = c("Peter"),                        family = "Dutey-Magni", role = "ctb", comment = c(ORCID = "0000-0002-8942-9836")),
-  person(given = c("Rogier", "P."),                 family = "Schade",      role = "ctb"),
+  person(given = c("Rogier", "P."),                 family = "Schade",      role = "ctb", comment = c(ORCID = "0000-0002-9487-4467")),
   person(given = c("Sofia"),                        family = "Ny",          role = "ctb", comment = c(ORCID = "0000-0002-2017-1363")),
   person(given = c("Alex", "W."),                   family = "Friedrich",   role = "ths", comment = c(ORCID = "0000-0003-4881-038X")),
   person(given = c("Bhanu", "N.", "M."),            family = "Sinha",       role = "ths", comment = c(ORCID = "0000-0003-1634-0010")),

NEWS.md

@@ -1,3 +1,9 @@
+# AMR 3.0.1.9001
+
+### Changed
+* Fixed a bug in `antibiogram()` for when no antimicrobials are set
+
+
 # AMR 3.0.1
 
 This is a bugfix release following the release of v3.0.0 in June 2025.

R/aa_helper_functions.R

@@ -1620,8 +1620,8 @@ get_n_cores <- function(max_cores = Inf) {
 
 # Support `where()` if tidyselect not installed ----
 if (!is.null(import_fn("where", "tidyselect", error_on_fail = FALSE))) {
-  # tidyselect::where() exists, load the namespace to make `where()`s work across the package in default arguments
+  # tidyselect::where() exists, retrieve from their namespace to make `where()`s work across the package in default arguments
-  loadNamespace("tidyselect")
+  where <- tidyselect::where
 } else {
   where <- function(fn) {
     # based on https://github.com/nathaneastwood/poorman/blob/52eb6947e0b4430cd588976ed8820013eddf955f/R/where.R#L17-L32

R/antibiogram.R

@@ -453,7 +453,7 @@ antibiogram.default <- function(x,
     deprecation_warning("antibiotics", "antimicrobials", fn = "antibiogram", is_argument = TRUE)
     antimicrobials <- list(...)$antibiotics
   }
-  meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer"), allow_NA = FALSE, allow_NULL = FALSE)
+  meet_criteria(antimicrobials, allow_class = c("character", "numeric", "integer", "function"), 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)
   }
@@ -518,6 +518,10 @@ antibiogram.default <- function(x,
 
   # get antimicrobials
   ab_trycatch <- tryCatch(colnames(suppressWarnings(x[, antimicrobials, drop = FALSE])), error = function(e) NULL)
+  if (is.null(ab_trycatch)) {
+    # try with tidyverse
+    ab_trycatch <- tryCatch(colnames(dplyr::select(x, {{ antimicrobials }})), error = function(e) NULL)
+  }
   if (is.null(ab_trycatch)) {
     stop_ifnot(is.character(suppressMessages(antimicrobials)), "`antimicrobials` must be an antimicrobial selector, or a character vector.")
     antimicrobials.bak <- antimicrobials

man/AMR.Rd

@@ -83,10 +83,10 @@ Other contributors:
   \item Judith M. Fonville [contributor]
   \item Kathryn Holt (\href{https://orcid.org/0000-0003-3949-2471}{ORCID}) [contributor]
   \item Larisse Bolton (\href{https://orcid.org/0000-0001-7879-2173}{ORCID}) [contributor]
-  \item Matthew Saab [contributor]
+  \item Matthew Saab (\href{https://orcid.org/0009-0008-6626-7919}{ORCID}) [contributor]
   \item Natacha Couto (\href{https://orcid.org/0000-0002-9152-5464}{ORCID}) [contributor]
   \item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
-  \item Rogier P. Schade [contributor]
+  \item Rogier P. Schade (\href{https://orcid.org/0000-0002-9487-4467}{ORCID}) [contributor]
   \item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
   \item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
   \item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]

tests/testthat/test-antibiogram.R

@@ -32,6 +32,9 @@ test_that("test-antibiogram.R", {
 
   # Traditional antibiogram ----------------------------------------------
 
+
+  ab0 <- antibiogram(example_isolates)
+
   ab1 <- antibiogram(example_isolates,
     antimicrobials = c(aminoglycosides(), carbapenems())
   )