(v3.0.1.9001) fix antibiogram

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
-  loadNamespace("tidyselect")
+  # tidyselect::where() exists, retrieve from their namespace to make `where()`s work across the package in default arguments
+  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

R/plotting.R

@@ -53,17 +53,17 @@
 #' ### The `scale_*_mic()` Functions
 #'
 #' The functions [scale_x_mic()], [scale_y_mic()], [scale_colour_mic()], and [scale_fill_mic()] functions allow to plot the [mic][as.mic()] class (MIC values) on a continuous, logarithmic scale.
-#' 
+#'
 #' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [mic][as.mic()].
-#' 
+#'
 #' When manually added though, they allow to rescale the MIC range with an 'inside' or 'outside' range if required, and provide the option to retain the operators in MIC values (such as `>=`). Missing intermediate log2 levels will always be plotted too.
 #'
 #' ### The `scale_*_sir()` Functions
 #'
 #' The functions [scale_x_sir()], [scale_colour_sir()], and [scale_fill_sir()] functions allow to plot the [sir][as.sir()] class in the right order (`r paste(levels(NA_sir_), collapse = " < ")`).
-#' 
+#'
 #' There is normally no need to add these scale functions to your plot, as they are applied automatically when plotting values of class [sir][as.sir()].
-#' 
+#'
 #' At default, they translate the S/I/R values to an interpretative text ("Susceptible", "Resistant", etc.) in any of the `r length(AMR:::LANGUAGES_SUPPORTED)` supported languages (use `language = NULL` to keep S/I/R). Also, except for [scale_x_sir()], they set colour-blind friendly colours to the `colour` and `fill` aesthetics.
 #'
 #' ### Additional `ggplot2` Functions
@@ -201,7 +201,7 @@
 #'     geom_boxplot(fill = NA, colour = "grey30") +
 #'     geom_jitter(width = 0.25)
 #'     labs(title = "scale_y_mic()/scale_colour_sir() automatically applied")
-#'     
+#'
 #'   mic_sir_plot
 #' }
 #' if (require("ggplot2")) {