website

R/aa_helper_functions.R

@@ -1139,7 +1139,7 @@ try_colour <- function(..., before, after, collapse = " ") {
 }
 is_dark <- function() {
   if (is.null(AMR_env$is_dark_theme)) {
-    AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
+    !has_colour() || AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
   }
   isTRUE(AMR_env$is_dark_theme)
 }

R/antibiogram.R

@@ -477,7 +477,9 @@ antibiogram <- function(x,
     colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N min-max)")
   }
 
-  structure(as_original_data_class(new_df, class(x), extra_class = "antibiogram"),
+  out <- as_original_data_class(new_df, class(x), extra_class = "antibiogram")
+  rownames(out) <- NULL
+  structure(out,
     long = long,
     combine_SI = combine_SI
   )

R/bug_drug_combinations.R

@@ -164,9 +164,9 @@ bug_drug_combinations <- function(x,
   } else {
     out <- run_it(x)
   }
-  rownames(out) <- NULL
   out <- out %pm>% pm_arrange(mo, ab)
   out <- as_original_data_class(out, class(x.bak)) # will remove tibble groups
+  rownames(out) <- NULL
   structure(out, class = c("bug_drug_combinations", ifelse(data_has_groups, "grouped", character(0)), class(out)))
 }