(v1.1.0.9016) small fix

R/aa_helper_functions.R

@@ -252,9 +252,9 @@ dataset_UTF8_to_ASCII <- function(df) {
 }
 
 
-# replace crayon::has_color
+# replace crayon::has_color, but now also FALSE on non-interactive mode
 has_colour <- function() {
-  if (Sys.getenv("TERM") == "dumb") {
+  if (Sys.getenv("TERM") == "dumb" | !interactive()) {
     return(FALSE)
   }
   if (tolower(Sys.info()["sysname"]) == "windows") {

R/ab.R

@@ -215,6 +215,8 @@ as.ab <- function(x, ...) {
     x_spelling <- gsub("(o\\+n|o\\+ne\\+)$", "o+ne*", x_spelling)
     # replace multiple same characters to single one with '+', like "ll" -> "l+"
     x_spelling <- gsub("(.)\\1+", "\\1+", x_spelling)
+    # replace spaces and slashes with a possibility on both
+    x_spelling <- gsub("[ /]", "( |/)", x_spelling)
   
     # try if name starts with it
     found <- antibiotics[which(antibiotics$name %like% paste0("^", x_spelling)), ]$ab

R/atc_online.R

@@ -128,7 +128,7 @@ atc_online_property <- function(atc_code,
     returnvalue <- rep(NA_character_, length(atc_code))
   }
 
-  progress <- progress_estimated(n = length(atc_code))
+  progress <- progress_estimated(n = length(atc_code), 3)
   on.exit(close(progress))
   
   for (i in seq_len(length(atc_code))) {
@@ -160,7 +160,7 @@ atc_online_property <- function(atc_code,
         as.data.frame(stringsAsFactors = FALSE)
 
       # case insensitive column names
-      colnames(tbl) <- tolower(colnames(tbl)) %>% gsub("^atc.*", "atc", .)
+      colnames(tbl) <- gsub("^atc.*", "atc", tolower(colnames(tbl)))
 
       if (length(tbl) == 0) {
         warning("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call. = FALSE)

R/eucast_rules.R

@@ -599,7 +599,7 @@ eucast_rules <- function(x,
     }
   }
   
-  if (!any(c("other", "all") %in% rules, na.rm = TRUE)) {
+  if (info == TRUE & !any(c("other", "all") %in% rules, na.rm = TRUE)) {
     cat(font_red("\nSkipping inheritance rules defined by this package, such as setting trimethoprim (TMP) = R where trimethoprim/sulfamethoxazole (SXT) = R.\nUse eucast_rules(..., rules = \"all\") to also apply those rules.\n"))
   }