(v1.5.0.9030) as.ab() speed improvement

R/ab.R

@@ -105,14 +105,29 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = TRUE, ...) {
   already_regex <- isTRUE(list(...)$already_regex)
   fast_mode <- isTRUE(list(...)$fast_mode)
   
-  if (all(toupper(x) %in% antibiotics$ab)) {
-    # valid AB code, but not yet right class
-    return(set_clean_class(toupper(x),
-                           new_class = c("ab", "character")))
-  }
 
   x_bak <- x
   x <- toupper(x)
+  x_nonNA <- x[!is.na(x)]
+  
+  if (all(x_nonNA %in% antibiotics$ab, na.rm = TRUE)) {
+    # all valid AB codes, but not yet right class
+    return(set_clean_class(x,
+                           new_class = c("ab", "character")))
+  }
+  if (all(x_nonNA %in% toupper(antibiotics$name), na.rm = TRUE)) {
+    # all valid AB names
+    out <- antibiotics$ab[match(x, toupper(antibiotics$name))]
+    out[is.na(x)] <- NA_character_
+    return(out)
+  }
+  if (all(x_nonNA %in% antibiotics$atc, na.rm = TRUE)) {
+    # all valid ATC codes
+    out <- antibiotics$ab[match(x, antibiotics$atc)]
+    out[is.na(x)] <- NA_character_
+    return(out)
+  }
+  
   # remove diacritics
   x <- iconv(x, from = "UTF-8", to = "ASCII//TRANSLIT")
   x <- gsub('"', "", x, fixed = TRUE)

R/catalogue_of_life.R

@@ -131,16 +131,15 @@ catalogue_of_life_version <- function() {
 #' @export
 #' @noRd
 print.catalogue_of_life_version <- function(x, ...) {
-  lst <- x
   cat(paste0(font_bold("Included in this AMR package (v", utils::packageDescription("AMR")$Version, ") are:\n\n", collapse = ""),
-             font_underline(lst$CoL$version), "\n",
-             "  Available at: ", lst$CoL$url, "\n",
-             "  Number of included species: ", format(lst$CoL$n, big.mark = ","), "\n",
-             font_underline(paste0(lst$LPSN$version, " (",
-                                   lst$LPSN$yearmonth, ")")), "\n",
-             "  Available at: ", lst$LPSN$url, "\n",
-             "  Number of included species: ", format(lst$LPSN$n, big.mark = ","), "\n\n",
-             "=> Total number of species included:  ", format(lst$total_included$n_total_species, big.mark = ","), "\n",
-             "=> Total number of synonyms included: ", format(lst$total_included$n_total_synonyms, big.mark = ","), "\n\n",
+             font_underline(x$CoL$version), "\n",
+             "  Available at: ", font_blue(x$CoL$url), "\n",
+             "  Number of included microbial species: ", format(x$CoL$n, big.mark = ","), "\n",
+             font_underline(paste0(x$LPSN$version, " (",
+                                   x$LPSN$yearmonth, ")")), "\n",
+             "  Available at: ", font_blue(x$LPSN$url), "\n",
+             "  Number of included bacterial species: ", format(x$LPSN$n, big.mark = ","), "\n\n",
+             "=> Total number of species included:  ", format(x$total_included$n_total_species, big.mark = ","), "\n",
+             "=> Total number of synonyms included: ", format(x$total_included$n_total_synonyms, big.mark = ","), "\n\n",
              "See for more info ?microorganisms and ?catalogue_of_life.\n"))
 }