From 551aaf651768b3faa884ce03994cefdf4099ca09 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Wed, 22 Feb 2023 16:00:52 +0100
Subject: [PATCH] auto-remove missing ABs in `antibiogram()`

---
 DESCRIPTION     |  2 +-
 NEWS.md         |  2 +-
 R/antibiogram.R | 20 ++++++++++++--------
 index.md        |  2 +-
 4 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fd06087f..f78e837c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9139
+Version: 1.8.2.9140
 Date: 2023-02-22
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 70b0e25f..2efd3b2a 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9139
+# AMR 1.8.2.9140
 
 *(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
 
diff --git a/R/antibiogram.R b/R/antibiogram.R
index 940bbd3d..c599a24e 100755
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -313,15 +313,19 @@ antibiogram <- function(x,
     df_ab <- get_column_abx(x, verbose = FALSE, info = FALSE)
     # get antibiotics from user
     user_ab <- suppressMessages(suppressWarnings(lapply(antibiotics, as.ab, flag_multiple_results = FALSE, info = FALSE)))
-    user_ab <- lapply(user_ab, function(x) unname(df_ab[match(x, names(df_ab))]))
-
-    # remove non-existing columns
-    # non_existing <- unlist(antibiotics)[is.na(unlist(abx_ab))]
-    # if (length(non_existing) > 0) {
-    #   warning_("The following antibiotics were not available and ignored: ", vector_and(non_existing, sort = FALSE))
-    #   abx_user <- Map(antibiotics, abx_user, f = function(input, ab) input[!is.na(ab)])
-    # }
+    non_existing <- character(0)
+    user_ab <- lapply(user_ab, function(x) {
+      out <- unname(df_ab[match(x, names(df_ab))])
+      non_existing <<- c(non_existing, x[is.na(out) & !is.na(x)])
+      # remove non-existing columns
+      out[!is.na(out)]
+    })
+    user_ab <- user_ab[unlist(lapply(user_ab, length)) > 0]
     
+    if (length(non_existing) > 0) {
+      warning_("The following antibiotics were not available and ignored: ", vector_and(ab_name(non_existing, language = NULL, tolower = TRUE), quotes = FALSE))
+    }
+
     # make list unique
     antibiotics <- unique(user_ab)
     # go through list to set AMR in combinations
diff --git a/index.md b/index.md
index 00358f38..e6d6134b 100644
--- a/index.md
+++ b/index.md
@@ -115,7 +115,7 @@ Like many other functions in this package, `antibiogram()` comes with support fo
 
 ```r
 antibiogram(example_isolates,
-            antibiotics = c("CIP", "TOB", "GEN"),
+            antibiotics = c("cipro", "tobra", "genta"), # any arbitrary name or code will work
             mo_transform = "gramstain",
             ab_transform = "name",
             language = "uk") # Ukrainian