From a84101db08d28afa55787539490e4fd29261f39a Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Wed, 22 Feb 2023 16:26:13 +0100
Subject: [PATCH] N for only 1 AB in

---
 DESCRIPTION        |  2 +-
 NEWS.md            |  2 +-
 R/antibiogram.R    | 36 +++++++++++++++++++++---------------
 man/antibiogram.Rd | 25 ++++++++++++-------------
 4 files changed, 35 insertions(+), 30 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f78e837c..f2afc73d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.8.2.9140
+Version: 1.8.2.9141
 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 2efd3b2a..e341c871 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.8.2.9140
+# AMR 1.8.2.9141
 
 *(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 c599a24e..3090a844 100755
--- a/R/antibiogram.R
+++ b/R/antibiogram.R
@@ -188,12 +188,11 @@
 #' # with a custom language, though this will be determined automatically
 #' # (i.e., this table will be in Spanish on Spanish systems)
 #' antibiogram(ex1,
-#'   antibiotics = aminoglycosides(),
-#'   ab_transform = "name",
-#'   syndromic_group = ifelse(ex1$ward == "ICU",
-#'     "UCI", "No UCI"
-#'   ),
-#'   language = "es"
+#'             antibiotics = aminoglycosides(),
+#'             ab_transform = "name",
+#'             syndromic_group = ifelse(ex1$ward == "ICU",
+#'                                      "UCI", "No UCI"),
+#'             language = "es"
 #' )
 #'
 #'
@@ -201,13 +200,13 @@
 #'
 #' # the data set could contain a filter for e.g. respiratory specimens/ICU
 #' antibiogram(example_isolates,
-#'   antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
-#'   mo_transform = "gramstain",
-#'   minimum = 10, # this should be >=30, but now just as example
-#'   syndromic_group = ifelse(example_isolates$age >= 65 &
-#'     example_isolates$gender == "M",
-#'   "WISCA Group 1", "WISCA Group 2"
-#'   )
+#'             antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
+#'             mo_transform = "gramstain",
+#'             minimum = 10, # this should be >=30, but now just as example
+#'             syndromic_group = ifelse(example_isolates$age >= 65 &
+#'                                        example_isolates$gender == "M",
+#'                                      "WISCA Group 1", "WISCA Group 2"
+#'             )
 #' )
 #'
 #' # Print the output for R Markdown / Quarto -----------------------------
@@ -488,8 +487,15 @@ antibiogram <- function(x,
       count_group <- n_per_mo$count[match(new_df[[1]], n_per_mo$mo)]
       edit_col <- 1
     }
-    new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", count_group, ")")
-    colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N min-max)")
+    if (NCOL(new_df) == edit_col + 1) {
+      # only 1 antibiotic
+      new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", unlist(lapply(strsplit(count_group, "-"), function(x) x[1])), ")")
+      colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N)")
+    } else {
+      # more than 1 antibiotic
+      new_df[[edit_col]] <- paste0(new_df[[edit_col]], " (", count_group, ")")
+      colnames(new_df)[edit_col] <- paste(colnames(new_df)[edit_col], "(N min-max)")
+    }
   }
 
   out <- as_original_data_class(new_df, class(x), extra_class = "antibiogram")
diff --git a/man/antibiogram.Rd b/man/antibiogram.Rd
index a18be744..a73d088b 100644
--- a/man/antibiogram.Rd
+++ b/man/antibiogram.Rd
@@ -217,12 +217,11 @@ ex1 <- example_isolates[which(mo_genus() == "Escherichia"), ]
 # with a custom language, though this will be determined automatically
 # (i.e., this table will be in Spanish on Spanish systems)
 antibiogram(ex1,
-  antibiotics = aminoglycosides(),
-  ab_transform = "name",
-  syndromic_group = ifelse(ex1$ward == "ICU",
-    "UCI", "No UCI"
-  ),
-  language = "es"
+            antibiotics = aminoglycosides(),
+            ab_transform = "name",
+            syndromic_group = ifelse(ex1$ward == "ICU",
+                                     "UCI", "No UCI"),
+            language = "es"
 )
 
 
@@ -230,13 +229,13 @@ antibiogram(ex1,
 
 # the data set could contain a filter for e.g. respiratory specimens/ICU
 antibiogram(example_isolates,
-  antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
-  mo_transform = "gramstain",
-  minimum = 10, # this should be >=30, but now just as example
-  syndromic_group = ifelse(example_isolates$age >= 65 &
-    example_isolates$gender == "M",
-  "WISCA Group 1", "WISCA Group 2"
-  )
+            antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
+            mo_transform = "gramstain",
+            minimum = 10, # this should be >=30, but now just as example
+            syndromic_group = ifelse(example_isolates$age >= 65 &
+                                       example_isolates$gender == "M",
+                                     "WISCA Group 1", "WISCA Group 2"
+            )
 )
 
 # Print the output for R Markdown / Quarto -----------------------------