From ba4dc20cf382fe1a064577d0a48bd95da8c05baa Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Thu, 30 May 2024 16:39:59 +0200
Subject: [PATCH] autoplot fix

---
 DESCRIPTION |  2 +-
 NEWS.md     |  2 +-
 R/plot.R    |  5 +++--
 R/sir.R     | 12 ++++++------
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0f0ff48a..95ce8820 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9034
+Version: 2.1.1.9035
 Date: 2024-05-30
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 363258d5..9ff6cb13 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9034
+# AMR 2.1.1.9035
 
 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*
 
diff --git a/R/plot.R b/R/plot.R
index 92da3a38..8cf4ab65 100755
--- a/R/plot.R
+++ b/R/plot.R
@@ -760,9 +760,10 @@ autoplot.sir <- function(object,
   }
 
   df <- as.data.frame(table(object), stringsAsFactors = TRUE)
-  colnames(df) <- c("sir", "count")
+  colnames(df) <- c("x", "n")
+  df <- df[!(df$n == 0 & df$x %in% c("SDD", "I", "N")), , drop = FALSE]
   ggplot2::ggplot(df) +
-    ggplot2::geom_col(ggplot2::aes(x = sir, y = count, fill = sir)) +
+    ggplot2::geom_col(ggplot2::aes(x = x, y = n, fill = x)) +
     # limits = force is needed because of a ggplot2 >= 3.3.4 bug (#4511)
     ggplot2::scale_fill_manual(
       values = c(
diff --git a/R/sir.R b/R/sir.R
index d264514f..78688c1f 100755
--- a/R/sir.R
+++ b/R/sir.R
@@ -907,15 +907,15 @@ as_sir_method <- function(method_short,
   same_ab <- generalise_antibiotic_name(ab) == generalise_antibiotic_name(agent_name)
   same_ab.bak <- generalise_antibiotic_name(ab.bak) == generalise_antibiotic_name(agent_name)
   agent_formatted[same_ab.bak] <- paste0(agent_formatted[same_ab.bak], " (", ab, ")")
-  agent_formatted[same_ab.bak & !same_ab] <- paste0(agent_formatted[same_ab.bak & !same_ab], 
-                                                    " (", ifelse(ab.bak[same_ab.bak & !same_ab] == ab[same_ab.bak & !same_ab],
+  agent_formatted[!same_ab.bak & !same_ab] <- paste0(agent_formatted[!same_ab.bak & !same_ab],
+                                                    " (", ifelse(ab.bak[!same_ab.bak & !same_ab] == ab[!same_ab.bak & !same_ab],
                                                                  "",
-                                                                 paste0(ab[same_ab.bak & !same_ab], ", ")),
-                                                    agent_name[same_ab.bak & !same_ab],
+                                                                 paste0(ab[!same_ab.bak & !same_ab], ", ")),
+                                                    agent_name[!same_ab.bak & !same_ab],
                                                     ")")
-  # this intro text will also be printed in the progress bar in the `progress` package is installed
+  # this intro text will also be printed in the progress bar if the `progress` package is installed
   intro_txt <- paste0("Interpreting ", method_long, ": ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
-                      ifelse(length(agent_formatted) == 1, agent_formatted, ""),
+                      ifelse(length(unique(agent_formatted)) == 1, unique(agent_formatted), vector_and(ab, quotes = FALSE)),
                       mo_var_found,
                       ifelse(identical(reference_data, AMR::clinical_breakpoints),
                              paste0(", ", font_bold(guideline_coerced)),