From e9e3de44698ca61b8fcc05f7ca6b275734cbb8f0 Mon Sep 17 00:00:00 2001
From: Nick Thomson <iglu.sitar@gmail.com>
Date: Thu, 17 Jul 2025 23:15:52 +0800
Subject: [PATCH] (v3.0.0.9009) fix as.sir when uti = FALSE

---
 DESCRIPTION |  2 +-
 NEWS.md     |  3 ++-
 R/sir.R     | 33 +++++++++++++++------------------
 3 files changed, 18 insertions(+), 20 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index cd143d099..92338a8c8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 3.0.0.9008
+Version: 3.0.0.9009
 Date: 2025-07-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 328620710..d9b5cbf59 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 3.0.0.9008
+# AMR 3.0.0.9009
 
 This is primarily a bugfix release, though we added one nice feature too.
 
@@ -13,6 +13,7 @@ This is primarily a bugfix release, though we added one nice feature too.
 * Fixed a bug in `as.ab()` for antimicrobial codes with a number in it if they are preceded by a space
 * Fixed a bug in `eucast_rules()` for using specific custom rules
 * Fixed a bug in `as.sir()` to allow any tidyselect language (#220)
+* Fixed a bug in `as.sir()` to pick right breakpoint when `uti = FALSE` (#216)
 * Fixed a bug in `ggplot_sir()` when using `combine_SI = FALSE` (#213)
 * Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent)
 * Fixed some specific Dutch translations for antimicrobials
diff --git a/R/sir.R b/R/sir.R
index 5ed895d46..2cff56159 100755
--- a/R/sir.R
+++ b/R/sir.R
@@ -1656,26 +1656,23 @@ as_sir_method <- function(method_short,
       next
     }
 
-    # sort on host and taxonomic rank
-    # (this will e.g. prefer 'species' breakpoints over 'order' breakpoints)
-    if (is.na(uti_current)) {
-      breakpoints_current <- breakpoints_current %pm>%
-        #  `uti` is a column in the data set
-        # this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE
-        pm_mutate(uti_index = ifelse(!is.na(uti) & uti == FALSE, 1,
-          ifelse(is.na(uti), 2,
-            3
-          )
-        )) %pm>%
-        # be as specific as possible (i.e. prefer species over genus):
-        pm_arrange(rank_index, uti_index)
-    } else if (uti_current == TRUE) {
-      breakpoints_current <- breakpoints_current %pm>%
-        subset(uti == TRUE) %pm>%
-        # be as specific as possible (i.e. prefer species over genus):
-        pm_arrange(rank_index)
+    # if the user explicitly set uti, keep only those rows
+    if (!is.na(uti_current)) {
+      breakpoints_current <- breakpoints_current[breakpoints_current$uti == uti_current, , drop = FALSE]
     }
 
+    # build a helper factor so FALSE < NA < TRUE
+    uti_index <- factor(
+      ifelse(is.na(breakpoints_current$uti), "NA",
+        as.character(breakpoints_current$uti)
+      ),
+      levels = c("FALSE", "NA", "TRUE")
+    )
+
+    # sort on host and taxonomic rank first, then by UTI
+    # (this will e.g. prefer 'species' breakpoints over 'order' breakpoints)
+    breakpoints_current <- breakpoints_current[order(breakpoints_current$rank_index, uti_index), , drop = FALSE]
+
     # throw messages for different body sites
     site <- breakpoints_current[1L, "site", drop = FALSE] # this is the one we'll take
     if (is.na(site)) {