From d9e66fb118a7927ad644b3a3e37409ec07c487e9 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Mon, 17 Jun 2024 14:52:18 +0200
Subject: [PATCH] (v2.1.1.9056) example fix

---
 DESCRIPTION                                |  2 +-
 NEWS.md                                    |  2 +-
 R/sir.R                                    | 12 ++++++------
 inst/tinytest/test-custom_microorganisms.R | 11 +++++++----
 man/as.sir.Rd                              | 12 ++++++------
 5 files changed, 21 insertions(+), 18 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e39714dc..033a8b86 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9055
+Version: 2.1.1.9056
 Date: 2024-06-17
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 45403b32..ce5b37db 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9055
+# AMR 2.1.1.9056
 
 *(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! Install this beta using [the instructions here](https://msberends.github.io/AMR/#latest-development-version).)*
 
diff --git a/R/sir.R b/R/sir.R
index 168ccff8..fd8a8638 100755
--- a/R/sir.R
+++ b/R/sir.R
@@ -199,13 +199,13 @@
 #'                                      ab = "antibiotic",
 #'                                      guideline = "CLSI")))
 #'   df_long %>%
-#'     # given certain columns, e.g. from AMP to TOB
-#'     mutate_at(vars(AMP:TOB), as.sir,
+#'     # given certain columns, e.g. from 'cipro' to 'genta'
+#'     mutate_at(vars(cipro:genta), as.sir,
 #'               mo = "bacteria",
 #'               ab = "antibiotic",
 #'               guideline = "CLSI")
 #'   df_long %>%
-#'     mutate(across(AMP:TOB,
+#'     mutate(across(cipro:genta,
 #'                        function(x) as.sir(x,
 #'                                           mo = "bacteria",
 #'                                           ab = "antibiotic",
@@ -229,13 +229,13 @@
 #'                                      guideline = "CLSI")))
 #'   df_long %>%
 #'     # given certain columns, e.g. from AMP to TOB
-#'     mutate_at(vars(AMP:TOB), as.sir,
+#'     mutate_at(vars(cipro:genta), as.sir,
 #'               mo = "bacteria",
 #'               ab = "antibiotic",
 #'               host = "animal_species",
 #'               guideline = "CLSI")
 #'   df_long %>%
-#'     mutate(across(AMP:TOB,
+#'     mutate(across(cipro:genta,
 #'                        function(x) as.sir(x,
 #'                                           mo = "bacteria",
 #'                                           ab = "antibiotic",
@@ -254,7 +254,7 @@
 #'     as.sir() # automatically determines urine isolates
 #'
 #'   df_wide %>%
-#'     mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
+#'     mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE)
 #' }
 #'
 #'
diff --git a/inst/tinytest/test-custom_microorganisms.R b/inst/tinytest/test-custom_microorganisms.R
index f7c45b77..040e3cb9 100644
--- a/inst/tinytest/test-custom_microorganisms.R
+++ b/inst/tinytest/test-custom_microorganisms.R
@@ -42,7 +42,10 @@ expect_identical(as.character(as.mo("ENT_ASB_CLO")), "ENT_ASB_CLO")
 expect_identical(mo_name("ENT_ASB_CLO"), "Enterobacter asburiae/cloacae")
 expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")
 
-expect_identical(paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
-                 as.character(as.mo("Klebsiella pneumoniae")))
-expect_identical(paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
-                 as.character(as.mo("Aerococcus urinae")))
+if (getRversion() >= "3.3.0") {
+  # until R 3.2, abbreviate() used a completely different algorithm, making these tests unreproducible
+  expect_identical(paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
+                   as.character(as.mo("Klebsiella pneumoniae")))
+  expect_identical(paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
+                   as.character(as.mo("Aerococcus urinae")))
+}
diff --git a/man/as.sir.Rd b/man/as.sir.Rd
index e72953b7..bd10d5d3 100644
--- a/man/as.sir.Rd
+++ b/man/as.sir.Rd
@@ -296,13 +296,13 @@ if (require("dplyr")) {
                                      ab = "antibiotic",
                                      guideline = "CLSI")))
   df_long \%>\%
-    # given certain columns, e.g. from AMP to TOB
-    mutate_at(vars(AMP:TOB), as.sir,
+    # given certain columns, e.g. from 'cipro' to 'genta'
+    mutate_at(vars(cipro:genta), as.sir,
               mo = "bacteria",
               ab = "antibiotic",
               guideline = "CLSI")
   df_long \%>\%
-    mutate(across(AMP:TOB,
+    mutate(across(cipro:genta,
                        function(x) as.sir(x,
                                           mo = "bacteria",
                                           ab = "antibiotic",
@@ -326,13 +326,13 @@ if (require("dplyr")) {
                                      guideline = "CLSI")))
   df_long \%>\%
     # given certain columns, e.g. from AMP to TOB
-    mutate_at(vars(AMP:TOB), as.sir,
+    mutate_at(vars(cipro:genta), as.sir,
               mo = "bacteria",
               ab = "antibiotic",
               host = "animal_species",
               guideline = "CLSI")
   df_long \%>\%
-    mutate(across(AMP:TOB,
+    mutate(across(cipro:genta,
                        function(x) as.sir(x,
                                           mo = "bacteria",
                                           ab = "antibiotic",
@@ -351,7 +351,7 @@ if (require("dplyr")) {
     as.sir() # automatically determines urine isolates
 
   df_wide \%>\%
-    mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
+    mutate_at(vars(cipro:genta), as.sir, mo = "E. coli", uti = TRUE)
 }