From 9e64d7708edf9eeb8ed8b657802b3615cd2e9569 Mon Sep 17 00:00:00 2001
From: Matthijs Berends <m.s.berends@umcg.nl>
Date: Sun, 20 Apr 2025 15:27:36 +0200
Subject: [PATCH] (v2.1.1.9248) unit test fix

---
 .github/workflows/check-current-testthat.yaml |   2 +-
 DESCRIPTION                                   |   2 +-
 NEWS.md                                       |   2 +-
 R/sir.R                                       |   7 +------
 data-raw/datasets/microorganisms.codes.dta    | Bin 133473 -> 133473 bytes
 .../datasets/microorganisms.codes.feather     | Bin 88882 -> 88882 bytes
 .../datasets/microorganisms.codes.parquet     | Bin 60219 -> 60215 bytes
 data-raw/datasets/microorganisms.codes.rds    | Bin 23464 -> 23464 bytes
 data-raw/datasets/microorganisms.codes.sav    | Bin 151215 -> 151215 bytes
 data-raw/datasets/microorganisms.codes.txt    |   2 +-
 data-raw/datasets/microorganisms.codes.xlsx   | Bin 85664 -> 85660 bytes
 data-raw/microorganisms.codes.md5             |   2 +-
 data/microorganisms.codes.rda                 | Bin 23496 -> 23496 bytes
 man/as.sir.Rd                                 |   9 +--------
 14 files changed, 7 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/check-current-testthat.yaml b/.github/workflows/check-current-testthat.yaml
index 961b79e9d..d59035888 100644
--- a/.github/workflows/check-current-testthat.yaml
+++ b/.github/workflows/check-current-testthat.yaml
@@ -53,7 +53,7 @@ jobs:
       matrix:
         config:
           # current development version, check all major OSes:
-          - {os: macOS-latest,   r: 'devel', allowfail: true}
+          # - {os: macOS-latest,   r: 'devel', allowfail: true}
           - {os: windows-latest, r: 'devel', allowfail: false}
           - {os: ubuntu-latest,  r: 'devel', allowfail: false, http-user-agent: 'release'}
 
diff --git a/DESCRIPTION b/DESCRIPTION
index ff9a90a06..b7ce75421 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: AMR
-Version: 2.1.1.9247
+Version: 2.1.1.9248
 Date: 2025-04-20
 Title: Antimicrobial Resistance Data Analysis
 Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index c649b1809..000032ca6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 2.1.1.9247
+# AMR 2.1.1.9248
 
 *(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://amr-for-r.org/#get-this-package).)*
 
diff --git a/R/sir.R b/R/sir.R
index 96136cea1..ad53151c9 100755
--- a/R/sir.R
+++ b/R/sir.R
@@ -31,12 +31,7 @@
 #'
 #' @description Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. [as.sir()] transforms the input to a new class [`sir`], which is an ordered [factor] containing the levels `S`, `SDD`, `I`, `R`, `NI`.
 #'
-#' These breakpoints are currently implemented:
-#' - For **clinical microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "human")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "human")$guideline)))`;
-#' - For **veterinary microbiology**: EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "animal")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "animal")$guideline)))`;
-#' - For **ECOFFs** (Epidemiological Cut-off Values): EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST" & type == "ECOFF")$guideline)))` and CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI" & type == "ECOFF")$guideline)))`.
-#'
-#' All breakpoints used for interpretation are available in our [clinical_breakpoints] data set.
+#' Breakpoints are currently implemented from EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, guideline %like% "CLSI")$guideline)))`), see *Details*. All breakpoints used for interpretation are available in our [clinical_breakpoints] data set.
 #' @rdname as.sir
 #' @param x Vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres).
 #' @param mo A vector (or column name) with [character]s that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically.
diff --git a/data-raw/datasets/microorganisms.codes.dta b/data-raw/datasets/microorganisms.codes.dta
index c10d4be5b7e6ac92eab3e1b0b9a591d465efc33d..12838b122616f7d3425b9a66fee506d84e914229 100644
GIT binary patch
delta 30
mcmaDjiR0lUjtQ+SrdCGgjh$ON8JGW=e2iUSyTe~bMIHdkmkeeA

delta 37
tcmaDjiR0lUjtQ+SMpmY#jh$ON8JGXz3UhaMc8(AB@%7to^_Nkd2LK(t4gCNB

diff --git a/data-raw/datasets/microorganisms.codes.feather b/data-raw/datasets/microorganisms.codes.feather
index ee5dfd6ef41a356550aa00c620e763f9c6626e8e..6d0427cdafdfdad2b53d6fd6a21c791d985d85a8 100644
GIT binary patch
delta 36
scmdnAjdjyD)`l&N+Ton6cNv&0I2m4XZ8r&LOk-q<5!yZ{f^ixX0N_Fk5&!@I

delta 36
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diff --git a/data-raw/datasets/microorganisms.codes.parquet b/data-raw/datasets/microorganisms.codes.parquet
index c082c3cfb14bc605b4d16de8ebee85f81f7fa9e3..b11391142e2ee2cfa712964b12e539b4b97cbb3a 100644
GIT binary patch
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diff --git a/data-raw/datasets/microorganisms.codes.rds b/data-raw/datasets/microorganisms.codes.rds
index f89de6fdce1f0b3786379f01deedc5e4319bad47..269f37ce24e014d91550ed8cb5b22f896948df24 100644
GIT binary patch
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delta 439
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diff --git a/data-raw/datasets/microorganisms.codes.sav b/data-raw/datasets/microorganisms.codes.sav
index 0af49e517cd90fe528673d4794074888a2c49ca0..4bbe35c79b78c73b1fcbda7405aba772a25bbab4 100644
GIT binary patch
delta 42
ycmZ2KmvjAG&IxJkrdCGgR>qbS3vDJgur#i1UCX$2EmMob<cCaR+ua?RGI#+|E)PTi

delta 49
zcmZ2KmvjAG&IxJkMpmY#R>qbS3vDJgur#i1UCX$2EmMmFSD3rAvvYi~kFVc$Ye%LM
FUI4jh5WfHb

diff --git a/data-raw/datasets/microorganisms.codes.txt b/data-raw/datasets/microorganisms.codes.txt
index 1bafd8a27..68cb37cab 100644
--- a/data-raw/datasets/microorganisms.codes.txt
+++ b/data-raw/datasets/microorganisms.codes.txt
@@ -4944,7 +4944,7 @@
 "VFL"	"B_VIBRI_FLVL"
 "VFU"	"B_VIBRI_FRNS"
 "VGC"	"B_VGCCC"
-"VGS"	"B_VGCCC_SLMN"
+"VGS"	"B_STRPT_VIRI"
 "VHI"	"B_VIBRI_CHLR"
 "VHO"	"B_GRMNT_HLLS"
 "VI-"	"B_VIBRI"
diff --git a/data-raw/datasets/microorganisms.codes.xlsx b/data-raw/datasets/microorganisms.codes.xlsx
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diff --git a/data-raw/microorganisms.codes.md5 b/data-raw/microorganisms.codes.md5
index e3fe15bdd..7a5e1fddb 100644
--- a/data-raw/microorganisms.codes.md5
+++ b/data-raw/microorganisms.codes.md5
@@ -1 +1 @@
-4862699a91a23f2fe6a790ac277697d0
+85b172c713e3e5aed32dc760c337ec34
diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda
index 8d2c1e57702550b205e1326ad85322f5d16848fb..41242ae3ac6c4a0783821e21435e7f5048b6692a 100644
GIT binary patch
delta 440
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delta 440
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diff --git a/man/as.sir.Rd b/man/as.sir.Rd
index dc1806752..337ca60f5 100644
--- a/man/as.sir.Rd
+++ b/man/as.sir.Rd
@@ -144,14 +144,7 @@ Ordered \link{factor} with new class \code{sir}
 \description{
 Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. \code{\link[=as.sir]{as.sir()}} transforms the input to a new class \code{\link{sir}}, which is an ordered \link{factor} containing the levels \code{S}, \code{SDD}, \code{I}, \code{R}, \code{NI}.
 
-These breakpoints are currently implemented:
-\itemize{
-\item For \strong{clinical microbiology}: EUCAST 2011-2025 and CLSI 2011-2025;
-\item For \strong{veterinary microbiology}: EUCAST 2021-2025 and CLSI 2019-2025;
-\item For \strong{ECOFFs} (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
-}
-
-All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
+Breakpoints are currently implemented from EUCAST (2011-2025) and CLSI (2011-2025), see \emph{Details}. All breakpoints used for interpretation are available in our \link{clinical_breakpoints} data set.
 }
 \details{
 \emph{Note: The clinical breakpoints in this package were validated through, and imported from, \href{https://whonet.org}{WHONET}. The public use of this \code{AMR} package has been endorsed by both CLSI and EUCAST. See \link{clinical_breakpoints} for more information.}