P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-04-04 02:56:00 +02:00
Code Releases Activity

(v3.0.1.9043) fix unit test

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-04-02 12:24:12 +02:00
parent 26613d774b
commit 225493192c
3 changed files with 5 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
DESCRIPTION
View File

@@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 3.0.1.9042 Version: 3.0.1.9043
Date: 2026-04-02 Date: 2026-04-02
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)

2
NEWS.md
View File

@@ -1,4 +1,4 @@
# AMR 3.0.1.9042 # AMR 3.0.1.9043
### New ### New
* Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations. * Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the `clinical_breakpoints` data set for usage in `as.sir()`. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.

6
tests/testthat/test-eucast_rules.R
View File

@@ -32,15 +32,15 @@ test_that("test-eucast_rules.R", {
# thoroughly check input table # thoroughly check input table
expect_equal( expect_equal(
colnames(AMR:::EUCAST_RULES_DF), sort(colnames(AMR:::EUCAST_RULES_DF)),
c( sort(c(
"if_mo_property", "like.is.one_of", "this_value", "if_mo_property", "like.is.one_of", "this_value",
"and_these_antibiotics", "have_these_values", "and_these_antibiotics", "have_these_values",
"then_change_these_antibiotics", "to_value", "then_change_these_antibiotics", "to_value",
"reference.rule", "reference.rule_group", "reference.rule", "reference.rule_group",
"reference.version", "reference.version",
"note" "note"
) ))
) )
MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value) MOs_mentioned <- unique(AMR:::EUCAST_RULES_DF$this_value)
MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE)))) MOs_mentioned <- sort(trimws(unlist(strsplit(MOs_mentioned[!AMR:::is_valid_regex(MOs_mentioned)], ",", fixed = TRUE))))