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(v2.1.1.9257) adjust unit tests

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dr. M.S. (Matthijs) Berends 2025-04-27 09:58:19 +02:00
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4 changed files with 10 additions and 13 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 2.1.1.9256 Version: 2.1.1.9257
Date: 2025-04-26 Date: 2025-04-27
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)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9256 # AMR 2.1.1.9257
*(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).)* *(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).)*

7
tests/testthat/test-antibiogram.R
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@ -53,7 +53,7 @@ test_that("test-antibiogram.R", {
expect_inherits(ab2, "antibiogram") expect_inherits(ab2, "antibiogram")
expect_inherits(ab3, "antibiogram") expect_inherits(ab3, "antibiogram")
expect_equal(colnames(ab1), c("Pathogen", "Amikacin", "Gentamicin", "Imipenem", "Kanamycin", "Meropenem", "Tobramycin")) expect_equal(colnames(ab1), c("Pathogen", "Amikacin", "Gentamicin", "Imipenem", "Kanamycin", "Meropenem", "Tobramycin"))
expect_equal(colnames(ab2), c("Pathogen (N min-max)", "J01GB01", "J01GB03", "J01GB04", "J01GB06")) expect_equal(colnames(ab2), c("Pathogen", "J01GB01", "J01GB03", "J01GB04", "J01GB06"))
expect_equal(colnames(ab3), c("Pathogen", "IPM", "MEM")) expect_equal(colnames(ab3), c("Pathogen", "IPM", "MEM"))
expect_equal(ab3$MEM, c(52, NA, 100, 100, NA)) expect_equal(ab3$MEM, c(52, NA, 100, 100, NA))
@ -96,14 +96,13 @@ test_that("test-antibiogram.R", {
syndromic_group = ifelse(ex1$ward == "ICU", syndromic_group = ifelse(ex1$ward == "ICU",
"IC", "Geen IC" "IC", "Geen IC"
), ),
language = "nl", language = "nl"
add_total_n = TRUE
) )
expect_inherits(ab6, "antibiogram") expect_inherits(ab6, "antibiogram")
expect_inherits(ab7, "antibiogram") expect_inherits(ab7, "antibiogram")
expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB")) expect_equal(colnames(ab6), c("Syndromic Group", "Pathogen", "AMK", "GEN", "IPM", "KAN", "MEM", "TOB"))
expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen (N min-max)", "Amikacine", "Gentamicine", "Tobramycine")) expect_equal(colnames(ab7), c("Syndroomgroep", "Pathogeen", "Amikacine", "Gentamicine", "Tobramycine"))
# Weighted-incidence syndromic combination antibiogram (WISCA) --------- # Weighted-incidence syndromic combination antibiogram (WISCA) ---------

10
tests/testthat/test-sir.R
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@ -325,15 +325,13 @@ test_that("test-sir.R", {
expect_message(as.sir(data.frame( expect_message(as.sir(data.frame(
mo = "E. coli", mo = "E. coli",
NIT = c("<= 2", 32), NIT = c("<= 2", 32),
uti = TRUE, uti = TRUE
info = TRUE ), info = TRUE))
)))
expect_message(as.sir(data.frame( expect_message(as.sir(data.frame(
mo = "E. coli", mo = "E. coli",
NIT = c("<= 2", 32), NIT = c("<= 2", 32),
specimen = c("urine", "blood"), specimen = c("urine", "blood")
info = TRUE ), info = TRUE))
)))
# SDD vs I in CLSI 2024 # SDD vs I in CLSI 2024
expect_identical( expect_identical(