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(v3.0.1.9020) unit test fixes

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dr. M.S. (Matthijs) Berends
2026-02-09 13:16:36 +01:00
parent ba4c159154
commit 499c830ee7
9 changed files with 42 additions and 30 deletions
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20
tests/testthat/test-sir.R
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@@ -354,11 +354,11 @@ test_that("test-sir.R", {
mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1])
)
out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
out_vet <- suppressWarnings(as.sir(vet, host = vet$animal, guideline = "CLSI 2023"))
# give host column name instead of values
expect_identical(
out_vet,
as.sir(vet, host = "animal", guideline = "CLSI 2023")
suppressWarnings(as.sir(vet, host = "animal", guideline = "CLSI 2023"))
)
# check outcomes
@@ -384,8 +384,12 @@ test_that("test-sir.R", {
# ECOFF -----------------------------------------------------------------
expect_equal(
suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF")),
as.sir("S")
suppressMessages(as.sir(as.mic(c(2, 32)), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF")),
as.sir(c("WT", "NWT")) # since ECOFF returns WT/NWT at default
)
expect_equal(
suppressMessages(as.sir(as.mic(c(2, 32)), "E. coli", "ampicillin", guideline = "EUCAST 2020", breakpoint_type = "ECOFF", as_wt_nwt = FALSE)),
as.sir(c("S", "R"))
)
# old method
expect_warning(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE))
@@ -397,10 +401,10 @@ test_that("test-sir.R", {
out2 <- as.sir(as.mic(c("0.125", "<0.125", ">0.125")), mo = "E. coli", ab = "Cipro", guideline = "EUCAST 2025", breakpoint_type = "ECOFF", capped_mic_handling = "conservative")
out3 <- as.sir(as.mic(c("0.125", "<0.125", ">0.125")), mo = "E. coli", ab = "Cipro", guideline = "EUCAST 2025", breakpoint_type = "ECOFF", capped_mic_handling = "standard")
out4 <- as.sir(as.mic(c("0.125", "<0.125", ">0.125")), mo = "E. coli", ab = "Cipro", guideline = "EUCAST 2025", breakpoint_type = "ECOFF", capped_mic_handling = "lenient")
expect_equal(out1, as.sir(c("R", "R", "R")))
expect_equal(out2, as.sir(c("R", "NI", "R")))
expect_equal(out3, as.sir(c("R", "S", "R")))
expect_equal(out4, as.sir(c("R", "S", "R")))
expect_equal(out1, as.sir(c("NWT", "NWT", "NWT")))
expect_equal(out2, as.sir(c("NWT", "NI", "NWT")))
expect_equal(out3, as.sir(c("NWT", "WT", "NWT")))
expect_equal(out4, as.sir(c("NWT", "WT", "NWT")))
# Parallel computing ----------------------------------------------------