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(v3.0.1.9004) Revamp as.sir() interpretation for capped MICs

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Fixes #243
Fixes #244
This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-12-15 13:18:13 +01:00
parent ba30b08f76
commit 225c73f7e7
7 changed files with 191 additions and 108 deletions
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11
tests/testthat/test-sir.R
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@@ -391,6 +391,17 @@ test_that("test-sir.R", {
expect_warning(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE))
# Capped MIC handling ---------------------------------------------------
out1 <- 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 = "none")
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")))
# Parallel computing ----------------------------------------------------
# MB 29 Apr 2025: I have run the code of AVC, PEI, Canada (dataset of 2854x65), and compared it like this: