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(v2.1.1.9195) add BTL-S, fix ranks in unknown microorganisms

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-13 14:30:14 +01:00
parent a7ef22a21e
commit 9aab129ea6
48 changed files with 1789 additions and 1710 deletions
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9
tests/testthat/test-data.R
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@ -49,6 +49,15 @@ test_that("data works", {
expect_false(anyNA(microorganisms.codes$mo))
expect_true(all(dosage$ab %in% AMR::antimicrobials$ab))
expect_true(all(dosage$name %in% AMR::antimicrobials$name))
eucast_abx <- AMR:::EUCAST_RULES_DF$and_these_antibiotics
eucast_abx <- unique(unlist(strsplit(eucast_abx[!is.na(eucast_abx)], ", +")))
expect_true(all(eucast_abx %in% AMR::antimicrobials$ab),
info = paste0(
"Missing in `antimicrobials` data set: ",
toString(eucast_abx[which(!eucast_abx %in% AMR::antimicrobials$ab)])
)
)
# check valid disks/MICs
expect_false(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_S", drop = TRUE])))
expect_true(anyNA(as.mic(clinical_breakpoints[which(clinical_breakpoints$method == "MIC" & clinical_breakpoints$ref_tbl != "ECOFF"), "breakpoint_R", drop = TRUE])))

3
tests/testthat/test-sir.R
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@ -124,6 +124,9 @@ test_that("sir works", {
# Human -------------------------------------------------------------------
# these are used in the script
expect_true(all(c("B_GRAMN", "B_GRAMP", "B_ANAER-NEG", "B_ANAER-POS", "B_ANAER") %in% AMR::microorganisms$mo))
mics <- as.mic(2^c(-4:6)) # 0.0625 to 64 in factors of 2
expect_identical(
as.character(as.sir(mics,