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(v2.1.1.9196) fix eucast, unit tests

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dr. M.S. (Matthijs) Berends
2025-03-13 15:38:39 +01:00
parent 9aab129ea6
commit 861331b1df
25 changed files with 114 additions and 97 deletions
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15
tests/testthat/test-sir.R
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@ -350,28 +350,29 @@ test_that("sir works", {
)
out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
# host column name instead of values
# give host column name instead of values
expect_identical(
out_vet,
as.sir(vet, host = "animal", guideline = "CLSI 2023")
)
# check outcomes
expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "R", NA)))
expect_identical(out_vet$FLR, as.sir(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "R", NA)))
out_vet <- as.sir(vet, host = "animal", guideline = "EUCAST 2023")
expect_identical(out_vet$PRA, rep(NA_sir_, 11))
expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
# expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
expect_identical(out_vet$FLR, as.sir(c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "R", NA)))
sir_history <- sir_interpretation_history()
expect_identical(
sort(sir_history$host),
c(
"cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats",
"cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
"horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "poultry", "poultry", "poultry", "poultry"
"cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cattle",
"cattle", "cattle", "cattle", "cattle", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs",
"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "horse", "horse", "horse", "horse", "horse", "horse", "horse", "horse",
"horse", "horse", "poultry", "poultry", "poultry", "poultry", "poultry"
)
)