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(v2.1.1.9073) unit tests

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dr. M.S. (Matthijs) Berends
2024-09-19 13:57:36 +02:00
parent ef8ef28650
commit 4e96a56b6a
5 changed files with 16 additions and 26 deletions
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2
inst/tinytest/test-mo_property.R
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@ -97,7 +97,7 @@ expect_equal(names(mo_info("Escherichia coli")), c(
"mo",
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"status", "synonyms", "gramstain", "oxygen_tolerance",
"url", "ref", "snomed", "lpsn", "gbif", "group_members"
"url", "ref", "snomed", "lpsn", "mycobank", "gbif", "group_members"
))
expect_inherits(mo_info(c("Escherichia coli", "Staphylococcus aureus")), "list")
expect_true(length(mo_group_members("B_HACEK")) > 1)

13
inst/tinytest/test-sir.R
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@ -312,14 +312,14 @@ vet <- data.frame(animal = c(rep("cat", 3), rep("dogs", 3), "canine", "equine",
FLR = mics,
mo = mo_name(rep(c("B_ESCHR_COLI", "B_PSTRL_MLTC", "B_MNNHM_HMLY"), 4)[-1]))
out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI")
out_vet <- as.sir(vet, host = vet$animal, guideline = "CLSI 2023")
# host column name instead of values
expect_identical(out_vet,
as.sir(vet, host = "animal", guideline = "CLSI 2023"))
# check outcomes
expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", "R", NA, "R", "R", NA, "R", "R", NA)))
expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA, "R", "R")))
expect_identical(out_vet$PRA, as.sir(c("S", NA, "S", NA, NA, "R", NA, NA, NA, "I", NA)))
expect_identical(out_vet$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$PRA, rep(NA_sir_, 11))
@ -327,9 +327,10 @@ expect_identical(out_vet$FLR, as.sir(c("S", "S", NA, "S", "S", NA, "I", "R", NA,
sir_history <- sir_interpretation_history()
expect_identical(sort(sir_history$host),
c("cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cats", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle",
"cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "cattle", "dogs",
"dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "dogs", "horse", "horse", "horse", "horse", "horse", "poultry","poultry"))
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"))
# ECOFF -------------------------------------------------------------------