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interpretation fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2023-07-11 09:50:45 +02:00
parent 5e1221bceb
commit 8df1cd8d97
10 changed files with 63 additions and 28 deletions
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2
inst/tinytest/test-data.R
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@ -38,6 +38,8 @@ expect_identical(class(antibiotics$ab), c("ab", "character"))
# check cross table reference
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
expect_true(all(example_isolates$mo %in% microorganisms$mo))
expect_true(all(microorganisms.groups$mo %in% microorganisms$mo))
expect_true(all(microorganisms.groups$mo_group %in% microorganisms$mo))
expect_true(all(clinical_breakpoints$mo %in% microorganisms$mo))
expect_true(all(clinical_breakpoints$ab %in% antibiotics$ab))
expect_true(all(intrinsic_resistant$mo %in% microorganisms$mo))

12
inst/tinytest/test-sir.R
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@ -108,6 +108,18 @@ if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir_))
mics <- as.mic(2 ^ c(-2:5)) # 0.25 to 32 in factors of 2
expect_identical(as.character(as.sir(mics, mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
uti = FALSE, include_PKPD = FALSE)),
c("S", "S", "S", "S", "S", "S", "R", "R"))
expect_identical(as.character(as.sir(mics, mo = "Enterobacterales", ab = "AMC", guideline = "EUCAST 2022",
uti = TRUE, include_PKPD = FALSE)),
c("S", "S", "S", "S", "S", "S", "S", "S"))
expect_identical(as.character(as.sir(mics, mo = "Escherichia coli", ab = "AMC", guideline = "EUCAST 2022",
uti = FALSE, include_PKPD = FALSE)),
c("S", "S", "S", "S", "S", "S", "R", "R"))
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
expect_equal(suppressMessages(
as.character(