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(v1.7.1.9063) not_intrinsic_resistant

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-12-09 10:48:25 +01:00
parent e63defe324
commit e18c49ed93
32 changed files with 275 additions and 185 deletions
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1
inst/tinytest/test-ab_property.R
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@ -69,6 +69,7 @@ expect_identical(colnames(set_ab_names(example_isolates[, 20:25], language = "nl
c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine"))
expect_identical(colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_identical(example_isolates %>% set_ab_names(),
example_isolates %>% rename_with(set_ab_names))

11
inst/tinytest/test-ab_class_selectors.R → inst/tinytest/test-ab_selectors.R
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@ -76,6 +76,17 @@ expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
x <- data.frame(x = 0,
mo = 0,
gen = "S",
genta = "S",
J01GB03 = "S",
tobra = "S",
Tobracin = "S")
# should have the first hits
expect_identical(colnames(x[, aminoglycosides()]),
c("gen", "tobra"))
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
expect_equal(example_isolates %>% select(administrable_per_os() & penicillins()) %>% ncol(), 5, tolerance = 0.5)
expect_equal(example_isolates %>% select(administrable_iv() & penicillins()) %>% ncol(), 7, tolerance = 0.5)

2
inst/tinytest/test-mo_property.R
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@ -92,6 +92,8 @@ expect_identical(mo_property("Escherichia coli", property = "genus"),
mo_genus("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "species"),
mo_species("Escherichia coli"))
expect_identical(mo_property("Escherichia coli", property = "species_id"),
mo_lpsn("Escherichia coli"))
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")