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(v0.7.1.9102) lintr
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@ -94,7 +94,7 @@ test_that("as.mo works", {
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rep("B_STPHY_AURS", 9))
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expect_identical(
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as.character(
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as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC', 'UPEC'))),
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as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))),
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rep("B_ESCHR_COLI", 6))
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# unprevalent MO
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expect_identical(
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@ -114,13 +114,13 @@ test_that("as.mo works", {
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c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
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# check for Becker classification
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expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
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expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
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expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
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expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
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expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
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# aureus must only be influenced if Becker = "all"
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expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
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expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
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@ -150,7 +150,7 @@ test_that("as.mo works", {
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# select with one column
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expect_identical(
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example_isolates[1:10,] %>%
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example_isolates[1:10, ] %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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as.mo() %>%
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@ -160,9 +160,9 @@ test_that("as.mo works", {
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# select with two columns
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expect_identical(
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example_isolates[1:10,] %>%
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example_isolates[1:10, ] %>%
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pull(mo),
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example_isolates[1:10,] %>%
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example_isolates[1:10, ] %>%
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left_join_microorganisms() %>%
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select(genus, species) %>%
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as.mo())
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@ -260,10 +260,6 @@ test_that("as.mo works", {
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expect_null(mo_failures())
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expect_true(example_isolates %>% pull(mo) %>% is.mo())
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# expect_equal(get_mo_code("test", "mo"), "test")
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# expect_equal(length(get_mo_code("Escherichia", "genus")),
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# nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
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expect_error(translate_allow_uncertain(5))
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# very old MO codes (<= v0.5.0)
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