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Merge branch 'premaster'
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@ -159,8 +159,7 @@ test_that("as.mo works", {
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septic_patients[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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as.character())
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as.mo())
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# unknown results
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expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
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@ -198,8 +197,8 @@ test_that("as.mo works", {
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print(mo_renamed())
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# check uncertain names
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expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
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expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
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expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AUR")
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expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
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expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
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expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
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expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
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@ -271,7 +270,7 @@ test_that("as.mo works", {
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expect_equal(as.character(as.mo("F_CANDD_GLB")), "F_CANDD_GLA")
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# debug mode
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expect_warning(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3))
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expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
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# ..coccus
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expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),
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