mirror of https://github.com/msberends/AMR.git
50 lines
1.4 KiB
R
50 lines
1.4 KiB
R
context("guess_bactid.R")
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test_that("guess_bactid works", {
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expect_identical(
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guess_bactid(c("E. coli", "H. influenzae")),
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c("ESCCOL", "HAEINF"))
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expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
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expect_equal(guess_bactid("P. aer"), "PSEAER") # not Pasteurella aerogenes
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expect_equal(guess_bactid("Negative rods"), "GNR")
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expect_equal(guess_bactid("MRSE"), "STAEPI")
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expect_equal(guess_bactid("VRE"), "ENC")
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expect_equal(guess_bactid("MRPA"), "PSEAER")
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expect_equal(guess_bactid("PISP"), "STCPNE")
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expect_equal(guess_bactid("PRSP"), "STCPNE")
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expect_equal(guess_bactid("VISP"), "STCPNE")
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expect_equal(guess_bactid("VRSP"), "STCPNE")
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expect_identical(
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guess_bactid(c("stau",
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"STAU",
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"staaur",
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"S. aureus",
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"S aureus",
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"Staphylococcus aureus",
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"MRSA",
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"VISA")),
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rep("STAAUR", 8))
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# select with one column
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expect_identical(
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septic_patients[1:10,] %>%
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left_join_microorganisms() %>%
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select(genus) %>%
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guess_bactid(),
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c("STC", "STC", "NEI", "STA", "STA",
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"NEI", "ENT", "ENT", "ESC", "KLE"))
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# select with two columns
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expect_identical(
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septic_patients[1:10,] %>%
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pull(bactid),
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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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guess_bactid())
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})
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