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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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66
tests/testthat/test-guess_ab_col.R
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@ -27,36 +27,38 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_equal(
guess_ab_col(example_isolates, "amox"),
"AMX"
)
expect_equal(
guess_ab_col(example_isolates, "amoxicillin"),
"AMX"
)
expect_equal(
guess_ab_col(example_isolates, "J01AA07"),
"TCY"
)
expect_equal(
guess_ab_col(example_isolates, "tetracycline"),
"TCY"
)
expect_equal(
guess_ab_col(example_isolates, "TETR"),
"TCY"
)
test_that("guess_ab_col works", {
expect_equal(
guess_ab_col(example_isolates, "amox"),
"AMX"
)
expect_equal(
guess_ab_col(example_isolates, "amoxicillin"),
"AMX"
)
expect_equal(
guess_ab_col(example_isolates, "J01AA07"),
"TCY"
)
expect_equal(
guess_ab_col(example_isolates, "tetracycline"),
"TCY"
)
expect_equal(
guess_ab_col(example_isolates, "TETR"),
"TCY"
)
df <- data.frame(
AMP_ND10 = "R",
AMC_ED20 = "S"
)
expect_equal(
guess_ab_col(df, "ampicillin"),
"AMP_ND10"
)
expect_equal(
guess_ab_col(df, "J01CR02"),
"AMC_ED20"
)
df <- data.frame(
AMP_ND10 = "R",
AMC_ED20 = "S"
)
expect_equal(
guess_ab_col(df, "ampicillin"),
"AMP_ND10"
)
expect_equal(
guess_ab_col(df, "J01CR02"),
"AMC_ED20"
)
})