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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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48
tests/testthat/test-join_microorganisms.R
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@ -27,35 +27,37 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
unjoined <- example_isolates
inner <- inner_join_microorganisms(example_isolates)
left <- left_join_microorganisms(example_isolates)
semi <- semi_join_microorganisms(example_isolates)
anti <- anti_join_microorganisms(example_isolates)
suppressWarnings(right <- right_join_microorganisms(example_isolates))
suppressWarnings(full <- full_join_microorganisms(example_isolates))
test_that("join_microorganisms works", {
unjoined <- example_isolates
inner <- inner_join_microorganisms(example_isolates)
left <- left_join_microorganisms(example_isolates)
semi <- semi_join_microorganisms(example_isolates)
anti <- anti_join_microorganisms(example_isolates)
suppressWarnings(right <- right_join_microorganisms(example_isolates))
suppressWarnings(full <- full_join_microorganisms(example_isolates))
expect_true(ncol(unjoined) < ncol(inner))
expect_true(nrow(unjoined) == nrow(inner))
expect_true(ncol(unjoined) < ncol(inner))
expect_true(nrow(unjoined) == nrow(inner))
expect_true(ncol(unjoined) < ncol(left))
expect_true(nrow(unjoined) == nrow(left))
expect_true(ncol(unjoined) < ncol(left))
expect_true(nrow(unjoined) == nrow(left))
expect_true(ncol(semi) == ncol(semi))
expect_true(nrow(semi) == nrow(semi))
expect_true(ncol(semi) == ncol(semi))
expect_true(nrow(semi) == nrow(semi))
expect_true(nrow(anti) == 0)
expect_true(nrow(anti) == 0)
expect_true(nrow(unjoined) < nrow(right))
expect_true(nrow(unjoined) < nrow(full))
expect_true(nrow(unjoined) < nrow(right))
expect_true(nrow(unjoined) < nrow(full))
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(inner_join_microorganisms("B_ESCHR_COLI", by = c("mo" = "mo"))), 1)
expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(left_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
expect_equal(nrow(semi_join_microorganisms("B_ESCHR_COLI")), 1)
expect_equal(nrow(anti_join_microorganisms("B_ESCHR_COLI")), 0)
# expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
# expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
# expect_warning(right_join_microorganisms("B_ESCHR_COLI"))
# expect_warning(full_join_microorganisms("B_ESCHR_COLI"))
})