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(v2.1.1.9186) replace antibiotics with antimicrobials!
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@ -27,90 +27,92 @@
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# antibiotic class selectors
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expect_equal(ncol(example_isolates[, amr_class("antimyco"), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, amr_selector(name %like% "trim"), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, aminoglycosides(), drop = FALSE]), 4, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, aminopenicillins(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, betalactams(), drop = FALSE]), 16, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, carbapenems(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins(), drop = FALSE]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]), 3, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, glycopeptides(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, isoxazolylpenicillins(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, lincosamides(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, macrolides(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, monobactams(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, nitrofurans(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, oxazolidinones(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, penicillins(), drop = FALSE]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, phenicols(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, polymyxins(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, rifamycins(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, streptogramins(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, quinolones(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, tetracyclines(), drop = FALSE]), 3, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, trimethoprims(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]), 1, tolerance = 0.5)
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test_that("amr selectors works", {
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# antibiotic class selectors
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expect_equal(ncol(example_isolates[, amr_class("antimyco"), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, amr_selector(name %like% "trim"), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, aminoglycosides(), drop = FALSE]), 4, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, aminopenicillins(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, betalactams(), drop = FALSE]), 16, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, carbapenems(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins(), drop = FALSE]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]), 3, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, glycopeptides(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, isoxazolylpenicillins(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, lincosamides(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, macrolides(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, monobactams(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, nitrofurans(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, oxazolidinones(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, penicillins(), drop = FALSE]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, phenicols(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, polymyxins(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, rifamycins(), drop = FALSE]), 1, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, streptogramins(), drop = FALSE]), 0, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, quinolones(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, tetracyclines(), drop = FALSE]), 3, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, trimethoprims(), drop = FALSE]), 2, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]), 1, tolerance = 0.5)
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expect_message(expect_stdout(print(carbapenems())))
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expect_error(administrable_per_os())
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expect_message(expect_output(print(carbapenems())))
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expect_error(administrable_per_os())
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# Examples:
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# Examples:
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# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
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# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
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expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_per_os() & penicillins())]), 5, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() & penicillins())]), 7, tolerance = 0.5)
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expect_equal(ncol(example_isolates[, c(administrable_iv() | penicillins())]), 37, tolerance = 0.5)
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# filter using any() or all()
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
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# filter using any() or all()
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
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# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
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expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
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expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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expect_equal(nrow(example_isolates[any(carbapenems() != "R"), ]), 910, tolerance = 0.5)
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expect_equal(nrow(example_isolates[carbapenems() != "R", ]), 704, tolerance = 0.5)
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# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
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expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
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expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
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expect_equal(nrow(example_isolates[any(carbapenems() != "R"), ]), 910, tolerance = 0.5)
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expect_equal(nrow(example_isolates[carbapenems() != "R", ]), 704, tolerance = 0.5)
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# filter with multiple antibiotic selectors using c()
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expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
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# filter with multiple antibiotic selectors using c()
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expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
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# filter + select in one go: get penicillins in carbapenems-resistant strains
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
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expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
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# filter + select in one go: get penicillins in carbapenems-resistant strains
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expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
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expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
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x <- data.frame(
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x = 0,
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mo = 0,
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gen = "S",
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genta = "S",
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J01GB03 = "S",
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tobra = "S",
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Tobracin = "S"
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)
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# should have the first hits
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expect_identical(
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colnames(x[, aminoglycosides(return_all = FALSE)]),
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c("gen", "tobra")
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)
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expect_identical(
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colnames(x[, aminoglycosides()]),
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c("gen", "genta", "J01GB03", "tobra", "Tobracin")
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)
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x <- data.frame(
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x = 0,
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mo = 0,
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gen = "S",
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genta = "S",
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J01GB03 = "S",
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tobra = "S",
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Tobracin = "S"
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)
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# should have the first hits
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expect_identical(
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colnames(x[, aminoglycosides(return_all = FALSE)]),
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c("gen", "tobra")
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)
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expect_identical(
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colnames(x[, aminoglycosides()]),
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c("gen", "genta", "J01GB03", "tobra", "Tobracin")
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)
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_equal(example_isolates %>% select(administrable_per_os() & penicillins()) %>% ncol(), 5, tolerance = 0.5)
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expect_equal(example_isolates %>% select(administrable_iv() & penicillins()) %>% ncol(), 7, tolerance = 0.5)
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expect_equal(example_isolates %>% select(administrable_iv() | penicillins()) %>% ncol(), 37, tolerance = 0.5)
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# expect_warning(example_isolates %>% select(GEH = GEN) %>% select(aminoglycosides(only_treatable = TRUE)))
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}
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
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expect_equal(example_isolates %>% select(administrable_per_os() & penicillins()) %>% ncol(), 5, tolerance = 0.5)
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expect_equal(example_isolates %>% select(administrable_iv() & penicillins()) %>% ncol(), 7, tolerance = 0.5)
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expect_equal(example_isolates %>% select(administrable_iv() | penicillins()) %>% ncol(), 37, tolerance = 0.5)
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# expect_warning(example_isolates %>% select(GEH = GEN) %>% select(aminoglycosides(only_treatable = TRUE)))
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}
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})
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