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(v1.7.1.9005) ab class selectors for R-3.0 and R-3.1

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dr. M.S. (Matthijs) Berends
2021-06-22 12:16:42 +02:00
parent c44d9392ca
commit d04e83f494
41 changed files with 227 additions and 279 deletions
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94
inst/tinytest/test-ab_class_selectors.R
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@ -23,52 +23,48 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (getRversion() < "3.2") {
expect_warning(example_isolates[, aminoglycosides(), drop = FALSE])
}
if (getRversion() >= "3.2") {
# antibiotic class selectors require at least R-3.2
expect_true(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, aminopenicillins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, carbapenems(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, glycopeptides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, lincosamides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, macrolides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, oxazolidinones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, penicillins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, polymyxins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, streptogramins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, quinolones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(example_isolates))
# Examples:
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
# filter using any() or all()
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
# filter with multiple antibiotic selectors using c()
expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
# filter + select in one go: get penicillins in carbapenems-resistant strains
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)
}
# antibiotic class selectors
expect_true(ncol(example_isolates[, ab_class("antimyco"), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, aminoglycosides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, aminopenicillins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, betalactams(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, carbapenems(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_1st(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_2nd(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_3rd(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, glycopeptides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, lincosamides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, macrolides(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, oxazolidinones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, penicillins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, polymyxins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, streptogramins(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, quinolones(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
expect_true(ncol(example_isolates[, ureidopenicillins(), drop = FALSE]) < ncol(example_isolates))
# Examples:
# select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'
expect_equal(ncol(example_isolates[, c("mo", aminoglycosides())]), 5, tolerance = 0.5)
# filter using any() or all()
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), ]), 55, tolerance = 0.5)
expect_equal(nrow(subset(example_isolates, any(carbapenems() == "R"))), 55, tolerance = 0.5)
# filter on any or all results in the carbapenem columns (i.e., IPM, MEM):
expect_equal(nrow(example_isolates[any(carbapenems()), ]), 962, tolerance = 0.5)
expect_equal(nrow(example_isolates[all(carbapenems()), ]), 756, tolerance = 0.5)
# filter with multiple antibiotic selectors using c()
expect_equal(nrow(example_isolates[all(c(carbapenems(), aminoglycosides()) == "R"), ]), 26, tolerance = 0.5)
# filter + select in one go: get penicillins in carbapenems-resistant strains
expect_equal(nrow(example_isolates[any(carbapenems() == "R"), penicillins()]), 55, tolerance = 0.5)
expect_equal(ncol(example_isolates[any(carbapenems() == "R"), penicillins()]), 7, tolerance = 0.5)