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(v1.6.0.9044) betalactams() selector

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dr. M.S. (Matthijs) Berends
2021-05-18 00:53:04 +02:00
parent be49131ed7
commit cfb7df823e
28 changed files with 275 additions and 200 deletions
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33
inst/tinytest/test-ab_class_selectors.R
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@ -23,20 +23,21 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (pkg_is_available("dplyr")) {
expect_true(example_isolates %>% select(aminoglycosides()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(carbapenems()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(cephalosporins()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(cephalosporins_1st()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(cephalosporins_2nd()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(cephalosporins_3rd()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(cephalosporins_4th()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(cephalosporins_5th()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(fluoroquinolones()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(glycopeptides()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(macrolides()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(oxazolidinones()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(penicillins()) %>% ncol() < ncol(example_isolates))
expect_true(example_isolates %>% select(tetracyclines()) %>% ncol() < ncol(example_isolates))
if (as.double(R.Version()$major) + (as.double(R.Version()$minor) / 10) >= 3.2) {
# antibiotic class selectors require at least R-3.2
expect_true(ncol(example_isolates[, aminoglycosides(), 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[, 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[, tetracyclines(), drop = FALSE]) < ncol(example_isolates))
}

3
inst/tinytest/test-filter_ab_class.R
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@ -26,13 +26,14 @@
if (pkg_is_available("dplyr")) {
expect_true(example_isolates %>% filter_ab_class("carbapenem") %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_aminoglycosides() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_betalactams() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_carbapenems() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_1st_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_2nd_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_3rd_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_4th_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_5th_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% mutate(ceftaroline = CTX) %>% filter_5th_cephalosporins() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_fluoroquinolones() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_glycopeptides() %>% nrow() < nrow(example_isolates))
expect_true(example_isolates %>% filter_macrolides() %>% nrow() < nrow(example_isolates))