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(v2.1.1.9141) new AMR selectors, eucast overwrite arg

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-02-07 18:01:22 +01:00
parent baea4323c7
commit 8ba2e4ed94
42 changed files with 282 additions and 197 deletions
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2
tests/testthat/test-ab_selectors.R → tests/testthat/test-amr_selectors.R
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@ -42,9 +42,11 @@ expect_equal(ncol(example_isolates[, cephalosporins_4th(), drop = FALSE]), 1, to
expect_equal(ncol(example_isolates[, cephalosporins_5th(), drop = FALSE]), 0, tolerance = 0.5)
expect_equal(ncol(example_isolates[, fluoroquinolones(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, glycopeptides(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, isoxazolylpenicillins(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, lincosamides(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, lipoglycopeptides(), drop = FALSE]), 0, tolerance = 0.5)
expect_equal(ncol(example_isolates[, macrolides(), drop = FALSE]), 2, tolerance = 0.5)
expect_equal(ncol(example_isolates[, monobactams(), drop = FALSE]), 0, tolerance = 0.5)
expect_equal(ncol(example_isolates[, nitrofurans(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, oxazolidinones(), drop = FALSE]), 1, tolerance = 0.5)
expect_equal(ncol(example_isolates[, penicillins(), drop = FALSE]), 7, tolerance = 0.5)

7
tests/testthat/test-zzz.R
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@ -141,11 +141,8 @@ call_functions <- c(
import_functions <- c(import_functions, call_functions)
suggests <- tryCatch(strsplit(utils::packageDescription(pkg = ".", lib.loc = ".", fields = "Suggests"), "[,\n ]+")[[1]],
error = function(e) {
print(list.files())
return(import_functions)
})
suggests <- tryCatch(strsplit(pkgload::pkg_desc()$get_field("Suggests"), "[,\n ]+")[[1]],
error = function(e) unname(import_functions))
for (i in seq_len(length(import_functions))) {
fn <- names(import_functions)[i]
pkg <- unname(import_functions[i])