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(v1.6.0.9041) filter_ab_class() fix

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-16 10:50:00 +02:00
parent 00496e45b7
commit 916df6e90c
41 changed files with 142 additions and 133 deletions
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10
inst/tinytest/test-data.R
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@ -23,7 +23,7 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
expect_true(check_dataset_integrity()) # in misc.R
expect_true(AMR:::check_dataset_integrity()) # in misc.R
# IDs should always be unique
expect_identical(nrow(microorganisms), length(unique(microorganisms$mo)))
@ -34,14 +34,14 @@ expect_identical(class(antibiotics$ab), c("ab", "character"))
# check cross table reference
expect_true(all(microorganisms.codes$mo %in% microorganisms$mo))
expect_true(all(example_isolates$mo %in% microorganisms$mo))
expect_true(all(microorganisms.translation$mo_new %in% microorganisms$mo))
expect_true(all(AMR:::microorganisms.translation$mo_new %in% microorganisms$mo))
expect_false(any(AMR:::microorganisms.translation$mo_old %in% microorganisms$mo))
expect_true(all(rsi_translation$mo %in% microorganisms$mo))
expect_true(all(rsi_translation$ab %in% antibiotics$ab))
expect_true(all(intrinsic_resistant$microorganism %in% microorganisms$fullname)) # also important for mo_is_intrinsic_resistant()
expect_true(all(intrinsic_resistant$antibiotic %in% antibiotics$name))
expect_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
expect_true(all(dosage$ab %in% antibiotics$ab))
expect_true(all(dosage$name %in% antibiotics$name))
@ -52,7 +52,7 @@ expect_identical(as.ab(antibiotics$name), antibiotics$ab)
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
for (i in seq_len(length(datasets))) {
dataset <- get(datasets[i], envir = asNamespace("AMR"))
expect_identical(dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
}
df <- AMR:::MO_lookup
@ -76,7 +76,7 @@ expect_stdout(print(catalogue_of_life_version()))
uncategorised <- subset(microorganisms,
genus == "Staphylococcus" &
!species %in% c("", "aureus") &
!mo %in% c(MO_CONS, MO_COPS))
!mo %in% c(AMR:::MO_CONS, AMR:::MO_COPS))
expect_true(NROW(uncategorised) == 0,
info = ifelse(NROW(uncategorised) == 0,
"All staphylococcal species categorised as CoNS/CoPS.",