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(v3.0.1.9059) Update taxonomy of microorganisms

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Matthijs Berends
2026-06-23 01:38:13 +02:00
committed by GitHub
parent 0af3f84655
commit 3f9f931777
123 changed files with 121928 additions and 94162 deletions
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3
tests/testthat/test-data.R
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@@ -81,12 +81,13 @@ test_that("test-data.R", {
}
}
AMR:::add_MO_lookup_to_AMR_env()
df <- AMR:::AMR_env$MO_lookup
expect_true(all(c(
"mo", "fullname", "status", "kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies", "rank", "ref", "source",
"lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence",
"snomed", "kingdom_index", "fullname_lower", "full_first", "species_first"
"snomed", "domain_index", "fullname_lower", "full_first", "species_first"
) %in% colnames(df)))
expect_inherits(AMR:::MO_CONS, "mo")