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(v1.5.0.9028) Updated taxonomy until March 2021

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dr. M.S. (Matthijs) Berends
2021-03-04 23:28:32 +01:00
parent 41f94cde97
commit ddf88345f1
95 changed files with 25868 additions and 21574 deletions
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8
tests/testthat/test-data.R
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@ -88,11 +88,13 @@ test_that("CoL version info works", {
})
test_that("CoNS/CoPS are up to date", {
skip_on_cran()
uncategorised <- subset(microorganisms,
genus == "Staphylococcus" &
!species %in% c("", "aureus") &
!mo %in% c(MO_CONS, MO_COPS))
expect(NROW(uncategorised) == 0,
failure_message = paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")"))
if (NROW(uncategorised) > 0) {
warning(paste0("Staphylococcal species not categorised as CoNS/CoPS: S. ",
uncategorised$species, " (", uncategorised$mo, ")\n"))
}
})