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(v1.5.0.9028) Updated taxonomy until March 2021

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This commit is contained in:
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"))
}
})

1
tests/testthat/test-mo.R
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@ -124,7 +124,6 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")

3
tests/testthat/test-mo_property.R
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@ -65,7 +65,8 @@ test_that("mo_property works", {
expect_equal(mo_shortname("Streptococcus agalactiae"), "S. agalactiae")
expect_equal(mo_shortname("Streptococcus agalactiae", Lancefield = TRUE), "GBS")
expect_true(mo_url("Escherichia coli") %like% "www.catalogueoflife.org")
expect_true(mo_url("Candida albicans") %like% "catalogueoflife.org")
expect_true(mo_url("Escherichia coli") %like% "lpsn.dsmz.de")
# test integrity
MOs <- microorganisms