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(v0.8.0.9007) Enterobacterales order

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dr. M.S. (Matthijs) Berends
2019-10-30 23:02:50 +01:00
parent 7ff2ad8188
commit 09c4b04cd0
22 changed files with 156 additions and 55 deletions
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2
tests/testthat/test-misc.R
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@ -44,6 +44,6 @@ test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
expect_message(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
})

2
tests/testthat/test-mo_property.R
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@ -28,7 +28,7 @@ test_that("mo_property works", {
expect_equal(mo_kingdom("Escherichia coli"), "Bacteria")
expect_equal(mo_phylum("Escherichia coli"), "Proteobacteria")
expect_equal(mo_class("Escherichia coli"), "Gammaproteobacteria")
expect_equal(mo_order("Escherichia coli"), "Enterobacteriales")
expect_equal(mo_order("Escherichia coli"), "Enterobacterales")
expect_equal(mo_family("Escherichia coli"), "Enterobacteriaceae")
expect_equal(mo_genus("Escherichia coli"), "Escherichia")
expect_equal(mo_species("Escherichia coli"), "coli")