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Merge branch 'premaster'

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-08-12 19:32:30 +02:00
parent 990709c151 5f2733349e
commit 6c4822164c
25 changed files with 453 additions and 300 deletions
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9
tests/testthat/test-mo.R
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@ -159,8 +159,7 @@ test_that("as.mo works", {
septic_patients[1:10,] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo() %>%
as.character())
as.mo())
# unknown results
expect_warning(as.mo(c("INVALID", "Yeah, unknown")))
@ -198,8 +197,8 @@ test_that("as.mo works", {
print(mo_renamed())
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), "UNKNOWN")
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = TRUE))), "B_ESCHR_COL")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = TRUE))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_warning(as.mo("esco extra_text", allow_uncertain = TRUE))
expect_equal(suppressWarnings(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AUR")
expect_equal(suppressWarnings(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
@ -271,7 +270,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("F_CANDD_GLB")), "F_CANDD_GLA")
# debug mode
expect_warning(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3))
expect_output(print(suppressMessages(suppressWarnings(as.mo("kshgcjkhsdgkshjdfsfvsdfv", debug = TRUE, allow_uncertain = 3)))))
# ..coccus
expect_equal(as.character(as.mo(c("meningococ", "gonococ", "pneumococ"))),