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(v1.3.0.9020) fix for uncertainty in as.mo()

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dr. M.S. (Matthijs) Berends
2020-09-14 19:41:48 +02:00
parent 354c606d6a
commit ab60f613aa
19 changed files with 100 additions and 84 deletions
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10
tests/testthat/test-mo.R
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@ -205,8 +205,8 @@ test_that("as.mo works", {
expect_equal(suppressWarnings(as.character(as.mo("staaur extratest", allow_uncertain = FALSE))), "UNKNOWN")
expect_message(as.mo("e coli extra_text", allow_uncertain = TRUE))
expect_equal(suppressMessages(as.character(as.mo("unexisting aureus", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY")
expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS")
expect_equal(suppressMessages(as.character(as.mo("unexisting staphy", allow_uncertain = 3))), "B_STPHY_COPS")
expect_equal(suppressMessages(as.character(as.mo("Staphylococcus aureus unexisting", allow_uncertain = 3))), "B_STPHY_AURS_ANRB")
# predefined reference_df
expect_equal(as.character(as.mo("TestingOwnID",
@ -228,15 +228,15 @@ test_that("as.mo works", {
c("B_PROTS_MRBL", "B_BCLLS_CERS", "B_ESCHR_COLI"))
# hard to find
expect_equal(as.character(suppressWarnings(as.mo(
expect_equal(as.character(suppressMessages(as.mo(
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena")))),
c("B_MCRBC_PRXY", "B_STRPT_SUIS", "B_RLTLL_TRRG"))
expect_output(print(mo_uncertainties()))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(suppressWarnings(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
expect_equal(suppressMessages(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
# no virusses