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(v1.7.0.9002) old MO codes

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dr. M.S. (Matthijs) Berends
2021-06-01 16:36:33 +02:00
parent bef0f42f66
commit 279376fccb
23 changed files with 44 additions and 45 deletions
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1
inst/tinytest/test-mo.R
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@ -48,7 +48,6 @@ expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo("Estreptococos grupo B")), "B_STRPT_GRPB")
expect_equal(as.character(as.mo("Group B Streptococci")), "B_STRPT_GRPB")
expect_equal(as.character(suppressWarnings(as.mo("B_STRPT_PNE"))), "B_STRPT_PNMN") # old MO code (<=v0.8.0)
expect_equal(as.character(as.mo(c("mycobacterie", "mycobakterium"))), c("B_MYCBC", "B_MYCBC"))
expect_equal(as.character(as.mo(c("GAS", "GBS", "a MGS", "haemoly strep"))), c("B_STRPT_GRPA", "B_STRPT_GRPB", "B_STRPT_MILL", "B_STRPT_HAEM"))

2
inst/tinytest/test-mo_property.R
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@ -98,7 +98,7 @@ expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
expect_true(112283007 %in% mo_snomed("Escherichia coli"))
# old codes must throw a warning in mo_* family
expect_message(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
# outcome of mo_fullname must always return the fullname from the data set
x <- data.frame(mo = microorganisms$mo,
# fullname from the original data: