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(v0.9.0.9016) Support SNOMED codes

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dr. M.S. (Matthijs) Berends committed 2020-01-27 19:14:23 +01:00
1 parent 42b079cdb7
commit a13c62e6e8
31 files changed
+456 -342
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tests/testthat/test-mo.R
+2 -1
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@@ -38,6 +38,7 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia coli")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(22242416)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo(112283007)), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("Escherichia species")), "B_ESCHR")
expect_equal(as.character(as.mo("Escherichia")), "B_ESCHR")
expect_equal(as.character(as.mo("Esch spp.")), "B_ESCHR")
@@ -240,7 +241,7 @@ test_that("as.mo works", {
expect_output(print(mo_uncertainties()))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A")),
expect_equal(suppressWarnings(mo_name(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
c("Salmonella enterica", "Salmonella typhimurium", "Salmonella"))
# no virusses
tests/testthat/test-mo_property.R
+3
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@@ -93,6 +93,9 @@ test_that("mo_property works", {
expect_identical(suppressWarnings(mo_ref("Chlamydia psittaci")), "Page, 1968")
expect_identical(mo_ref("Chlamydophila psittaci"), "Everett et al., 1999")
expect_equal(mo_snomed("Escherichia coli"),
c(112283007, 116395006, 116396007, 103429008, 83285000, 116394005, 407166006, 457914007))
# old codes must throw a warning in mo_* family
expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))