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(v0.7.0.9001) new pathovars, small fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-06-07 22:47:37 +02:00
parent 04c75e8e36
commit f02679fb63
83 changed files with 686 additions and 583 deletions
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4
tests/testthat/test-ab.R
View File

@ -59,4 +59,8 @@ test_that("as.ab works", {
expect_equal(as.character(as.ab("Phloxapen")),
"FLC")
expect_equal(suppressWarnings(as.character(as.ab(c("Bacteria", "Bacterial")))),
c(NA, "TMP"))
})

8
tests/testthat/test-mo.R
View File

@ -74,7 +74,7 @@ test_that("as.mo works", {
# prevalent MO
expect_identical(
as.character(
suppressWarnings(as.character(
as.mo(c("stau",
"STAU",
"staaur",
@ -83,12 +83,12 @@ test_that("as.mo works", {
"Sthafilokkockus aureeuzz",
"Staphylococcus aureus",
"MRSA",
"VISA"))),
"VISA")))),
rep("B_STPHY_AUR", 9))
expect_identical(
as.character(
as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC'))),
rep("B_ESCHR_COL", 5))
as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC', 'UPEC'))),
rep("B_ESCHR_COL", 6))
# unprevalent MO
expect_identical(
as.character(