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(v0.7.1.9102) lintr

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dr. M.S. (Matthijs) Berends
2019-10-11 17:21:02 +02:00
parent 59af355a89
commit 00cdb498a0
65 changed files with 620 additions and 812 deletions
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26
tests/testthat/test-mo.R
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@ -94,7 +94,7 @@ test_that("as.mo works", {
rep("B_STPHY_AURS", 9))
expect_identical(
as.character(
as.mo(c('EHEC', 'EPEC', 'EIEC', 'STEC', 'ATEC', 'UPEC'))),
as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))),
rep("B_ESCHR_COLI", 6))
# unprevalent MO
expect_identical(
@ -114,13 +114,13 @@ test_that("as.mo works", {
c("UNKNOWN", NA_character_, "B_STNTR_MLTP", "B_KLBSL_PNMN_RHNS", "B_ESCHR_COLI"))
# check for Becker classification
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPDR")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CONS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius", Becker = FALSE)), "B_STPHY_INTR")
expect_identical(as.character(as.mo("Sta intermedius", Becker = TRUE)), "B_STPHY_COPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_COPS")
# aureus must only be influenced if Becker = "all"
expect_identical(as.character(as.mo("STAAUR", Becker = FALSE)), "B_STPHY_AURS")
expect_identical(as.character(as.mo("STAAUR", Becker = TRUE)), "B_STPHY_AURS")
@ -150,7 +150,7 @@ test_that("as.mo works", {
# select with one column
expect_identical(
example_isolates[1:10,] %>%
example_isolates[1:10, ] %>%
left_join_microorganisms() %>%
select(genus) %>%
as.mo() %>%
@ -160,9 +160,9 @@ test_that("as.mo works", {
# select with two columns
expect_identical(
example_isolates[1:10,] %>%
example_isolates[1:10, ] %>%
pull(mo),
example_isolates[1:10,] %>%
example_isolates[1:10, ] %>%
left_join_microorganisms() %>%
select(genus, species) %>%
as.mo())
@ -260,10 +260,6 @@ test_that("as.mo works", {
expect_null(mo_failures())
expect_true(example_isolates %>% pull(mo) %>% is.mo())
# expect_equal(get_mo_code("test", "mo"), "test")
# expect_equal(length(get_mo_code("Escherichia", "genus")),
# nrow(AMR::microorganisms[base::which(AMR::microorganisms[, "genus"] %in% "Escherichia"),]))
expect_error(translate_allow_uncertain(5))
# very old MO codes (<= v0.5.0)