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(v0.7.1.9075) new microorganism codes

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dr. M.S. (Matthijs) Berends
2019-09-18 15:46:09 +02:00
parent f553a08a7b
commit e2aa4f996b
53 changed files with 636 additions and 475 deletions
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6
tests/testthat/test-first_isolate.R
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@ -190,19 +190,19 @@ test_that("first isolates work", {
# unknown MOs
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = FALSE)) %>%
.$first %>%
sum(),
1062)
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", "UNKNOWN", mo)) %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", "UNKNOWN", mo)) %>%
mutate(first = first_isolate(., include_unknown = TRUE)) %>%
.$first %>%
sum(),
1529)
expect_equal(example_isolates %>%
mutate(mo = ifelse(mo == "B_ESCHR_COL", NA, mo)) %>%
mutate(mo = ifelse(mo == "B_ESCHR_COLI", NA, mo)) %>%
mutate(first = first_isolate(.)) %>%
.$first %>%
sum(),