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mdro and 1st isolate improvements

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-10-23 11:15:05 +02:00
parent 299c5bea43
commit 7997de6a6d
8 changed files with 138 additions and 95 deletions
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9
tests/testthat/test-first_isolate.R
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@ -119,11 +119,18 @@ test_that("first isolates work", {
# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
expect_error(first_isolate(septic_patients))
expect_error(first_isolate(septic_patients,
col_date = "non-existing col",
col_mo = "mo"))
# look for columns itself
expect_message(first_isolate(septic_patients))
expect_message(first_isolate(septic_patients %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms(),
col_genus = "genus",
col_species = "species"))
# if mo is not an mo class, result should be the same
expect_identical(septic_patients %>%
mutate(mo = as.character(mo)) %>%

2
tests/testthat/test-mdro.R
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@ -20,7 +20,7 @@ test_that("MDRO works", {
# septic_patients should have these finding using Dutch guidelines
expect_equal(outcome %>% freq() %>% pull(count),
c(2, 14)) # 2 unconfirmed, 14 positive
c(1167, 817, 14, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))