mdro and 1st isolate improvements

tests/testthat/test-first_isolate.R

@@ -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)) %>%

tests/testthat/test-mdro.R

@@ -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))