more MOs

tests/testthat/test-atc.R

@@ -14,3 +14,18 @@ test_that("abname works", {
   expect_equal(abname("amox", from = 'molis'), "Amoxicillin")
   expect_equal(abname("J01CA04", from = 'atc'), "Amoxicillin")
 })
+
+test_that("guess_bactid works", {
+  expect_identical(guess_bactid(c("E. coli", "H. influenzae")), c("ESCCOL", "HAEINF"))
+  expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
+  expect_equal(guess_bactid("Negative rods"), "GNR")
+  expect_equal(guess_bactid(c("stau",
+                              "STAU",
+                              "staaur",
+                              "S. aureus",
+                              "S aureus",
+                              "Staphylococcus aureus",
+                              "MRSA",
+                              "VISA")),
+               rep("STAAUR", 8))
+})

tests/testthat/test-first_isolates.R

@@ -7,11 +7,6 @@ test_that("keyantibiotics work", {
   expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
 })
 
-test_that("guess_bactid works", {
-  expect_equal(guess_bactid("E. coli"), "ESCCOL")
-  expect_equal(guess_bactid("Escherichia coli"), "ESCCOL")
-})
-
 test_that("first isolates work", {
   # septic_patients contains 1960 out of 2000 first isolates
   #septic_ptns <- septic_patients