new MOs, cleanup

tests/testthat/test-eucast.R

@@ -20,7 +20,6 @@ test_that("EUCAST rules work", {
                       "ENTAER"), # Enterobacter aerogenes
                   amox = "R",           # Amoxicillin
                   stringsAsFactors = FALSE)
-  expect_warning(EUCAST_rules(a, info = FALSE))
   expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
   expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
 

tests/testthat/test-first_isolate.R

@@ -124,10 +124,15 @@ test_that("first isolates work", {
                              col_date = "non-existing col",
                              col_mo = "mo"))
 
-  expect_warning(septic_patients %>%
+  # if mo is not an mo class, result should be the same
+  expect_identical(septic_patients %>%
                    mutate(mo = as.character(mo)) %>%
                    first_isolate(col_date = "date",
                                  col_mo = "mo",
-                                 col_patient_id = "patient_id"))
+                                 col_patient_id = "patient_id"),
+                   septic_patients %>%
+                     first_isolate(col_date = "date",
+                                   col_mo = "mo",
+                                   col_patient_id = "patient_id"))
 
 })

tests/testthat/test-mo.R

@@ -11,6 +11,7 @@ test_that("as.mo works", {
   expect_equal(as.character(as.mo(" ESCCOL ")), "ESCCOL")
   expect_equal(as.character(as.mo("klpn")), "KLEPNE")
   expect_equal(as.character(as.mo("Klebsiella")), "KLE")
+  expect_equal(as.character(as.mo("K. pneu rhino")), "KLEPNERH") # K. pneumoniae subspp. rhinoscleromatis
   expect_equal(as.character(as.mo("coagulase negative")), "STACNS")
 
   expect_equal(as.character(as.mo("P. aer")), "PSEAER") # not Pasteurella aerogenes