implement ecoffs

inst/tinytest/test-mo_property.R

@@ -166,15 +166,13 @@ expect_identical(mo_ref("Chlamydia psittaci"), "Garcia-Lopez et al., 2019")
 expect_identical(mo_ref("Chlamydophila psittaci", keep_synonyms = TRUE), "Everett et al., 1999")
 
 expect_true(112283007 %in% mo_snomed("Escherichia coli")[[1]])
-# old codes must throw a warning in mo_* family
-# expect_warning(mo_name(c("B_ESCHR_COL", "B_STPHY_AUR")))
 # outcome of mo_fullname must always return the fullname from the data set
 x <- data.frame(
   mo = microorganisms$mo,
   # fullname from the original data:
   f1 = microorganisms$fullname,
   # newly created fullname based on MO code:
-  f2 = mo_fullname(microorganisms$mo, language = "en"),
+  f2 = mo_fullname(microorganisms$mo, language = "en", keep_synonyms = TRUE),
   stringsAsFactors = FALSE
 )
 expect_equal(nrow(subset(x, f1 != f2)), 0)

inst/tinytest/test-sir.R

@@ -142,6 +142,10 @@ expect_equal(
   suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
   as.sir("S")
 )
+expect_equal(
+  suppressMessages(as.sir(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020", ecoff = TRUE)),
+  as.sir("S")
+)
 expect_equal(
   suppressMessages(as.sir(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020")),
   as.sir("R")