(v1.3.0.9035) mdro() for EUCAST 3.2, examples cleanup

tests/testthat/test-data.R

@@ -66,6 +66,8 @@ test_that("creation of data sets is valid", {
   expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
                     "fullname_lower", "g_species") %in% colnames(olddf)))
   
+  expect_s3_class(create_species_cons_cops("CoNS"), "mo")
+  
 })
 
 test_that("CoL version info works", {

tests/testthat/test-mdro.R

@@ -31,14 +31,16 @@ test_that("mdro works", {
   expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
 
   outcome <- suppressWarnings(mdro(example_isolates))
+  outcome <- mdro(example_isolates, "eucast3.1", info = TRUE)
   outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
   # check class
-  expect_equal(outcome %>% class(), c("ordered", "factor"))
+  expect_equal(class(outcome), c("ordered", "factor"))
 
   outcome <- mdro(example_isolates, "nl", info = TRUE)
   # check class
-  expect_equal(outcome %>% class(), c("ordered", "factor"))
+  expect_equal(class(outcome), c("ordered", "factor"))
 
+  library(dplyr)
   # example_isolates should have these finding using Dutch guidelines
   expect_equal(outcome %>% cleaner::freq() %>% pull(count),
                c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos

tests/testthat/test-rsi.R

@@ -84,18 +84,20 @@ test_that("mic2rsi works", {
   
   skip_on_cran()
   
+  # S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
   expect_equal(as.character(
-    as.rsi(x = as.mic(0.125),
-                      mo = "B_STRPT_PNMN",
-                      ab = "AMX",
-                      guideline = "EUCAST")),
-    "S")
+    as.rsi(x = as.mic(c(0.125, 0.5, 1, 2, 4)),
+           mo = "B_STRPT_PNMN",
+           ab = "AMP",
+           guideline = "EUCAST 2020")),
+    c("S", "S", "I", "I", "R"))
+  # S. pneumoniae/amoxicillin in CLSI 2019: 2-8 ug/ml (R is 8 and > 8)
   expect_equal(as.character(
-    as.rsi(x = as.mic(4),
+    as.rsi(x = as.mic(c(1, 2, 4, 8, 16)),
            mo = "B_STRPT_PNMN",
            ab = "AMX",
-           guideline = "EUCAST")),
-    "I")
+           guideline = "CLSI 2019")),
+    c("S", "S", "I", "R", "R"))
 
   # cutoffs at MIC = 8
   expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020"),