unit test fix

inst/tinytest/test-_misc.R

@@ -47,7 +47,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
 }
 
-# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
+# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
   expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
 }

inst/tinytest/test-ab_property.R

@@ -68,15 +68,15 @@ expect_true(ab_url("AMX") %like% "whocc.no")
 expect_warning(ab_url("ASP"))
 
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 20:25])),
+  colnames(set_ab_names(example_isolates[, 17:22])),
   c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
 )
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
+  colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
   c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
 )
 expect_identical(
-  colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
+  colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
   c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
 )
 

inst/tinytest/test-count.R

@@ -79,7 +79,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
         combination = count_susceptible(CIP, GEN)
       ) %>%
       pull(combination),
-    c(253, 465, 192, 558)
+    c(946, 428, 94)
   )
 
   # count_df

inst/tinytest/test-data.R

@@ -57,7 +57,6 @@ expect_identical(as.ab(antibiotics$name), antibiotics$ab)
 datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
 for (i in seq_len(length(datasets))) {
   dataset <- get(datasets[i], envir = asNamespace("AMR"))
-  expect_identical(class(dataset), "data.frame")
   expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
 }
 

inst/tinytest/test-first_isolate.R

@@ -75,7 +75,7 @@ expect_equal(
     ),
     na.rm = TRUE
   ),
-  941
+  942
 )
 
 # set 1500 random observations to be of specimen type 'Urine'
@@ -160,7 +160,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
 
   # support for WHONET
   expect_message(example_isolates %>%
-    select(-patient_id) %>%
+    select(-patient) %>%
     mutate(
       `First name` = "test",
       `Last name` = "test",

inst/tinytest/test-proportion.R

@@ -84,7 +84,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
         combination_n = n_rsi(CIP, GEN)
       ) %>%
       pull(combination_n),
-    c(305, 617, 241, 711)
+    c(1181, 577, 116)
   )
 
   # proportion_df