(v3.0.0.9027) skimr update and as.ab warning - fixes #234, fixes #232

tests/testthat/test-ab.R

@@ -96,6 +96,14 @@ test_that("test-ab.R", {
     rep("GEH", 8)
   )
 
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(clinical_breakpoints$ab),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "ab.n_unique", "ab.top_ab", "ab.top_ab_name", "ab.top_group")
+    )
+  }
+
   # assigning and subsetting
   x <- AMR::antimicrobials$ab
   expect_inherits(x[1], "ab")

tests/testthat/test-disk.R

@@ -60,4 +60,12 @@ test_that("test-disk.R", {
   if (AMR:::pkg_is_available("tibble")) {
     expect_output(print(tibble::tibble(d = as.disk(12))))
   }
+
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(random_disk(100)),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "disk.p0", "disk.p25", "disk.p50", "disk.p75", "disk.p100", "disk.hist")
+    )
+  }
 })

tests/testthat/test-mic.R

@@ -81,6 +81,14 @@ test_that("test-mic.R", {
     expect_output(print(tibble::tibble(m = as.mic(2:4))))
   }
 
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(random_mic(100)),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "mic.p0", "mic.p25", "mic.p50", "mic.p75", "mic.p100", "mic.hist")
+    )
+  }
+
   # all mathematical operations
   x <- random_mic(50)
   x_double <- as.double(gsub("[<=>]+", "", as.character(x)))

tests/testthat/test-mo.R

@@ -321,4 +321,12 @@ test_that("test-mo.R", {
   if (AMR:::pkg_is_available("cleaner")) {
     expect_inherits(cleaner::freq(example_isolates$mo), "freq")
   }
+
+  # skimr
+  if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
+    expect_named(
+      skim(example_isolates$mo),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "mo.n_unique", "mo.gram_negative", "mo.gram_positive", "mo.yeast", "mo.top_genus", "mo.top_species")
+    )
+  }
 })

tests/testthat/test-sir.R

@@ -103,22 +103,13 @@ test_that("test-sir.R", {
       pull(MEM) %>%
       is.sir())
   }
+
+  # skimr
   if (AMR:::pkg_is_available("skimr", min_version = "2.0.0", also_load = TRUE)) {
-    expect_inherits(
-      skim(example_isolates),
-      "data.frame"
+    expect_named(
+      skim(example_isolates$PEN),
+      c("skim_type", "skim_variable", "n_missing", "complete_rate", "sir.count_S", "sir.count_I", "sir.count_R", "sir.prop_S", "sir.prop_I", "sir.prop_R", "sir.hist")
     )
-    if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
-      expect_inherits(
-        example_isolates %>%
-          mutate(
-            m = as.mic(2),
-            d = as.disk(20)
-          ) %>%
-          skim(),
-        "data.frame"
-      )
-    }
   }
 
   expect_equal(as.sir(c("", "-", NA, "NULL")), c(NA_sir_, NA_sir_, NA_sir_, NA_sir_))