styled, unit test fix

2025-07-12 21:41:55 +02:00 · 2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
--- a/inst/tinytest/test-first_isolate.R
+++ b/inst/tinytest/test-first_isolate.R
@ -9,7 +9,7 @@
 # (c) 2018-2022 Berends MS, Luz CF et al.                              #
 # Developed at the University of Groningen, the Netherlands, in        #
 # collaboration with non-profit organisations Certe Medical            #
-# Diagnostics & Advice, and University Medical Center Groningen.       # 
+# Diagnostics & Advice, and University Medical Center Groningen.       #
 #                                                                      #
 # This R package is free software; you can freely use and distribute   #
 # it for both personal and commercial purposes under the terms of the  #
@ -24,40 +24,59 @@
 # ==================================================================== #

 # all four methods
-expect_equal(sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),
-             1984)
-expect_equal(sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE),
-             1265)
-expect_equal(sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE),
-             1300)
-expect_equal(sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
-             1379)
+expect_equal(
+  sum(first_isolate(x = example_isolates, method = "isolate-based", info = TRUE), na.rm = TRUE),
+  1984
+)
+expect_equal(
+  sum(first_isolate(x = example_isolates, method = "patient-based", info = TRUE), na.rm = TRUE),
+  1265
+)
+expect_equal(
+  sum(first_isolate(x = example_isolates, method = "episode-based", info = TRUE), na.rm = TRUE),
+  1300
+)
+expect_equal(
+  sum(first_isolate(x = example_isolates, method = "phenotype-based", info = TRUE), na.rm = TRUE),
+  1379
+)

 # Phenotype-based, using key antimicrobials
-expect_equal(sum(first_isolate(x = example_isolates,
-                               method = "phenotype-based",
-                               type = "keyantimicrobials",
-                               antifungal = NULL, info = TRUE), na.rm = TRUE),
-             1395)
-expect_equal(sum(first_isolate(x = example_isolates,
-                               method = "phenotype-based",
-                               type = "keyantimicrobials",
-                               antifungal = NULL, info = TRUE, ignore_I = FALSE), na.rm = TRUE),
-             1418)
+expect_equal(
+  sum(first_isolate(
+    x = example_isolates,
+    method = "phenotype-based",
+    type = "keyantimicrobials",
+    antifungal = NULL, info = TRUE
+  ), na.rm = TRUE),
+  1395
+)
+expect_equal(
+  sum(first_isolate(
+    x = example_isolates,
+    method = "phenotype-based",
+    type = "keyantimicrobials",
+    antifungal = NULL, info = TRUE, ignore_I = FALSE
+  ), na.rm = TRUE),
+  1418
+)


 # first non-ICU isolates
 expect_equal(
  sum(
    first_isolate(example_isolates,
-                  col_mo = "mo",
-                  col_date = "date",
-                  col_patient_id = "patient",
-                  col_icu = example_isolates$ward == "ICU",
-                  info = TRUE,
-                  icu_exclude = TRUE),
-    na.rm = TRUE),
-  941)
+      col_mo = "mo",
+      col_date = "date",
+      col_patient_id = "patient",
+      col_icu = example_isolates$ward == "ICU",
+      info = TRUE,
+      icu_exclude = TRUE
+    ),
+    na.rm = TRUE
+  ),
+  941
+)

 # set 1500 random observations to be of specimen type 'Urine'
 random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
@ -65,78 +84,98 @@ x <- example_isolates
 x$specimen <- "Other"
 x[random_rows, "specimen"] <- "Urine"
 expect_true(
-  sum(first_isolate(x = x,
-                    col_date = "date",
-                    col_patient_id = "patient",
-                    col_mo = "mo",
-                    col_specimen = "specimen",
-                    filter_specimen = "Urine",
-                    info = TRUE), na.rm = TRUE) < 1501)
+  sum(first_isolate(
+    x = x,
+    col_date = "date",
+    col_patient_id = "patient",
+    col_mo = "mo",
+    col_specimen = "specimen",
+    filter_specimen = "Urine",
+    info = TRUE
+  ), na.rm = TRUE) < 1501
+)
 # same, but now exclude ICU
 expect_true(
-  sum(first_isolate(x = x,
-                    col_date = "date",
-                    col_patient_id = "patient",
-                    col_mo = "mo",
-                    col_specimen = "specimen",
-                    filter_specimen = "Urine",
-                    col_icu = x$ward == "ICU",
-                    icu_exclude = TRUE,
-                    info = TRUE), na.rm = TRUE) < 1501)
+  sum(first_isolate(
+    x = x,
+    col_date = "date",
+    col_patient_id = "patient",
+    col_mo = "mo",
+    col_specimen = "specimen",
+    filter_specimen = "Urine",
+    col_icu = x$ward == "ICU",
+    icu_exclude = TRUE,
+    info = TRUE
+  ), na.rm = TRUE) < 1501
+)

 # "No isolates found"
 test_iso <- example_isolates
 test_iso$specimen <- "test"
-expect_message(first_isolate(test_iso, 
-                             "date", 
-                             "patient",
-                             col_mo = "mo",
-                             col_specimen = "specimen",
-                             filter_specimen = "something_unexisting",
-                             info = TRUE))
+expect_message(first_isolate(test_iso,
+  "date",
+  "patient",
+  col_mo = "mo",
+  col_specimen = "specimen",
+  filter_specimen = "something_unexisting",
+  info = TRUE
+))

 # printing of exclusion message
 expect_message(first_isolate(example_isolates,
-                             col_date = "date",
-                             col_mo = "mo",
-                             col_patient_id = "patient",
-                             col_testcode = "gender",
-                             testcodes_exclude = "M",
-                             info = TRUE))
+  col_date = "date",
+  col_mo = "mo",
+  col_patient_id = "patient",
+  col_testcode = "gender",
+  testcodes_exclude = "M",
+  info = TRUE
+))

 # errors
 expect_error(first_isolate("date", "patient", col_mo = "mo"))
 expect_error(first_isolate(example_isolates,
-                           col_date = "non-existing col",
-                           col_mo = "mo"))
+  col_date = "non-existing col",
+  col_mo = "mo"
+))

 if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
  # if mo is not an mo class, result should be the same
-  expect_identical(example_isolates %>%
-                     mutate(mo = as.character(mo)) %>%
-                     first_isolate(col_date = "date",
-                                   col_mo = "mo",
-                                   col_patient_id = "patient",
-                                   info = FALSE),
-                   example_isolates %>%
-                     first_isolate(col_date = "date",
-                                   col_mo = "mo",
-                                   col_patient_id = "patient",
-                                   info = FALSE))
-  
+  expect_identical(
+    example_isolates %>%
+      mutate(mo = as.character(mo)) %>%
+      first_isolate(
+        col_date = "date",
+        col_mo = "mo",
+        col_patient_id = "patient",
+        info = FALSE
+      ),
+    example_isolates %>%
+      first_isolate(
+        col_date = "date",
+        col_mo = "mo",
+        col_patient_id = "patient",
+        info = FALSE
+      )
+  )
+
  # support for WHONET
  expect_message(example_isolates %>%
-                   select(-patient_id) %>%
-                   mutate(`First name` = "test",
-                          `Last name` = "test", 
-                          Sex = "Female") %>% 
-                   first_isolate(info = TRUE))
-  
+    select(-patient_id) %>%
+    mutate(
+      `First name` = "test",
+      `Last name` = "test",
+      Sex = "Female"
+    ) %>%
+    first_isolate(info = TRUE))
+
  # groups
-  x <- example_isolates %>% group_by(ward) %>% mutate(first = first_isolate())
-  y <- example_isolates %>% group_by(ward) %>% mutate(first = first_isolate(.))
+  x <- example_isolates %>%
+    group_by(ward) %>%
+    mutate(first = first_isolate())
+  y <- example_isolates %>%
+    group_by(ward) %>%
+    mutate(first = first_isolate(.))
  expect_identical(x, y)
-  
 }

 # missing dates should be no problem
@ -144,33 +183,47 @@ df <- example_isolates
 df[1:100, "date"] <- NA
 expect_equal(
  sum(
-    first_isolate(x = df,
-                  col_date = "date",
-                  col_patient_id = "patient",
-                  col_mo = "mo",
-                  info = TRUE),
-    na.rm = TRUE),
-  1382)
+    first_isolate(
+      x = df,
+      col_date = "date",
+      col_patient_id = "patient",
+      col_mo = "mo",
+      info = TRUE
+    ),
+    na.rm = TRUE
+  ),
+  1382
+)

 # unknown MOs
 test_unknown <- example_isolates
 test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
-expect_equal(sum(first_isolate(test_unknown, include_unknown = FALSE)), 
-             1108)
-expect_equal(sum(first_isolate(test_unknown, include_unknown = TRUE)),
-             1591)
+expect_equal(
+  sum(first_isolate(test_unknown, include_unknown = FALSE)),
+  1108
+)
+expect_equal(
+  sum(first_isolate(test_unknown, include_unknown = TRUE)),
+  1591
+)

 test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
-expect_equal(sum(first_isolate(test_unknown)),
-             1108)
+expect_equal(
+  sum(first_isolate(test_unknown)),
+  1108
+)

 # empty rsi results
-expect_equal(sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
-             1366)
+expect_equal(
+  sum(first_isolate(example_isolates, include_untested_rsi = FALSE)),
+  1366
+)

 # shortcuts
-expect_identical(filter_first_isolate(example_isolates),
-                 subset(example_isolates, first_isolate(example_isolates)))
+expect_identical(
+  filter_first_isolate(example_isolates),
+  subset(example_isolates, first_isolate(example_isolates))
+)


 # notice that all mo's are distinct, so all are TRUE