(v2.1.1.9186) replace antibiotics with antimicrobials!

2025-07-08 09:51:48 +02:00 · 2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@ -27,234 +27,236 @@
 # how to conduct AMR data analysis: https://msberends.github.io/AMR/   #
 # ==================================================================== #

-# 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),
-  1387
-)
-
-# for phenotype determination
-expect_equal(
-  AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
-  FALSE
-)
-expect_equal(
-  AMR:::duplicated_antibiogram(c("RRR", "SSS"),
-    points_threshold = 2, ignore_I = TRUE, type = "points"
-  ),
-  c(FALSE, FALSE)
-)
-expect_equal(
-  AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
-    points_threshold = 2, ignore_I = TRUE, type = "points"
-  ),
-  c(FALSE, TRUE, FALSE)
-)
-expect_equal(
-  AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
-    points_threshold = 2, ignore_I = TRUE, type = "points"
-  ),
-  c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)
-)
-
-# 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),
-  1383
-)
-expect_equal(
-  sum(first_isolate(
-    x = example_isolates,
-    method = "phenotype-based",
-    type = "keyantimicrobials",
-    antifungal = NULL, info = TRUE, ignore_I = FALSE
-  ), na.rm = TRUE),
-  1397
-)
-
-
-# first non-ICU isolates
-expect_true(
-  sum(
-    first_isolate(example_isolates,
-      col_mo = "mo",
-      col_date = "date",
-      col_patient_id = "patient",
-      col_icu = example_isolates$ward == "ICU",
-      info = TRUE,
-      icu_exclude = TRUE
-    ),
-    na.rm = TRUE
-  ) < 950
-)
-
-# set 1500 random observations to be of specimen type 'Urine'
-random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
-x <- example_isolates
-x$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) < 1400
-)
-# 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$ward == "ICU",
-    icu_exclude = TRUE,
-    info = TRUE
-  ), na.rm = TRUE) < 1000
-)
-
-# "No isolates found"
-test_iso <- example_isolates
-test_iso$specimen <- "test"
-expect_message(first_isolate(test_iso,
-  "date",
-  "patient",
-  col_mo = "mo",
-  col_specimen = "specimen",
-  filter_specimen = "something_unexisting",
-  info = TRUE
-))
-
-# 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
-))
-
-# errors
-expect_error(first_isolate("date", "patient", col_mo = "mo"))
-expect_error(first_isolate(example_isolates,
-  col_date = "non-existing col",
-  col_mo = "mo"
-))
-
-if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
-  # 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
-      )
+test_that("first_isolate works", {
+  # 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),
+    1387
  )

-  # support for WHONET
-  expect_message(example_isolates %>%
-    select(-patient) %>%
-    mutate(
-      `First name` = "test",
-      `Last name` = "test",
-      Sex = "Female"
-    ) %>%
-    first_isolate(info = TRUE))
+  # for phenotype determination
+  expect_equal(
+    AMR:::duplicated_antibiogram("SSSS", points_threshold = 2, ignore_I = TRUE, type = "points"),
+    FALSE
+  )
+  expect_equal(
+    AMR:::duplicated_antibiogram(c("RRR", "SSS"),
+      points_threshold = 2, ignore_I = TRUE, type = "points"
+    ),
+    c(FALSE, FALSE)
+  )
+  expect_equal(
+    AMR:::duplicated_antibiogram(c("RRR", "RRR", "SSS"),
+      points_threshold = 2, ignore_I = TRUE, type = "points"
+    ),
+    c(FALSE, TRUE, FALSE)
+  )
+  expect_equal(
+    AMR:::duplicated_antibiogram(c("RRR", "RSS", "SSS", "RSS", "RRR", "RRR", "SSS", "RSS", "RSR", "RRR"),
+      points_threshold = 2, ignore_I = TRUE, type = "points"
+    ),
+    c(FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE)
+  )

-  # groups
-  x <- example_isolates %>%
-    group_by(ward) %>%
-    mutate(first = first_isolate())
-  y <- example_isolates %>%
-    group_by(ward) %>%
-    mutate(first = first_isolate(.))
-  expect_identical(x, y)
-}
+  # 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),
+    1383
+  )
+  expect_equal(
+    sum(first_isolate(
+      x = example_isolates,
+      method = "phenotype-based",
+      type = "keyantimicrobials",
+      antifungal = NULL, info = TRUE, ignore_I = FALSE
+    ), na.rm = TRUE),
+    1397
+  )

-# missing dates should be no problem
-df <- example_isolates
-df[1:100, "date"] <- NA
-expect_equal(
-  sum(
-    first_isolate(
-      x = df,
+
+  # first non-ICU isolates
+  expect_true(
+    sum(
+      first_isolate(example_isolates,
+        col_mo = "mo",
+        col_date = "date",
+        col_patient_id = "patient",
+        col_icu = example_isolates$ward == "ICU",
+        info = TRUE,
+        icu_exclude = TRUE
+      ),
+      na.rm = TRUE
+    ) < 950
+  )
+
+  # set 1500 random observations to be of specimen type 'Urine'
+  random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
+  x <- example_isolates
+  x$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) < 1400
+  )
+  # 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$ward == "ICU",
+      icu_exclude = TRUE,
+      info = TRUE
+    ), na.rm = TRUE) < 1000
+  )
+
+  # "No isolates found"
+  test_iso <- example_isolates
+  test_iso$specimen <- "test"
+  expect_message(first_isolate(test_iso,
+    "date",
+    "patient",
+    col_mo = "mo",
+    col_specimen = "specimen",
+    filter_specimen = "something_unexisting",
+    info = TRUE
+  ))
+
+  # 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
+  ))
+
+  # errors
+  expect_error(first_isolate("date", "patient", col_mo = "mo"))
+  expect_error(first_isolate(example_isolates,
+    col_date = "non-existing col",
+    col_mo = "mo"
+  ))
+
+  if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0", also_load = TRUE)) {
+    # 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
+        )
+    )
+
+    # support for WHONET
+    expect_message(example_isolates %>%
+      select(-patient) %>%
+      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(.))
+    expect_identical(x, y)
+  }
+
+  # missing dates should be no problem
+  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
    ),
-    na.rm = TRUE
-  ),
-  1390
-)
+    1390
+  )

-# unknown MOs
-test_unknown <- example_isolates
-test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
-expect_equal(
-  sum(first_isolate(test_unknown, include_unknown = FALSE)),
-  1116
-)
-expect_equal(
-  sum(first_isolate(test_unknown, include_unknown = TRUE)),
-  1599
-)
+  # unknown MOs
+  test_unknown <- example_isolates
+  test_unknown$mo <- ifelse(test_unknown$mo == "B_ESCHR_COLI", "UNKNOWN", test_unknown$mo)
+  expect_equal(
+    sum(first_isolate(test_unknown, include_unknown = FALSE)),
+    1116
+  )
+  expect_equal(
+    sum(first_isolate(test_unknown, include_unknown = TRUE)),
+    1599
+  )

-test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
-expect_equal(
-  sum(first_isolate(test_unknown)),
-  1116
-)
+  test_unknown$mo <- ifelse(test_unknown$mo == "UNKNOWN", NA, test_unknown$mo)
+  expect_equal(
+    sum(first_isolate(test_unknown)),
+    1116
+  )

-# empty sir results
-expect_equal(
-  sum(first_isolate(example_isolates, include_untested_sir = FALSE)),
-  1374
-)
+  # empty sir results
+  expect_equal(
+    sum(first_isolate(example_isolates, include_untested_sir = FALSE)),
+    1374
+  )

-# shortcuts
-expect_identical(
-  filter_first_isolate(example_isolates),
-  subset(example_isolates, first_isolate(example_isolates))
-)
+  # shortcuts
+  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
-expect_true(all(first_isolate(AMR:::pm_distinct(example_isolates, mo, .keep_all = TRUE), info = TRUE) == TRUE))
+  # notice that all mo's are distinct, so all are TRUE
+  expect_true(all(first_isolate(AMR:::pm_distinct(example_isolates, mo, .keep_all = TRUE), info = TRUE) == TRUE))

-# only one isolate, so return fast
-expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
+  # only one isolate, so return fast
+  expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
+})