mirror of https://github.com/msberends/AMR.git
134 lines
4.9 KiB
R
Executable File
134 lines
4.9 KiB
R
Executable File
context("first_isolate.R")
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test_that("first isolates work", {
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# septic_patients contains 1331 out of 2000 first isolates
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expect_equal(
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sum(
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first_isolate(tbl = septic_patients,
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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info = TRUE),
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na.rm = TRUE),
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1331)
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# septic_patients contains 1426 out of 2000 first *weighted* isolates
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1426)
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# and 1449 when not ignoring I
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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ignore_I = FALSE,
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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1449)
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# and 1430 when using points
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expect_equal(
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suppressWarnings(
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sum(
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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type = "points",
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info = TRUE),
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na.rm = TRUE)),
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1430)
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# septic_patients contains 1176 out of 2000 first non-ICU isolates
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expect_equal(
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sum(
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first_isolate(septic_patients,
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col_mo = "mo",
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col_date = "date",
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col_patient_id = "patient_id",
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col_icu = "ward_icu",
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info = TRUE,
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icu_exclude = TRUE),
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na.rm = TRUE),
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1176)
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# set 1500 random observations to be of specimen type 'Urine'
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random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
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expect_lt(
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sum(
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first_isolate(tbl = mutate(septic_patients,
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specimen = if_else(row_number() %in% random_rows,
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"Urine",
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"Other")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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col_specimen = "specimen",
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filter_specimen = "Urine",
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info = TRUE),
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na.rm = TRUE),
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1501)
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# same, but now exclude ICU
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expect_lt(
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sum(
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first_isolate(tbl = mutate(septic_patients,
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specimen = if_else(row_number() %in% random_rows,
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"Urine",
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"Other")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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col_specimen = "specimen",
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filter_specimen = "Urine",
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col_icu = "ward_icu",
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icu_exclude = TRUE,
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info = TRUE),
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na.rm = TRUE),
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1501)
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# "No isolates found"
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expect_message(septic_patients %>%
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mutate(specimen = "test") %>%
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mutate(first = first_isolate(., "date", "patient_id",
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col_mo = "mo",
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col_specimen = "specimen",
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filter_specimen = "something_unexisting",
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output_logical = FALSE)))
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# printing of exclusion message
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expect_output(septic_patients %>%
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first_isolate(col_date = "date",
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col_mo = "mo",
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col_patient_id = "patient_id",
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col_testcode = "sex",
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testcodes_exclude = "M"))
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# errors
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expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
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expect_error(first_isolate(septic_patients))
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expect_error(first_isolate(septic_patients,
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col_date = "non-existing col",
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col_mo = "mo"))
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expect_warning(septic_patients %>%
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mutate(mo = as.character(mo)) %>%
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first_isolate(col_date = "date",
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col_mo = "mo",
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col_patient_id = "patient_id"))
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})
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