2018-03-27 17:43:42 +02:00
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context("first_isolates.R")
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test_that("keyantibiotics work", {
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expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
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expect_true(key_antibiotics_equal("SSS", "SSS"))
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expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
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expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
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})
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test_that("first isolates work", {
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2018-06-19 10:05:38 +02:00
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# septic_patients contains 1959 out of 2000 first isolates
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2018-04-02 16:05:09 +02:00
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expect_equal(
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2018-06-19 10:05:38 +02:00
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sum(
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first_isolate(tbl = septic_patients,
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2018-04-02 16:05:09 +02:00
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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2018-06-19 10:05:38 +02:00
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info = FALSE),
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2018-07-02 09:34:20 +02:00
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na.rm = TRUE),
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1959)
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2018-06-19 10:05:38 +02:00
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2018-07-15 22:56:41 +02:00
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# septic_patients contains 1963 out of 2000 first *weighted* isolates
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2018-06-19 10:05:38 +02:00
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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_bactid = "bactid",
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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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2018-07-15 22:56:41 +02:00
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1963)
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2018-07-02 09:34:20 +02:00
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# and 1998 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_bactid = "bactid",
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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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1998)
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2018-04-03 11:08:31 +02:00
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2018-06-19 10:05:38 +02:00
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# septic_patients contains 1732 out of 2000 first non-ICU isolates
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2018-04-20 13:45:34 +02:00
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expect_equal(
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sum(
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2018-06-19 10:05:38 +02:00
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first_isolate(septic_patients,
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col_bactid = "bactid",
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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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1732)
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2018-04-20 13:45:34 +02:00
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2018-04-03 11:08:31 +02:00
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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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2018-06-19 10:05:38 +02:00
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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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"Unknown")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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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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2018-04-03 11:08:31 +02:00
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1501)
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2018-07-02 09:34:20 +02:00
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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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"Unknown")),
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col_date = "date",
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col_patient_id = "patient_id",
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col_bactid = "bactid",
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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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2018-03-27 17:43:42 +02:00
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})
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