AMR/tests/testthat/test-first_isolates.R

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context("first_isolates.R")
test_that("keyantibiotics work", {
expect_equal(length(key_antibiotics(septic_patients, info = FALSE)), nrow(septic_patients))
expect_true(key_antibiotics_equal("SSS", "SSS"))
expect_true(key_antibiotics_equal("SSS", "SIS", ignore_I = TRUE))
expect_false(key_antibiotics_equal("SSS", "SIS", ignore_I = FALSE))
})
test_that("first isolates work", {
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# septic_patients contains 1959 out of 2000 first isolates
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expect_equal(
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sum(
first_isolate(tbl = septic_patients,
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col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
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info = FALSE),
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na.rm = TRUE),
1959)
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# septic_patients contains 1963 out of 2000 first *weighted* isolates
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expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_keyantibiotics = "keyab",
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
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1963)
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# and 1998 when using points
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_keyantibiotics = "keyab",
type = "points",
info = TRUE),
na.rm = TRUE)),
1998)
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# septic_patients contains 1732 out of 2000 first non-ICU isolates
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expect_equal(
sum(
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first_isolate(septic_patients,
col_bactid = "bactid",
col_date = "date",
col_patient_id = "patient_id",
col_icu = "ward_icu",
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1732)
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# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
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expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Unknown")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_specimen = "specimen",
filter_specimen = "Urine",
info = TRUE),
na.rm = TRUE),
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1501)
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# same, but now exclude ICU
expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Unknown")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_specimen = "specimen",
filter_specimen = "Urine",
col_icu = "ward_icu",
icu_exclude = TRUE,
info = TRUE),
na.rm = TRUE),
1501)
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})