AMR/tests/testthat/test-first_isolates.R

96 lines
3.4 KiB
R
Executable File

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", {
# septic_patients contains 1959 out of 2000 first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
info = FALSE),
na.rm = TRUE),
1959)
# septic_patients contains 1961 out of 2000 first *weighted* isolates
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)),
1961)
# 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)
# septic_patients contains 1732 out of 2000 first non-ICU isolates
expect_equal(
sum(
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)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
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),
1501)
# 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)
})