mirror of https://github.com/msberends/AMR.git
48 lines
1.9 KiB
R
48 lines
1.9 KiB
R
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 1960 out of 2000 first isolates
|
|
#septic_ptns <- septic_patients
|
|
expect_equal(sum(first_isolate(tbl = septic_patients,
|
|
col_date = "date",
|
|
col_patient_id = "patient_id",
|
|
col_bactid = "bactid",
|
|
info = FALSE)), 1960)
|
|
|
|
# septic_patients contains 1962 out of 2000 first *weighted* isolates
|
|
#septic_ptns$keyab <- suppressWarnings(key_antibiotics(septic_ptns))
|
|
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))),
|
|
1962)
|
|
|
|
# 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)),
|
|
1501)
|
|
|
|
})
|