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new class bactid

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dr. M.S. (Matthijs) Berends
2018-07-23 14:14:03 +02:00
parent 40de1b4ac2
commit 8421638b60
21 changed files with 408 additions and 251 deletions
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88
tests/testthat/test-first_isolate.R Executable file
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context("first_isolate.R")
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 1962 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)),
1962)
# and 1997 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)),
1997)
# 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)
})