tests/testthat/test-validate_data.R
In ramses-antibiotics/ramses-package: R Package for Antimicrobial Stewardship & Surveillance
date1 <- structure(1585220000, class = c("POSIXct", "POSIXt"))
# .validate_variable_exist ------------------------------------------------
test_that(".validate_variable_exist", {
testdata <- dplyr::tibble(
bidule = 1,
truc = 2
)
testdatatable <- data.table::data.table(
bidule = 1,
truc = 2
)
expect_true(.validate_variable_exist(testdata, c("bidule", "truc")))
expect_error(.validate_variable_exist(testdata, c("bidule", "truc", "bidul"), "error"))
expect_warning(.validate_variable_exist(testdata, c("bidule", "truc", "TRUC")))
expect_true(.validate_variable_exist(testdatatable, c("bidule", "truc")))
expect_error(.validate_variable_exist(testdatatable, c("bidule", "truc", "bidul"), "error"))
expect_warning(.validate_variable_exist(testdatatable, c("bidule", "truc", "TRUC")))
})
# .validate_variable_no_missing -------------------------------------------
test_that(".validate_variable_no_missing() on data.frame", {
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = "bidule"))
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = NULL))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = "error"))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.frame(foo = c("1", NA)),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", NA)),
vectorname = "foo",
action = "error"))
expect_true(.validate_variable_no_missing(
data = data.frame(foo = c("1", NA)),
vectorname = character(0),
action = "error"))
expect_true(.validate_variable_no_missing(
data.frame(bar = c("1", NA)),
vectorname = "foo",
action = "error"))
})
test_that(".validate_variable_no_missing() on data.table", {
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = "bidule"))
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = NULL))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = "error"))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", NA)),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", NA)),
vectorname = "foo",
action = "error"))
expect_true(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", NA)),
vectorname = character(0),
action = "error"))
expect_true(.validate_variable_no_missing(
data.table::data.table(bar = c("1", NA)),
vectorname = "foo",
action = "error"))
})
# .validate_inpatient_encounters/validate_inpatient_episodes -------------------
test_that("validate_inpatient_episodes on test dataset", {
expect_true(validate_inpatient_episodes(.ramses_mock_dataset$patients,
.ramses_mock_dataset$episodes))
expect_true(validate_inpatient_episodes(patients = .ramses_mock_dataset$patients,
episodes = .ramses_mock_dataset$episodes,
wards = inpatient_wards))
})
test_that(".validate_inpatient_encounters()/validate_inpatient_episodes() on data.frame", {
faulty_encounters <- data.frame(list(
patient_id = c(1, 2, 2),
encounter_id = c(1, 2, 3),
admission_date = c(date1, date1, date1 + 3*3600),
discharge_date = c(date1 - 12*3600,
date1 + 6*3600,
date1 + 6*3600)
))
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[1, ])))
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[-1, ])))
healthy_episodes <- data.frame(list(
patient_id = "1",
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
expect_equal(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes),
TRUE
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(wrong_variable = "1"),
episodes = healthy_episodes)
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "2"),
episodes = healthy_episodes)
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes[, -3])
)
expect_equal(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes,
wards = dplyr::tibble(
patient_id = "1",
encounter_id = 2,
ward_start = date1,
ward_end = date1 + 3*3600,
ward_code = "3E",
ward_display_name = "3 East",
ward_description = "3 East"
)),
TRUE
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes,
wards = dplyr::tibble(
patient_id = "1",
encounter_id = 2,
ward_start = date1,
ward_end = date1 + 3*3600,
ward_code = "3E",
ward_description = "3 East"
))
)
overlap_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 0.5*3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
missing_first_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 2:4,
last_episode_in_encounter = 2,
episode_start = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 2*3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
missing_intermediate_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = c(1, 3, 4),
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
missing_final_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
expect_true(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
missing_first_episode)))
expect_true(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
missing_intermediate_episode)))
expect_true(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
missing_final_episode)))
expect_false(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
overlap_episode)))
})
test_that(".validate_inpatient_encounters()/validate_inpatient_episodes() on data.table", {
faulty_encounters <- data.table::data.table(
patient_id = c(1, 2, 2),
encounter_id = c(1, 2, 3),
admission_date = c(date1, date1, date1 + 3*3600),
discharge_date = c(date1 - 12*3600,
date1 + 6*3600,
date1 + 6*3600)
)
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[1, ])))
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[-1, ])))
healthy_episodes <- data.table::data.table(
patient_id = "1",
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
expect_equal(
validate_inpatient_episodes(patients = data.table::data.table(patient_id = "1"),
episodes = healthy_episodes),
TRUE
)
expect_error(
validate_inpatient_episodes(patients = data.table::data.table(wrong_variable = "1"),
episodes = healthy_episodes)
)
expect_error(
validate_inpatient_episodes(patients = data.table::data.table(patient_id = "2"),
episodes = healthy_episodes)
)
overlap_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 0.5*3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
missing_first_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 2:4,
last_episode_in_encounter = 2,
episode_start = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 2*3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
missing_intermediate_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = c(1, 3, 4),
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
missing_final_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
episode_dates_inverted <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1, date1 + 3600, date1 + 2*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
encounter_dates_inverted <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1 + 4*3600,
discharge_date = date1,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
episode_spilling_out_of_encounter <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 5*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
expect_true(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
missing_first_episode)))
expect_true(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
missing_intermediate_episode)))
expect_true(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
missing_final_episode)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
overlap_episode)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
episode_dates_inverted)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
encounter_dates_inverted)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
episode_spilling_out_of_encounter)))
})
# validate_inpatient_diagnoses --------------------------------------------
test_that("validate_inpatient_diagnoses on test dataset", {
expect_warning(
validate_inpatient_diagnoses(
diagnoses_data = .ramses_mock_dataset$diagnoses,
diagnoses_lookup = .ramses_mock_dataset$icd10cm_2020))
})
test_that("validate_inpatient_diagnoses() on data.frame", {
test_diagnoses <- data.frame(list(
patient_id = 1,
encounter_id = 1,
episode_number = 1,
icd_code = c("J440", "N39", "N81", NA),
diagnosis_position = 1,
last_episode_in_encounter = "2"
))
test_lookup <- data.frame(list(
icd_code = c("J44", "N39"),
icd_display = c("J44", "N39"),
icd_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system"),
category_code = c("J44", "N39"),
category_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system")
))
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[1,],
diagnoses_lookup = test_lookup)))
expect_true(validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[2,],
diagnoses_lookup = test_lookup))
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = test_lookup)))
expect_error(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = dplyr::select(test_lookup, icd_code)))
expect_false(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[4,],
diagnoses_lookup = test_lookup)
))
expect_error(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,-2],
diagnoses_lookup = test_lookup))
})
test_that("validate_inpatient_diagnoses() on data.table", {
test_diagnoses <- data.table::data.table(
patient_id = 1,
encounter_id = 1,
episode_number = 1,
icd_code = c("J440", "N39", "N81", NA),
diagnosis_position = 1,
last_episode_in_encounter = "2"
)
test_lookup <- data.table::data.table(
icd_code = c("J44", "N39"),
icd_display = c("J44", "N39"),
icd_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system"),
category_code = c("J44", "N39"),
category_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system")
)
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[1,],
diagnoses_lookup = test_lookup)))
expect_true(validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[2,],
diagnoses_lookup = test_lookup))
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = test_lookup)))
expect_error(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = test_lookup[, icd_code]))
expect_false(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[4,],
diagnoses_lookup = test_lookup)
))
})
# validate_prescriptions --------------------------------------------------
test_that("validate_prescriptions on test dataset", {
expect_null(validate_prescriptions(.ramses_mock_dataset$drug_rx))
})
test_that("validate_prescriptions() on data.frame", {
expect_null(
validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
)
)
expect_error(validate_prescriptions(
data.frame(list(
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "biduletrucc'estleurtruc",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 400, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = NA,
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = "INVALID DATA",
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "ERROR!!!!!!!",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_null(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_warning(validate_prescriptions(
data.frame(list(
patient_id = c("5593245762", "5593245762"),
prescription_id = c("6025e96e1cc750dc6ec7fb9aadca0dbd", "2"),
prescription_text = c("Flucloxacillin IV 2g 3 days", "Flucloxacillin IV 2g 4 days"),
drug_code = c("FLC","FLC"), drug_name = c("Flucloxacillin", "Flucloxacillin"),
drug_display_name = c("Flucloxacillin", "Flucloxacillin"),
drug_group = c("Beta-lactams/penicillins",
"Beta-lactams/penicillins"),
antiinfective_type = c("antibacterial", "antibacterial"),
ATC_code = c("J01CF05","J01CF05"),
ATC_route = c("P", "P"),
authoring_date = rep(structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_start = rep(structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_end = rep(structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),2),
prescription_status = c("completed", "completed"),
prescription_context = c("inpatient", "inpatient"),
dose = c(2, 2), unit = c("g", "g"), route = c("IV", "IV"),
frequency = c("6H", "6H"),
daily_frequency = c(4, 4), DDD = c( 4, 4)), stringsAsFactors = F)
))
expect_null(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = as.POSIXct(NA),
prescription_status = "cancelled",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4))
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = as.POSIXct(NA),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4))
))
})
test_that("validate_prescriptions() on data.table", {
expect_error(validate_prescriptions(
data.table::data.table(
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_error(validate_prescriptions(
data.table::data.table(
patient_id = NA,
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_error(validate_prescriptions(
data.table::data.table(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = "INVALID DATA",
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_error(validate_prescriptions(
data.table::data.table(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "ERROR!!!!!!!",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_null(validate_prescriptions(
data.table::data.table(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_warning(validate_prescriptions(
data.table::data.table(
patient_id = c("5593245762", "5593245762"),
prescription_id = c("6025e96e1cc750dc6ec7fb9aadca0dbd", "2"),
prescription_text = c("Flucloxacillin IV 2g 3 days", "Flucloxacillin IV 2g 4 days"),
drug_code = c("FLC","FLC"), drug_name = c("Flucloxacillin", "Flucloxacillin"),
drug_display_name = c("Flucloxacillin", "Flucloxacillin"),
drug_group = c("Beta-lactams/penicillins",
"Beta-lactams/penicillins"),
antiinfective_type = c("antibacterial", "antibacterial"),
ATC_code = c("J01CF05","J01CF05"),
ATC_route = c("P", "P"),
authoring_date = rep(structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_start = rep(structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_end = rep(structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),2),
prescription_status = c("completed", "completed"),
prescription_context = c("inpatient", "inpatient"),
dose = c(2, 2), unit = c("g", "g"), route = c("IV", "IV"),
frequency = c("6H", "6H"),
daily_frequency = c(4, 4), DDD = c( 4, 4))
))
})
# validate_administrations ------------------------------------------------
test_that("validate_administrations on test dataset", {
expect_null(validate_administrations(.ramses_mock_dataset$drug_admins))
})
test_that("validate_administrations", {
test_admin <- data.frame(list(
patient_id = "3462786743",
administration_id = c("644", "645", "646"),
prescription_id = "a094fad22985020999e6a1773dfc87e3",
administration_text = "Meropenem IV 1g",
drug_code = "MEM", drug_name = "Meropenem", drug_display_name = "Meropenem",
drug_group = "Carbapenems",
antiinfective_type = "antibacterial",
ATC_code = "J01DH02", ATC_route = "P",
dose = 1, unit = "g",
route = "IV",
administration_date = structure(
c(1491142845, 1491142846, 1491142845),
tzone = "Europe/London",
class = c("POSIXct", "POSIXt")
),
administration_status = "completed",
DDD = 0.333333333333333
))
expect_null(validate_administrations(test_admin[1,]))
expect_null(validate_administrations(test_admin[1:2,]))
expect_warning(
expect_null(
expect_null(validate_administrations(test_admin[1:3,])))
)
})
# arrange_variables -------------------------------------------------------
test_that("arrange_variables", {
testdf <- data.frame(list(
misc = 3,
encounter_id = 2,
patient_id = 1
))
testDT <- data.table::data.table(
misc = 3,
encounter_id = 2,
patient_id = 1
)
expect_error(arrange_variables(testdf, "missing variable"))
expect_equal(
colnames(arrange_variables(testdf, c("patient_id", "encounter_id"))),
c("patient_id", "encounter_id", "misc"))
expect_error(arrange_variables(testDT, "missing variable"))
expect_equal(
colnames(arrange_variables(testDT, c("patient_id", "encounter_id"))),
c("patient_id", "encounter_id", "misc"))
})
# .validate_values_unique -------------------------------------------------
test_that(".validate_values_unique()", {
testdata <- data.frame(list(a = 1:4, b = rep(4, 4)))
testdatatable <- data.table::data.table(a = 1:4, b = rep(4, 4))
expect_true(.validate_values_unique(testdata, c("a")))
expect_error(.validate_values_unique(testdata, c("a", "b")))
expect_error(.validate_values_unique(testdata, c("b")))
expect_true(.validate_values_unique(testdata, c("a", "c")))
expect_true(.validate_values_unique(testdata, c("c")))
expect_true(.validate_values_unique(testdata, c()))
expect_true(.validate_values_unique(testdata, NULL))
expect_true(.validate_values_unique(testdatatable, c("a")))
expect_error(.validate_values_unique(testdatatable, c("a", "b")))
expect_error(.validate_values_unique(testdatatable, c("b")))
expect_true(.validate_values_unique(testdatatable, c("a", "c")))
expect_true(.validate_values_unique(testdatatable, c("c")))
expect_true(.validate_values_unique(testdatatable, c()))
expect_true(.validate_values_unique(testdatatable, NULL))
})
# .validate_UCUM_codes ----------------------------------------------------
test_that(".validate_UCUM_codes()", {
testdata <- c('absurd_code', NA, '', '%', 'degree_Celsius', 'mm_Hg', '10^9/L',
'mmol/L', 'fL', 'g/L', 'pg', 'micromol/L', 'mg/L')
expect_error(.validate_UCUM_codes(testdata[1:5]))
expect_true(.validate_UCUM_codes(testdata[-1]))
})
# validate_microbiology ---------------------------------------------------
test_that("validate_microbiology on test dataset", {
expect_true(validate_microbiology(
.ramses_mock_dataset$micro$specimens,
.ramses_mock_dataset$micro$isolates,
.ramses_mock_dataset$micro$susceptibilities
))
})
test_that("validate_microbiology on data.frame", {
testdata = list(
specimens = data.frame(list(
specimen_id = "1",
patient_id = "1",
status = "available",
specimen_datetime = Sys.time(),
specimen_type_code = "122575003",
specimen_type_name = "Urine specimen",
specimen_type_display = "Urine"
), stringsAsFactors = FALSE),
isolates = data.frame(
list(isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = structure("B_ESCHR_COLI", class = c("mo", "character")),
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
multidrug_resistance = "Multi-drug-resistant (MDR)",
isolation_datetime = Sys.time() + 259200
), stringsAsFactors = FALSE),
susceptibilities = data.frame(list(
isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = "B_ESCHR_COLI",
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
agent_code = c("AMP", "AMC", "CAZ", "CTX", "CIP", "LEX", "CXM", "ETP",
"FOS", "GEN", "MEM", "NIT", "TZP", "TMP"),
agent_name = c("Ampicillin", "Amoxicillin/clavulanic acid", "Ceftazidime", "Cefotaxime",
"Ciprofloxacin", "Cephalexin", "Cefuroxime", "Ertapenem", "Fosfomycin",
"Gentamicin", "Meropenem", "Nitrofurantoin", "Piperacillin/tazobactam",
"Trimethoprim"),
agent_display_name = c("Ampicillin", "Co-amoxiclav", "Ceftazidime", "Cefotaxime", "Ciprofloxacin",
"Cefalexin", "Cefuroxime", "Ertapenem", "Fosfomycin", "Gentamicin",
"Meropenem", "Nitrofurantoin", "Piperacillin + Tazobactam", "Trimethoprim"),
rsi_code = c("R", "R", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "R", "R")
), stringsAsFactors = FALSE)
)
expect_true(validate_microbiology(
testdata$specimens,
testdata$isolates,
testdata$susceptibilities
))
# wrong specimen code
testdata_spec_code <- testdata
testdata_spec_code$specimens$specimen_type_code <- "biduletruccleurtruc"
expect_warning(validate_microbiology(
testdata_spec_code$specimens,
testdata_spec_code$isolates,
testdata_spec_code$susceptibilities
))
# missing relations
testdata_missing_id1 <- testdata
testdata_missing_id1$susceptibilities$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id1$specimens,
testdata_missing_id1$isolates,
testdata_missing_id1$susceptibilities
))
testdata_missing_id2 <- testdata
testdata_missing_id2$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id2$specimens,
testdata_missing_id2$isolates,
testdata_missing_id2$susceptibilities
))
testdata_missing_id3 <- testdata
testdata_missing_id3$isolates$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id3$specimens,
testdata_missing_id3$isolates,
testdata_missing_id3$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$isolates$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_drug_codes <- testdata
testdata_invalid_drug_codes$susceptibilities$agent_code[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_drug_codes$specimens,
testdata_invalid_drug_codes$isolates,
testdata_invalid_drug_codes$susceptibilities
))
})
test_that("validate_microbiology on data.table", {
testdata = list(
specimens = data.table::data.table(
specimen_id = "1",
patient_id = "1",
status = "available",
specimen_datetime = Sys.time(),
specimen_type_code = "122575003",
specimen_type_name = "Urine specimen",
specimen_type_display = "Urine"
),
isolates = data.table::data.table(
isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = structure("B_ESCHR_COLI", class = c("mo", "character")),
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
multidrug_resistance = "Multi-drug-resistant (MDR)",
isolation_datetime = Sys.time() + 259200
),
susceptibilities = data.table::data.table(
isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = "B_ESCHR_COLI",
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
agent_code = c("AMP", "AMC", "CAZ", "CTX", "CIP", "LEX", "CXM", "ETP",
"FOS", "GEN", "MEM", "NIT", "TZP", "TMP"),
agent_name = c("Ampicillin", "Amoxicillin/clavulanic acid", "Ceftazidime", "Cefotaxime",
"Ciprofloxacin", "Cephalexin", "Cefuroxime", "Ertapenem", "Fosfomycin",
"Gentamicin", "Meropenem", "Nitrofurantoin", "Piperacillin/tazobactam",
"Trimethoprim"),
agent_display_name = c("Ampicillin", "Co-amoxiclav", "Ceftazidime", "Cefotaxime", "Ciprofloxacin",
"Cefalexin", "Cefuroxime", "Ertapenem", "Fosfomycin", "Gentamicin",
"Meropenem", "Nitrofurantoin", "Piperacillin + Tazobactam", "Trimethoprim"),
rsi_code = c("R", "R", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "R", "R")
)
)
expect_true(validate_microbiology(
testdata$specimens,
testdata$isolates,
testdata$susceptibilities
))
# wrong specimen code
testdata_spec_code <- testdata
testdata_spec_code$specimens$specimen_type_code <- "biduletruccleurtruc"
expect_warning(validate_microbiology(
testdata_spec_code$specimens,
testdata_spec_code$isolates,
testdata_spec_code$susceptibilities
))
# missing relations
testdata_missing_id1 <- testdata
testdata_missing_id1$susceptibilities$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id1$specimens,
testdata_missing_id1$isolates,
testdata_missing_id1$susceptibilities
))
testdata_missing_id2 <- testdata
testdata_missing_id2$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id2$specimens,
testdata_missing_id2$isolates,
testdata_missing_id2$susceptibilities
))
testdata_missing_id3 <- testdata
testdata_missing_id3$isolates$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id3$specimens,
testdata_missing_id3$isolates,
testdata_missing_id3$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$isolates$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_drug_codes <- testdata
testdata_invalid_drug_codes$susceptibilities$agent_code[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_drug_codes$specimens,
testdata_invalid_drug_codes$isolates,
testdata_invalid_drug_codes$susceptibilities
))
})
# validate_investigations -------------------------------------------------
test_that("validate_investigations on test dataset", {
expect_true(validate_investigations(inpatient_investigations))
})
test_that("validate_investigations", {
example_data <- dplyr::tibble(
observation_id = c("1", "2"),
patient_id = "99999999999",
encounter_id = "9278078393", status = "final",
request_datetime = as.POSIXct("2016-03-30 13:51:13"),
observation_datetime = as.POSIXct("2016-03-30 13:51:45"),
observation_value_text = "",
observation_value_numeric = c(35.7, 100.4),
observation_name = "Body temperature",
observation_display = "Temperature",
observation_code_system = "http://loinc.org",
observation_code = "8310-5",
observation_unit = c("degree_Celsius", "degree_F")
)
example_datatable <- data.table::data.table(
observation_id = c("1", "2"),
patient_id = "99999999999",
encounter_id = "9278078393", status = "final",
request_datetime = as.POSIXct("2016-03-30 13:51:13"),
observation_datetime = as.POSIXct("2016-03-30 13:51:45"),
observation_value_text = "",
observation_value_numeric = c(35.7, 100.4),
observation_name = "Body temperature",
observation_display = "Temperature",
observation_code_system = "http://loinc.org",
observation_code = "8310-5",
observation_unit = c("degree_Celsius", "degree_F")
)
expect_true(validate_investigations(example_data[1,]))
expect_error(validate_investigations(example_data))
expect_true(validate_investigations(example_datatable[1,]))
expect_error(validate_investigations(example_datatable))
non_unique_metadata <- dplyr::tibble(
observation_id = c("1", "2"),
patient_id = "99999999999",
encounter_id = "9278078393", status = "final",
request_datetime = as.POSIXct("2016-03-30 13:51:13"),
observation_datetime = as.POSIXct("2016-03-30 13:51:45"),
observation_value_text = "",
observation_value_numeric = c(35.7, 100.4),
observation_name = "Body temperature",
observation_display = c("Body temperature", "Temperature"),
observation_code_system = "http://loinc.org",
observation_code = "8310-5",
observation_unit = c("degree_Celsius", "degree_Celsius")
)
expect_error(
validate_investigations(non_unique_metadata),
"^Every `observation_code` must only be associated with one `observation_name` and `observation_display` only"
)
})
# Bug 85 ------------------------------------------------------------------
test_that("Bug 85 - uniqueness of patient_id in patient dataset", {
expect_error(
validate_inpatient_episodes(
patients = data.frame(
patient_id = c("1253675584", "1253675584"),
NHS_number = c("5632763868", "5632763868"),
forename = c("jflmnfcjnc", "jflmnfcjnc"),
surname = c("mljkaigaji", "mljkaigaji"),
sex = c("1", "1"), ethnic_category_UK = c("A", "A"),
date_of_birth = c("1999-11-21", "1999-11-21"),
date_of_death = c(NA_character_, NA_character_)
),
episodes = data.frame(
patient_id = "1253675584", encounter_id = "8751633817",
admission_method = "2",
admission_date = as.POSIXct("2015-02-26 18:30:55"),
discharge_date = as.POSIXct("2015-03-17 17:23:49"),
episode_number = 1L, last_episode_in_encounter = "2",
episode_start = as.POSIXct("2015-02-26 18:30:55"),
episode_end = as.POSIXct("2015-03-17 17:23:49"),
consultant_code = "C1000002",
main_specialty_code = "100",
last_episode_in_encounter = 2,
ramses_bed_days = 1.72303240740741
)
)
)
})
ramses-antibiotics/ramses-package documentation built on Feb. 13, 2024, 1:01 p.m.
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date1 <- structure(1585220000, class = c("POSIXct", "POSIXt"))
# .validate_variable_exist ------------------------------------------------
test_that(".validate_variable_exist", {
testdata <- dplyr::tibble(
bidule = 1,
truc = 2
)
testdatatable <- data.table::data.table(
bidule = 1,
truc = 2
)
expect_true(.validate_variable_exist(testdata, c("bidule", "truc")))
expect_error(.validate_variable_exist(testdata, c("bidule", "truc", "bidul"), "error"))
expect_warning(.validate_variable_exist(testdata, c("bidule", "truc", "TRUC")))
expect_true(.validate_variable_exist(testdatatable, c("bidule", "truc")))
expect_error(.validate_variable_exist(testdatatable, c("bidule", "truc", "bidul"), "error"))
expect_warning(.validate_variable_exist(testdatatable, c("bidule", "truc", "TRUC")))
})
# .validate_variable_no_missing -------------------------------------------
test_that(".validate_variable_no_missing() on data.frame", {
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = "bidule"))
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = NULL))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", "")),
vectorname = "foo",
action = "error"))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.frame(foo = c("1", NA)),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.frame(foo = c("1", NA)),
vectorname = "foo",
action = "error"))
expect_true(.validate_variable_no_missing(
data = data.frame(foo = c("1", NA)),
vectorname = character(0),
action = "error"))
expect_true(.validate_variable_no_missing(
data.frame(bar = c("1", NA)),
vectorname = "foo",
action = "error"))
})
test_that(".validate_variable_no_missing() on data.table", {
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = "bidule"))
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = NULL))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", "")),
vectorname = "foo",
action = "error"))
expect_false(expect_warning(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", NA)),
vectorname = "foo",
action = "warning")))
expect_error(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", NA)),
vectorname = "foo",
action = "error"))
expect_true(.validate_variable_no_missing(
data = data.table::data.table(foo = c("1", NA)),
vectorname = character(0),
action = "error"))
expect_true(.validate_variable_no_missing(
data.table::data.table(bar = c("1", NA)),
vectorname = "foo",
action = "error"))
})
# .validate_inpatient_encounters/validate_inpatient_episodes -------------------
test_that("validate_inpatient_episodes on test dataset", {
expect_true(validate_inpatient_episodes(.ramses_mock_dataset$patients,
.ramses_mock_dataset$episodes))
expect_true(validate_inpatient_episodes(patients = .ramses_mock_dataset$patients,
episodes = .ramses_mock_dataset$episodes,
wards = inpatient_wards))
})
test_that(".validate_inpatient_encounters()/validate_inpatient_episodes() on data.frame", {
faulty_encounters <- data.frame(list(
patient_id = c(1, 2, 2),
encounter_id = c(1, 2, 3),
admission_date = c(date1, date1, date1 + 3*3600),
discharge_date = c(date1 - 12*3600,
date1 + 6*3600,
date1 + 6*3600)
))
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[1, ])))
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[-1, ])))
healthy_episodes <- data.frame(list(
patient_id = "1",
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
expect_equal(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes),
TRUE
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(wrong_variable = "1"),
episodes = healthy_episodes)
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "2"),
episodes = healthy_episodes)
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes[, -3])
)
expect_equal(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes,
wards = dplyr::tibble(
patient_id = "1",
encounter_id = 2,
ward_start = date1,
ward_end = date1 + 3*3600,
ward_code = "3E",
ward_display_name = "3 East",
ward_description = "3 East"
)),
TRUE
)
expect_error(
validate_inpatient_episodes(patients = dplyr::tibble(patient_id = "1"),
episodes = healthy_episodes,
wards = dplyr::tibble(
patient_id = "1",
encounter_id = 2,
ward_start = date1,
ward_end = date1 + 3*3600,
ward_code = "3E",
ward_description = "3 East"
))
)
overlap_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 0.5*3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
missing_first_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 2:4,
last_episode_in_encounter = 2,
episode_start = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 2*3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
missing_intermediate_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = c(1, 3, 4),
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
missing_final_episode <- data.frame(list(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
))
expect_true(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
missing_first_episode)))
expect_true(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
missing_intermediate_episode)))
expect_true(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
missing_final_episode)))
expect_false(expect_warning(validate_inpatient_episodes(dplyr::tibble(patient_id = 1),
overlap_episode)))
})
test_that(".validate_inpatient_encounters()/validate_inpatient_episodes() on data.table", {
faulty_encounters <- data.table::data.table(
patient_id = c(1, 2, 2),
encounter_id = c(1, 2, 3),
admission_date = c(date1, date1, date1 + 3*3600),
discharge_date = c(date1 - 12*3600,
date1 + 6*3600,
date1 + 6*3600)
)
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[1, ])))
expect_false(expect_warning(.validate_inpatient_encounters(faulty_encounters[-1, ])))
healthy_episodes <- data.table::data.table(
patient_id = "1",
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
expect_equal(
validate_inpatient_episodes(patients = data.table::data.table(patient_id = "1"),
episodes = healthy_episodes),
TRUE
)
expect_error(
validate_inpatient_episodes(patients = data.table::data.table(wrong_variable = "1"),
episodes = healthy_episodes)
)
expect_error(
validate_inpatient_episodes(patients = data.table::data.table(patient_id = "2"),
episodes = healthy_episodes)
)
overlap_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 3*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 0.5*3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
missing_first_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 2:4,
last_episode_in_encounter = 2,
episode_start = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 2*3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
missing_intermediate_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = c(1, 3, 4),
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1 + 3600, date1 + 3*3600, date1 + 4*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
missing_final_episode <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
episode_dates_inverted <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
episode_end = c(date1, date1 + 3600, date1 + 2*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
encounter_dates_inverted <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1 + 4*3600,
discharge_date = date1,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 3*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
episode_spilling_out_of_encounter <- data.table::data.table(
patient_id = 1,
encounter_id = 2,
admission_date = date1,
discharge_date = date1 + 4*3600,
episode_number = 1:3,
last_episode_in_encounter = 2,
episode_start = c(date1, date1 + 3600, date1 + 2*3600),
episode_end = c(date1 + 3600, date1 + 2*3600, date1 + 5*3600),
admission_method = "2",
consultant_code = "CXXXXXX",
main_specialty_code = "100"
)
expect_true(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
missing_first_episode)))
expect_true(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
missing_intermediate_episode)))
expect_true(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
missing_final_episode)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
overlap_episode)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
episode_dates_inverted)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
encounter_dates_inverted)))
expect_false(expect_warning(validate_inpatient_episodes(data.table::data.table(patient_id = 1),
episode_spilling_out_of_encounter)))
})
# validate_inpatient_diagnoses --------------------------------------------
test_that("validate_inpatient_diagnoses on test dataset", {
expect_warning(
validate_inpatient_diagnoses(
diagnoses_data = .ramses_mock_dataset$diagnoses,
diagnoses_lookup = .ramses_mock_dataset$icd10cm_2020))
})
test_that("validate_inpatient_diagnoses() on data.frame", {
test_diagnoses <- data.frame(list(
patient_id = 1,
encounter_id = 1,
episode_number = 1,
icd_code = c("J440", "N39", "N81", NA),
diagnosis_position = 1,
last_episode_in_encounter = "2"
))
test_lookup <- data.frame(list(
icd_code = c("J44", "N39"),
icd_display = c("J44", "N39"),
icd_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system"),
category_code = c("J44", "N39"),
category_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system")
))
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[1,],
diagnoses_lookup = test_lookup)))
expect_true(validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[2,],
diagnoses_lookup = test_lookup))
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = test_lookup)))
expect_error(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = dplyr::select(test_lookup, icd_code)))
expect_false(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[4,],
diagnoses_lookup = test_lookup)
))
expect_error(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,-2],
diagnoses_lookup = test_lookup))
})
test_that("validate_inpatient_diagnoses() on data.table", {
test_diagnoses <- data.table::data.table(
patient_id = 1,
encounter_id = 1,
episode_number = 1,
icd_code = c("J440", "N39", "N81", NA),
diagnosis_position = 1,
last_episode_in_encounter = "2"
)
test_lookup <- data.table::data.table(
icd_code = c("J44", "N39"),
icd_display = c("J44", "N39"),
icd_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system"),
category_code = c("J44", "N39"),
category_description = c("Other chronic obstructive pulmonary disease",
"Other disorders of urinary system")
)
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[1,],
diagnoses_lookup = test_lookup)))
expect_true(validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[2,],
diagnoses_lookup = test_lookup))
expect_true(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = test_lookup)))
expect_error(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[3,],
diagnoses_lookup = test_lookup[, icd_code]))
expect_false(expect_warning(
validate_inpatient_diagnoses(diagnoses_data = test_diagnoses[4,],
diagnoses_lookup = test_lookup)
))
})
# validate_prescriptions --------------------------------------------------
test_that("validate_prescriptions on test dataset", {
expect_null(validate_prescriptions(.ramses_mock_dataset$drug_rx))
})
test_that("validate_prescriptions() on data.frame", {
expect_null(
validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
)
)
expect_error(validate_prescriptions(
data.frame(list(
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "biduletrucc'estleurtruc",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 400, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = NA,
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = "INVALID DATA",
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "ERROR!!!!!!!",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_null(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4), stringsAsFactors = F)
))
expect_warning(validate_prescriptions(
data.frame(list(
patient_id = c("5593245762", "5593245762"),
prescription_id = c("6025e96e1cc750dc6ec7fb9aadca0dbd", "2"),
prescription_text = c("Flucloxacillin IV 2g 3 days", "Flucloxacillin IV 2g 4 days"),
drug_code = c("FLC","FLC"), drug_name = c("Flucloxacillin", "Flucloxacillin"),
drug_display_name = c("Flucloxacillin", "Flucloxacillin"),
drug_group = c("Beta-lactams/penicillins",
"Beta-lactams/penicillins"),
antiinfective_type = c("antibacterial", "antibacterial"),
ATC_code = c("J01CF05","J01CF05"),
ATC_route = c("P", "P"),
authoring_date = rep(structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_start = rep(structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_end = rep(structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),2),
prescription_status = c("completed", "completed"),
prescription_context = c("inpatient", "inpatient"),
dose = c(2, 2), unit = c("g", "g"), route = c("IV", "IV"),
frequency = c("6H", "6H"),
daily_frequency = c(4, 4), DDD = c( 4, 4)), stringsAsFactors = F)
))
expect_null(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = as.POSIXct(NA),
prescription_status = "cancelled",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4))
))
expect_error(validate_prescriptions(
data.frame(list(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = as.POSIXct(NA),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4))
))
})
test_that("validate_prescriptions() on data.table", {
expect_error(validate_prescriptions(
data.table::data.table(
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_error(validate_prescriptions(
data.table::data.table(
patient_id = NA,
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_error(validate_prescriptions(
data.table::data.table(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = "INVALID DATA",
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_error(validate_prescriptions(
data.table::data.table(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_group = "Beta-lactam antibacterials, penicillins",
ATC_route = "ERROR!!!!!!!",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_null(validate_prescriptions(
data.table::data.table(
patient_id = "5593245762",
prescription_id = "6025e96e1cc750dc6ec7fb9aadca0dbd",
prescription_text = "Flucloxacillin IV 2g 3 days",
drug_code = "FLC", drug_name = "Flucloxacillin",
drug_display_name = "Flucloxacillin",
drug_group = "Beta-lactams/penicillins",
antiinfective_type = c("antibacterial"),
ATC_code = "J01CF05",
ATC_route = "P",
authoring_date = structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_start = structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_end = structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),
prescription_status = "completed",
prescription_context = "inpatient",
dose = 2, unit = "g", route = "IV", frequency = "6H",
daily_frequency = 4, DDD = 4)
))
expect_warning(validate_prescriptions(
data.table::data.table(
patient_id = c("5593245762", "5593245762"),
prescription_id = c("6025e96e1cc750dc6ec7fb9aadca0dbd", "2"),
prescription_text = c("Flucloxacillin IV 2g 3 days", "Flucloxacillin IV 2g 4 days"),
drug_code = c("FLC","FLC"), drug_name = c("Flucloxacillin", "Flucloxacillin"),
drug_display_name = c("Flucloxacillin", "Flucloxacillin"),
drug_group = c("Beta-lactams/penicillins",
"Beta-lactams/penicillins"),
antiinfective_type = c("antibacterial", "antibacterial"),
ATC_code = c("J01CF05","J01CF05"),
ATC_route = c("P", "P"),
authoring_date = rep(structure(1421048831,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_start = rep(structure(1421051891,
class = c("POSIXct", "POSIXt"),
tzone = ""), 2),
prescription_end = rep(structure(1421311091,
class = c("POSIXct", "POSIXt"),
tzone = ""),2),
prescription_status = c("completed", "completed"),
prescription_context = c("inpatient", "inpatient"),
dose = c(2, 2), unit = c("g", "g"), route = c("IV", "IV"),
frequency = c("6H", "6H"),
daily_frequency = c(4, 4), DDD = c( 4, 4))
))
})
# validate_administrations ------------------------------------------------
test_that("validate_administrations on test dataset", {
expect_null(validate_administrations(.ramses_mock_dataset$drug_admins))
})
test_that("validate_administrations", {
test_admin <- data.frame(list(
patient_id = "3462786743",
administration_id = c("644", "645", "646"),
prescription_id = "a094fad22985020999e6a1773dfc87e3",
administration_text = "Meropenem IV 1g",
drug_code = "MEM", drug_name = "Meropenem", drug_display_name = "Meropenem",
drug_group = "Carbapenems",
antiinfective_type = "antibacterial",
ATC_code = "J01DH02", ATC_route = "P",
dose = 1, unit = "g",
route = "IV",
administration_date = structure(
c(1491142845, 1491142846, 1491142845),
tzone = "Europe/London",
class = c("POSIXct", "POSIXt")
),
administration_status = "completed",
DDD = 0.333333333333333
))
expect_null(validate_administrations(test_admin[1,]))
expect_null(validate_administrations(test_admin[1:2,]))
expect_warning(
expect_null(
expect_null(validate_administrations(test_admin[1:3,])))
)
})
# arrange_variables -------------------------------------------------------
test_that("arrange_variables", {
testdf <- data.frame(list(
misc = 3,
encounter_id = 2,
patient_id = 1
))
testDT <- data.table::data.table(
misc = 3,
encounter_id = 2,
patient_id = 1
)
expect_error(arrange_variables(testdf, "missing variable"))
expect_equal(
colnames(arrange_variables(testdf, c("patient_id", "encounter_id"))),
c("patient_id", "encounter_id", "misc"))
expect_error(arrange_variables(testDT, "missing variable"))
expect_equal(
colnames(arrange_variables(testDT, c("patient_id", "encounter_id"))),
c("patient_id", "encounter_id", "misc"))
})
# .validate_values_unique -------------------------------------------------
test_that(".validate_values_unique()", {
testdata <- data.frame(list(a = 1:4, b = rep(4, 4)))
testdatatable <- data.table::data.table(a = 1:4, b = rep(4, 4))
expect_true(.validate_values_unique(testdata, c("a")))
expect_error(.validate_values_unique(testdata, c("a", "b")))
expect_error(.validate_values_unique(testdata, c("b")))
expect_true(.validate_values_unique(testdata, c("a", "c")))
expect_true(.validate_values_unique(testdata, c("c")))
expect_true(.validate_values_unique(testdata, c()))
expect_true(.validate_values_unique(testdata, NULL))
expect_true(.validate_values_unique(testdatatable, c("a")))
expect_error(.validate_values_unique(testdatatable, c("a", "b")))
expect_error(.validate_values_unique(testdatatable, c("b")))
expect_true(.validate_values_unique(testdatatable, c("a", "c")))
expect_true(.validate_values_unique(testdatatable, c("c")))
expect_true(.validate_values_unique(testdatatable, c()))
expect_true(.validate_values_unique(testdatatable, NULL))
})
# .validate_UCUM_codes ----------------------------------------------------
test_that(".validate_UCUM_codes()", {
testdata <- c('absurd_code', NA, '', '%', 'degree_Celsius', 'mm_Hg', '10^9/L',
'mmol/L', 'fL', 'g/L', 'pg', 'micromol/L', 'mg/L')
expect_error(.validate_UCUM_codes(testdata[1:5]))
expect_true(.validate_UCUM_codes(testdata[-1]))
})
# validate_microbiology ---------------------------------------------------
test_that("validate_microbiology on test dataset", {
expect_true(validate_microbiology(
.ramses_mock_dataset$micro$specimens,
.ramses_mock_dataset$micro$isolates,
.ramses_mock_dataset$micro$susceptibilities
))
})
test_that("validate_microbiology on data.frame", {
testdata = list(
specimens = data.frame(list(
specimen_id = "1",
patient_id = "1",
status = "available",
specimen_datetime = Sys.time(),
specimen_type_code = "122575003",
specimen_type_name = "Urine specimen",
specimen_type_display = "Urine"
), stringsAsFactors = FALSE),
isolates = data.frame(
list(isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = structure("B_ESCHR_COLI", class = c("mo", "character")),
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
multidrug_resistance = "Multi-drug-resistant (MDR)",
isolation_datetime = Sys.time() + 259200
), stringsAsFactors = FALSE),
susceptibilities = data.frame(list(
isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = "B_ESCHR_COLI",
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
agent_code = c("AMP", "AMC", "CAZ", "CTX", "CIP", "LEX", "CXM", "ETP",
"FOS", "GEN", "MEM", "NIT", "TZP", "TMP"),
agent_name = c("Ampicillin", "Amoxicillin/clavulanic acid", "Ceftazidime", "Cefotaxime",
"Ciprofloxacin", "Cephalexin", "Cefuroxime", "Ertapenem", "Fosfomycin",
"Gentamicin", "Meropenem", "Nitrofurantoin", "Piperacillin/tazobactam",
"Trimethoprim"),
agent_display_name = c("Ampicillin", "Co-amoxiclav", "Ceftazidime", "Cefotaxime", "Ciprofloxacin",
"Cefalexin", "Cefuroxime", "Ertapenem", "Fosfomycin", "Gentamicin",
"Meropenem", "Nitrofurantoin", "Piperacillin + Tazobactam", "Trimethoprim"),
rsi_code = c("R", "R", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "R", "R")
), stringsAsFactors = FALSE)
)
expect_true(validate_microbiology(
testdata$specimens,
testdata$isolates,
testdata$susceptibilities
))
# wrong specimen code
testdata_spec_code <- testdata
testdata_spec_code$specimens$specimen_type_code <- "biduletruccleurtruc"
expect_warning(validate_microbiology(
testdata_spec_code$specimens,
testdata_spec_code$isolates,
testdata_spec_code$susceptibilities
))
# missing relations
testdata_missing_id1 <- testdata
testdata_missing_id1$susceptibilities$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id1$specimens,
testdata_missing_id1$isolates,
testdata_missing_id1$susceptibilities
))
testdata_missing_id2 <- testdata
testdata_missing_id2$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id2$specimens,
testdata_missing_id2$isolates,
testdata_missing_id2$susceptibilities
))
testdata_missing_id3 <- testdata
testdata_missing_id3$isolates$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id3$specimens,
testdata_missing_id3$isolates,
testdata_missing_id3$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$isolates$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_drug_codes <- testdata
testdata_invalid_drug_codes$susceptibilities$agent_code[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_drug_codes$specimens,
testdata_invalid_drug_codes$isolates,
testdata_invalid_drug_codes$susceptibilities
))
})
test_that("validate_microbiology on data.table", {
testdata = list(
specimens = data.table::data.table(
specimen_id = "1",
patient_id = "1",
status = "available",
specimen_datetime = Sys.time(),
specimen_type_code = "122575003",
specimen_type_name = "Urine specimen",
specimen_type_display = "Urine"
),
isolates = data.table::data.table(
isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = structure("B_ESCHR_COLI", class = c("mo", "character")),
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
multidrug_resistance = "Multi-drug-resistant (MDR)",
isolation_datetime = Sys.time() + 259200
),
susceptibilities = data.table::data.table(
isolate_id = "1",
specimen_id = "1",
patient_id = "1",
organism_code = "B_ESCHR_COLI",
organism_name = "Escherichia coli",
organism_display_name = "Escherichia coli",
agent_code = c("AMP", "AMC", "CAZ", "CTX", "CIP", "LEX", "CXM", "ETP",
"FOS", "GEN", "MEM", "NIT", "TZP", "TMP"),
agent_name = c("Ampicillin", "Amoxicillin/clavulanic acid", "Ceftazidime", "Cefotaxime",
"Ciprofloxacin", "Cephalexin", "Cefuroxime", "Ertapenem", "Fosfomycin",
"Gentamicin", "Meropenem", "Nitrofurantoin", "Piperacillin/tazobactam",
"Trimethoprim"),
agent_display_name = c("Ampicillin", "Co-amoxiclav", "Ceftazidime", "Cefotaxime", "Ciprofloxacin",
"Cefalexin", "Cefuroxime", "Ertapenem", "Fosfomycin", "Gentamicin",
"Meropenem", "Nitrofurantoin", "Piperacillin + Tazobactam", "Trimethoprim"),
rsi_code = c("R", "R", "S", "S", "R", "S", "S", "S", "S", "S", "S", "S", "R", "R")
)
)
expect_true(validate_microbiology(
testdata$specimens,
testdata$isolates,
testdata$susceptibilities
))
# wrong specimen code
testdata_spec_code <- testdata
testdata_spec_code$specimens$specimen_type_code <- "biduletruccleurtruc"
expect_warning(validate_microbiology(
testdata_spec_code$specimens,
testdata_spec_code$isolates,
testdata_spec_code$susceptibilities
))
# missing relations
testdata_missing_id1 <- testdata
testdata_missing_id1$susceptibilities$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id1$specimens,
testdata_missing_id1$isolates,
testdata_missing_id1$susceptibilities
))
testdata_missing_id2 <- testdata
testdata_missing_id2$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id2$specimens,
testdata_missing_id2$isolates,
testdata_missing_id2$susceptibilities
))
testdata_missing_id3 <- testdata
testdata_missing_id3$isolates$specimen_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_missing_id3$specimens,
testdata_missing_id3$isolates,
testdata_missing_id3$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$isolates$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_organism_codes <- testdata
testdata_invalid_organism_codes$susceptibilities$isolate_id[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_organism_codes$specimens,
testdata_invalid_organism_codes$isolates,
testdata_invalid_organism_codes$susceptibilities
))
testdata_invalid_drug_codes <- testdata
testdata_invalid_drug_codes$susceptibilities$agent_code[1] <- "biduletruccleurtruc"
expect_error(validate_microbiology(
testdata_invalid_drug_codes$specimens,
testdata_invalid_drug_codes$isolates,
testdata_invalid_drug_codes$susceptibilities
))
})
# validate_investigations -------------------------------------------------
test_that("validate_investigations on test dataset", {
expect_true(validate_investigations(inpatient_investigations))
})
test_that("validate_investigations", {
example_data <- dplyr::tibble(
observation_id = c("1", "2"),
patient_id = "99999999999",
encounter_id = "9278078393", status = "final",
request_datetime = as.POSIXct("2016-03-30 13:51:13"),
observation_datetime = as.POSIXct("2016-03-30 13:51:45"),
observation_value_text = "",
observation_value_numeric = c(35.7, 100.4),
observation_name = "Body temperature",
observation_display = "Temperature",
observation_code_system = "http://loinc.org",
observation_code = "8310-5",
observation_unit = c("degree_Celsius", "degree_F")
)
example_datatable <- data.table::data.table(
observation_id = c("1", "2"),
patient_id = "99999999999",
encounter_id = "9278078393", status = "final",
request_datetime = as.POSIXct("2016-03-30 13:51:13"),
observation_datetime = as.POSIXct("2016-03-30 13:51:45"),
observation_value_text = "",
observation_value_numeric = c(35.7, 100.4),
observation_name = "Body temperature",
observation_display = "Temperature",
observation_code_system = "http://loinc.org",
observation_code = "8310-5",
observation_unit = c("degree_Celsius", "degree_F")
)
expect_true(validate_investigations(example_data[1,]))
expect_error(validate_investigations(example_data))
expect_true(validate_investigations(example_datatable[1,]))
expect_error(validate_investigations(example_datatable))
non_unique_metadata <- dplyr::tibble(
observation_id = c("1", "2"),
patient_id = "99999999999",
encounter_id = "9278078393", status = "final",
request_datetime = as.POSIXct("2016-03-30 13:51:13"),
observation_datetime = as.POSIXct("2016-03-30 13:51:45"),
observation_value_text = "",
observation_value_numeric = c(35.7, 100.4),
observation_name = "Body temperature",
observation_display = c("Body temperature", "Temperature"),
observation_code_system = "http://loinc.org",
observation_code = "8310-5",
observation_unit = c("degree_Celsius", "degree_Celsius")
)
expect_error(
validate_investigations(non_unique_metadata),
"^Every `observation_code` must only be associated with one `observation_name` and `observation_display` only"
)
})
# Bug 85 ------------------------------------------------------------------
test_that("Bug 85 - uniqueness of patient_id in patient dataset", {
expect_error(
validate_inpatient_episodes(
patients = data.frame(
patient_id = c("1253675584", "1253675584"),
NHS_number = c("5632763868", "5632763868"),
forename = c("jflmnfcjnc", "jflmnfcjnc"),
surname = c("mljkaigaji", "mljkaigaji"),
sex = c("1", "1"), ethnic_category_UK = c("A", "A"),
date_of_birth = c("1999-11-21", "1999-11-21"),
date_of_death = c(NA_character_, NA_character_)
),
episodes = data.frame(
patient_id = "1253675584", encounter_id = "8751633817",
admission_method = "2",
admission_date = as.POSIXct("2015-02-26 18:30:55"),
discharge_date = as.POSIXct("2015-03-17 17:23:49"),
episode_number = 1L, last_episode_in_encounter = "2",
episode_start = as.POSIXct("2015-02-26 18:30:55"),
episode_end = as.POSIXct("2015-03-17 17:23:49"),
consultant_code = "C1000002",
main_specialty_code = "100",
last_episode_in_encounter = 2,
ramses_bed_days = 1.72303240740741
)
)
)
})
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