Nothing
tests/testthat/test-airway_18_population.R
In nemsqar: National Emergency Medical Service Quality Alliance Measure Calculations
testthat::test_that("Test for non-missing table and df arguments", {
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(df = tibble::tibble(),
patient_scene_table = tibble::tibble(),
procedures_table = tibble::tibble(),
vitals_table = tibble::tibble(),
airway_table = tibble::tibble(),
response_table = tibble::tibble(),
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "Please choose"
)
})
testthat::test_that("Test for df argument with wrong format", {
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(df = list(),
patient_scene_table = NULL,
procedures_table = NULL,
vitals_table = NULL,
airway_table = NULL,
response_table = NULL,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "An object of class"
)
})
testthat::test_that("Test for incorrectly formatted DOB / incident date", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
wrong_data <- nemsqar_patient_scene_table
wrong_data$`Incident Date` <- as.character(nemsqar_patient_scene_table$`Incident Date`)
wrong_data$`Patient Date Of Birth (ePatient.17)` <- as.character(nemsqar_patient_scene_table$`Patient Date Of Birth (ePatient.17)`)
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(
df = NULL,
patient_scene_table = wrong_data,
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
})
testthat::test_that("Test for correctly formatted dates/times in df", {
# get a big df with useful data
big_df <- tibble::tibble(
`Incident Patient Care Report Number - PCR (eRecord.01)` = c("a", "b", "c", "d", "e"),
`Incident Date` = c(
as.Date("2023-01-01"),
as.Date("2023-06-01"),
as.Date("2023-05-01"),
as.Date("2023-12-01"),
as.Date("2023-12-01")
), `Patient Date Of Birth (ePatient.17)` = c(
as.Date("2005-01-01"),
as.Date("2000-06-01"),
as.Date("1995-05-01"),
as.Date("2018-12-01"),
as.Date("1970-12-01")
), `Patient Age (ePatient.15)` = c(18, 23, 28, 5, 53),
`Patient Age Units (ePatient.16)` = c("Years", "Years", "Years", "Years", "Years"),
`Response Type Of Service Requested With Code (eResponse.05)` = rep("2205001", 5),
`Procedure Performed Date Time (eProcedures.01)` = c(
lubridate::as_datetime("2023-01-01 15:00:00"),
lubridate::as_datetime("2023-06-01 14:00:00"),
lubridate::as_datetime("2023-05-01 13:00:00"),
lubridate::as_datetime("2023-12-01 12:00:00"),
lubridate::as_datetime("2023-12-01 06:00:00")
),
`Procedure Performed Prior To EMS Care (eProcedures.02)` = rep("No", 5),
`Procedure Performed Description And Code (eProcedures.03)` = rep("112798008", 5),
`Procedure Number Of Attempts (eProcedures.05)` = rep(1, 5),
`Procedure Successful (eProcedures.06)` = rep("Yes", 5),
`Airway Device Placement Confirmation Date Time (eAirway.02)` = c(
lubridate::as_datetime("2023-01-01 15:05:00"),
lubridate::as_datetime("2023-06-01 14:05:00"),
lubridate::as_datetime("2023-05-01 13:05:00"),
lubridate::as_datetime("2023-12-01 12:05:00"),
lubridate::as_datetime("2023-12-01 06:05:00")
),
`Airway Device Placement Confirmed Method List (eAirway.04)` = rep("4004019", 5),
`Vitals Signs Taken Date Time (eVitals.01)` = c(
lubridate::as_datetime("2023-01-01 15:03:00"),
lubridate::as_datetime("2023-06-01 14:03:00"),
lubridate::as_datetime("2023-05-01 13:03:00"),
lubridate::as_datetime("2023-12-01 12:03:00"),
lubridate::as_datetime("2023-12-01 06:03:00")
),
`Vitals Carbon Dioxide CO2 (eVitals.16)` = rep(6, 5)
)
# incorrectly formatted date columns
big_df_demo <- big_df |>
dplyr::mutate(dplyr::across(matches("birth|incident date"), ~ as.character(.)
)
)
big_df_dates <- big_df |>
dplyr::mutate(dplyr::across(matches("date time"), ~ as.character(.))
)
# all character arguments to incident date and
# the patient DOB
# expect an error
testthat::expect_error(
airway_18_population(
df = big_df_demo,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
# all character arguments to vitals, airway, and
# the procedures date time fields
# expect an error
testthat::expect_error(
airway_18_population(
df = big_df_dates,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
# all character arguments to vitals and
# the procedures date time fields
# expect an error
testthat::expect_error(
airway_18_population(
df = big_df_dates,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = NULL,
eairway_04_col = NULL,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
})
testthat::test_that("Ensure the function runs with the df method", {
# get a big df with useful data
big_df <- tibble::tibble(
`Incident Patient Care Report Number - PCR (eRecord.01)` = c("a", "b", "c", "d", "e"),
`Incident Date` = c(
as.Date("2023-01-01"),
as.Date("2023-06-01"),
as.Date("2023-05-01"),
as.Date("2023-12-01"),
as.Date("2023-12-01")
), `Patient Date Of Birth (ePatient.17)` = c(
as.Date("2005-01-01"),
as.Date("2000-06-01"),
as.Date("1995-05-01"),
as.Date("2018-12-01"),
as.Date("1970-12-01")
), `Patient Age (ePatient.15)` = c(18, 23, 28, 5, 53),
`Patient Age Units (ePatient.16)` = c("Years", "Years", "Years", "Years", "Years"),
`Response Type Of Service Requested With Code (eResponse.05)` = rep("2205001", 5),
`Procedure Performed Date Time (eProcedures.01)` = c(
lubridate::as_datetime("2023-01-01 15:00:00"),
lubridate::as_datetime("2023-06-01 14:00:00"),
lubridate::as_datetime("2023-05-01 13:00:00"),
lubridate::as_datetime("2023-12-01 12:00:00"),
lubridate::as_datetime("2023-12-01 06:00:00")
),
`Procedure Performed Prior To EMS Care (eProcedures.02)` = rep("No", 5),
`Procedure Performed Description And Code (eProcedures.03)` = rep("112798008", 5),
`Procedure Number Of Attempts (eProcedures.05)` = rep(1, 5),
`Procedure Successful (eProcedures.06)` = rep("Yes", 5),
`Airway Device Placement Confirmation Date Time (eAirway.02)` = c(
lubridate::as_datetime("2023-01-01 15:05:00"),
lubridate::as_datetime("2023-06-01 14:05:00"),
lubridate::as_datetime("2023-05-01 13:05:00"),
lubridate::as_datetime("2023-12-01 12:05:00"),
lubridate::as_datetime("2023-12-01 06:05:00")
),
`Airway Device Placement Confirmed Method List (eAirway.04)` = rep("4004019", 5),
`Vitals Signs Taken Date Time (eVitals.01)` = c(
lubridate::as_datetime("2023-01-01 15:03:00"),
lubridate::as_datetime("2023-06-01 14:03:00"),
lubridate::as_datetime("2023-05-01 13:03:00"),
lubridate::as_datetime("2023-12-01 12:03:00"),
lubridate::as_datetime("2023-12-01 06:03:00")
),
`Vitals Carbon Dioxide CO2 (eVitals.16)` = rep(6, 5)
)
# all arguments correct
# expect success
result <- airway_18_population(
df = big_df,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
)
testthat::expect_type(result, "list")
testthat::expect_equal(nrow(result$filter_process), 12)
testthat::expect_equal(nrow(result$initial_population), 5)
})
testthat::test_that("Test for incorrectly formatted vitals/airway times", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
# get wrong data
wrong_data_vitals <- nemsqar_vitals_table
wrong_data_airway <- nemsqar_airway_table
wrong_data_proc <- nemsqar_procedures_table
wrong_data_vitals$`Vitals Signs Taken Date Time (eVitals.01)` <- as.character(nemsqar_vitals_table$`Vitals Signs Taken Date Time (eVitals.01)`)
wrong_data_proc$`Procedure Performed Date Time (eProcedures.01)` <- as.character(nemsqar_procedures_table$`Procedure Performed Date Time (eProcedures.01)`)
wrong_data_airway$`Airway Device Placement Confirmation Date Time (eAirway.02)` <- as.character(nemsqar_airway_table$`Airway Device Placement Confirmation Date Time (eAirway.02)`)
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(
df = NULL,
patient_scene_table = nemsqar_patient_scene_table,
procedures_table = wrong_data_proc,
vitals_table = wrong_data_vitals,
airway_table = wrong_data_airway,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
})
testthat::test_that("Test for incorrectly formatted table argument", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(
df = NULL,
patient_scene_table = list(),
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "One or more"
)
})
testthat::test_that("Test for missing column names", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
testthat::expect_error(airway_18_population(
df = NULL,
patient_scene_table = nemsqar_patient_scene_table,
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`
), "arguments is missing")
})
testthat::test_that("Test for missing df and tables", {
testthat::expect_error(airway_18_population(
df = NULL,
patient_scene_table = NULL,
procedures_table = NULL,
vitals_table = NULL,
airway_table = NULL,
response_table = NULL,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
))
})
testthat::test_that("Test for correct input handling (table method)", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01 = 1:5,
incident_date = as.Date(c("2025-01-01", "2025-01-05", "2025-02-01", "2025-01-01", "2025-06-01")),
patient_dob = as.Date(c("2000-01-01", "2020-01-01", "2023-02-01", "2023-01-01", "1970-06-01")),
epatient_15 = c(25, 5, 2, 2, 55), # Ages
epatient_16 = rep("Years", 5)
)
procedures_table <- tibble::tibble(
erecord_01 = 1:5,
eprocedures_01 = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02 = rep("No", 5),
eprocedures_03 = rep("44738004", 5),
eprocedures_05 = c(1, 1, 1, 1, 1),
eprocedures_06 = rep("Yes", 5)
)
response_table <- tibble::tibble(
erecord_01 = 1:5,
eresponse_05 = rep("2205001", 5)
)
vitals_table <- tibble::tibble(
erecord_01 = 1:5,
evitals_01 = Sys.time() + c(0, 1, 2, 3, 4),
evitals_16 = c(6, 5, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01 = 1:5,
eairway_02 = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04 = rep("4004019", 5)
)
result <- airway_18_population(
df = NULL,
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01,
incident_date_col = incident_date,
patient_DOB_col = patient_dob,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05,
eprocedures_01_col = eprocedures_01,
eprocedures_02_col = eprocedures_02,
eprocedures_03_col = eprocedures_03,
eprocedures_06_col = eprocedures_06,
eairway_02_col = eairway_02,
eairway_04_col = eairway_04,
evitals_01_col = evitals_01,
evitals_16_col = evitals_16
)
testthat::expect_type(result, "list")
testthat::expect_true(all(names(result) %in% c("filter_process", "adults", "peds", "initial_population", "computing_population")))
})
testthat::test_that("Test for invalid column names", {
testthat::expect_error(airway_18_population(
df = nemsqar_airway_18_df,
patient_scene_table = NULL,
procedures_table = NULL,
vitals_table = NULL,
airway_table = NULL,
response_table = NULL,
erecord_01_col = `Invalid Column Name`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
))
})
testthat::test_that("Test for table and df input conflicts", {
df <- tibble::tibble()
testthat::expect_error(airway_18_population(
df = nemsqar_airway_18_df,
patient_scene_table = nemsqar_patient_scene_table,
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
))
})
# Example test: Check if intubation data is correctly filtered
testthat::test_that("incident date is correctly validated", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01_col = 1:5,
incident_date_col = c(5, 10, 15, 20, 25),
patient_DOB_col = c(20, 25, 30, 35, 40),
epatient_15 = c(20, 30, 40, 50, 60),
epatient_16 = c("Years", "Months", "Days", "Years", "Months")
)
procedures_table <- tibble::tibble(
erecord_01_col = 1:5,
eprocedures_01_col = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02_col = c("Yes", "No", "Yes", "No", "Yes"),
eprocedures_03_col = c("endotracheal intubation", "other", "endotracheal intubation", "other", "endotracheal intubation"),
eprocedures_06_col = c("yes", "no", "yes", "no", "yes")
)
response_table <- tibble::tibble(
erecord_01_col = 1:5,
eresponse_05_col = c("911", "911", "other", "other", "911")
)
vitals_table <- tibble::tibble(
erecord_01_col = 1:5,
evitals_01_col = Sys.time() + c(0, 1, 2, 3, 4),
evitals_16_col = c(6, 4, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01_col = 1:5,
eairway_02_col = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04_col = c("waveform etco2", "other", "waveform etco2", "other", "waveform etco2")
)
testthat::expect_error(airway_18_population(
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01_col,
incident_date_col = incident_date_col,
patient_DOB_col = patient_DOB_col,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05_col,
eprocedures_01_col = eprocedures_01_col,
eprocedures_02_col = eprocedures_02_col,
eprocedures_03_col = eprocedures_03_col,
eprocedures_06_col = eprocedures_06_col,
eairway_02_col = eairway_02_col,
eairway_04_col = eairway_04_col,
evitals_01_col = evitals_01_col,
evitals_16_col = evitals_16_col
))
})
# Test case 1: Verify patient age calculation when both dates are provided
testthat::test_that("vitals times are correctly validated", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01_col = 1:5,
incident_date_col = Sys.time() - c(5, 10, 15, 20, 25),
patient_DOB_col = Sys.time() - c(1120, 1125, 1130, 1135, 1140),
epatient_15 = c(20, 30, 40, 50, 60),
epatient_16 = c("Years", "Months", "Days", "Years", "Months")
)
procedures_table <- tibble::tibble(
erecord_01_col = 1:5,
eprocedures_01_col = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02_col = c("Yes", "No", "Yes", "No", "Yes"),
eprocedures_03_col = c("endotracheal intubation", "other", "endotracheal intubation", "other", "endotracheal intubation"),
eprocedures_06_col = c("yes", "no", "yes", "no", "yes")
)
response_table <- tibble::tibble(
erecord_01_col = 1:5,
eresponse_05_col = c("911", "911", "other", "other", "911")
)
vitals_table <- tibble::tibble(
erecord_01_col = 1:5,
evitals_01_col = c(0, 1, 2, 3, 4),
evitals_16_col = c(6, 4, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01_col = 1:5,
eairway_02_col = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04_col = c("waveform etco2", "other", "waveform etco2", "other", "waveform etco2")
)
testthat::expect_error(airway_18_population(
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01_col,
incident_date_col = incident_date_col,
patient_DOB_col = patient_DOB_col,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05_col,
eprocedures_01_col = eprocedures_01_col,
eprocedures_02_col = eprocedures_02_col,
eprocedures_03_col = eprocedures_03_col,
eprocedures_06_col = eprocedures_06_col,
eairway_02_col = eairway_02_col,
eairway_04_col = eairway_04_col,
evitals_01_col = evitals_01_col,
evitals_16_col = evitals_16_col
))
})
# Test case 2: Check if the numerator data extraction works
testthat::test_that("denominator data is correctly extracted", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01 = 1:5,
incident_date = as.Date(c("2025-01-01", "2025-01-05", "2025-02-01", "2025-01-01", "2025-06-01")),
patient_dob = as.Date(c("2000-01-01", "2020-01-01", "2023-02-01", "2023-01-01", "1970-06-01")),
epatient_15 = c(25, 5, 2, 2, 55), # Ages
epatient_16 = rep("Years", 5)
)
procedures_table <- tibble::tibble(
erecord_01 = 1:5,
eprocedures_01 = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02 = rep("No", 5),
eprocedures_03 = rep("44738004", 5),
eprocedures_05 = c(1, 1, 1, 1, 1),
eprocedures_06 = rep("Yes", 5)
)
response_table <- tibble::tibble(
erecord_01 = 1:5,
eresponse_05 = rep("2205001", 5)
)
vitals_table <- tibble::tibble(
erecord_01 = 1:5,
evitals_01 = Sys.time() + c(0, 1, 2, 3, 4),
evitals_16 = c(6, 5, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01 = 1:5,
eairway_02 = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04 = rep("4004019", 5)
)
result <- airway_18_population(
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01,
incident_date_col = incident_date,
patient_DOB_col = patient_dob,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05,
eprocedures_01_col = eprocedures_01,
eprocedures_02_col = eprocedures_02,
eprocedures_03_col = eprocedures_03,
eprocedures_06_col = eprocedures_06,
eairway_02_col = eairway_02,
eairway_04_col = eairway_04,
evitals_01_col = evitals_01,
evitals_16_col = evitals_16
)
filters <- result$filter_process
testthat::expect_equal(nrow(filters), 12)
})
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testthat::test_that("Test for non-missing table and df arguments", {
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(df = tibble::tibble(),
patient_scene_table = tibble::tibble(),
procedures_table = tibble::tibble(),
vitals_table = tibble::tibble(),
airway_table = tibble::tibble(),
response_table = tibble::tibble(),
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "Please choose"
)
})
testthat::test_that("Test for df argument with wrong format", {
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(df = list(),
patient_scene_table = NULL,
procedures_table = NULL,
vitals_table = NULL,
airway_table = NULL,
response_table = NULL,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "An object of class"
)
})
testthat::test_that("Test for incorrectly formatted DOB / incident date", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
wrong_data <- nemsqar_patient_scene_table
wrong_data$`Incident Date` <- as.character(nemsqar_patient_scene_table$`Incident Date`)
wrong_data$`Patient Date Of Birth (ePatient.17)` <- as.character(nemsqar_patient_scene_table$`Patient Date Of Birth (ePatient.17)`)
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(
df = NULL,
patient_scene_table = wrong_data,
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
})
testthat::test_that("Test for correctly formatted dates/times in df", {
# get a big df with useful data
big_df <- tibble::tibble(
`Incident Patient Care Report Number - PCR (eRecord.01)` = c("a", "b", "c", "d", "e"),
`Incident Date` = c(
as.Date("2023-01-01"),
as.Date("2023-06-01"),
as.Date("2023-05-01"),
as.Date("2023-12-01"),
as.Date("2023-12-01")
), `Patient Date Of Birth (ePatient.17)` = c(
as.Date("2005-01-01"),
as.Date("2000-06-01"),
as.Date("1995-05-01"),
as.Date("2018-12-01"),
as.Date("1970-12-01")
), `Patient Age (ePatient.15)` = c(18, 23, 28, 5, 53),
`Patient Age Units (ePatient.16)` = c("Years", "Years", "Years", "Years", "Years"),
`Response Type Of Service Requested With Code (eResponse.05)` = rep("2205001", 5),
`Procedure Performed Date Time (eProcedures.01)` = c(
lubridate::as_datetime("2023-01-01 15:00:00"),
lubridate::as_datetime("2023-06-01 14:00:00"),
lubridate::as_datetime("2023-05-01 13:00:00"),
lubridate::as_datetime("2023-12-01 12:00:00"),
lubridate::as_datetime("2023-12-01 06:00:00")
),
`Procedure Performed Prior To EMS Care (eProcedures.02)` = rep("No", 5),
`Procedure Performed Description And Code (eProcedures.03)` = rep("112798008", 5),
`Procedure Number Of Attempts (eProcedures.05)` = rep(1, 5),
`Procedure Successful (eProcedures.06)` = rep("Yes", 5),
`Airway Device Placement Confirmation Date Time (eAirway.02)` = c(
lubridate::as_datetime("2023-01-01 15:05:00"),
lubridate::as_datetime("2023-06-01 14:05:00"),
lubridate::as_datetime("2023-05-01 13:05:00"),
lubridate::as_datetime("2023-12-01 12:05:00"),
lubridate::as_datetime("2023-12-01 06:05:00")
),
`Airway Device Placement Confirmed Method List (eAirway.04)` = rep("4004019", 5),
`Vitals Signs Taken Date Time (eVitals.01)` = c(
lubridate::as_datetime("2023-01-01 15:03:00"),
lubridate::as_datetime("2023-06-01 14:03:00"),
lubridate::as_datetime("2023-05-01 13:03:00"),
lubridate::as_datetime("2023-12-01 12:03:00"),
lubridate::as_datetime("2023-12-01 06:03:00")
),
`Vitals Carbon Dioxide CO2 (eVitals.16)` = rep(6, 5)
)
# incorrectly formatted date columns
big_df_demo <- big_df |>
dplyr::mutate(dplyr::across(matches("birth|incident date"), ~ as.character(.)
)
)
big_df_dates <- big_df |>
dplyr::mutate(dplyr::across(matches("date time"), ~ as.character(.))
)
# all character arguments to incident date and
# the patient DOB
# expect an error
testthat::expect_error(
airway_18_population(
df = big_df_demo,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
# all character arguments to vitals, airway, and
# the procedures date time fields
# expect an error
testthat::expect_error(
airway_18_population(
df = big_df_dates,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
# all character arguments to vitals and
# the procedures date time fields
# expect an error
testthat::expect_error(
airway_18_population(
df = big_df_dates,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = NULL,
eairway_04_col = NULL,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
})
testthat::test_that("Ensure the function runs with the df method", {
# get a big df with useful data
big_df <- tibble::tibble(
`Incident Patient Care Report Number - PCR (eRecord.01)` = c("a", "b", "c", "d", "e"),
`Incident Date` = c(
as.Date("2023-01-01"),
as.Date("2023-06-01"),
as.Date("2023-05-01"),
as.Date("2023-12-01"),
as.Date("2023-12-01")
), `Patient Date Of Birth (ePatient.17)` = c(
as.Date("2005-01-01"),
as.Date("2000-06-01"),
as.Date("1995-05-01"),
as.Date("2018-12-01"),
as.Date("1970-12-01")
), `Patient Age (ePatient.15)` = c(18, 23, 28, 5, 53),
`Patient Age Units (ePatient.16)` = c("Years", "Years", "Years", "Years", "Years"),
`Response Type Of Service Requested With Code (eResponse.05)` = rep("2205001", 5),
`Procedure Performed Date Time (eProcedures.01)` = c(
lubridate::as_datetime("2023-01-01 15:00:00"),
lubridate::as_datetime("2023-06-01 14:00:00"),
lubridate::as_datetime("2023-05-01 13:00:00"),
lubridate::as_datetime("2023-12-01 12:00:00"),
lubridate::as_datetime("2023-12-01 06:00:00")
),
`Procedure Performed Prior To EMS Care (eProcedures.02)` = rep("No", 5),
`Procedure Performed Description And Code (eProcedures.03)` = rep("112798008", 5),
`Procedure Number Of Attempts (eProcedures.05)` = rep(1, 5),
`Procedure Successful (eProcedures.06)` = rep("Yes", 5),
`Airway Device Placement Confirmation Date Time (eAirway.02)` = c(
lubridate::as_datetime("2023-01-01 15:05:00"),
lubridate::as_datetime("2023-06-01 14:05:00"),
lubridate::as_datetime("2023-05-01 13:05:00"),
lubridate::as_datetime("2023-12-01 12:05:00"),
lubridate::as_datetime("2023-12-01 06:05:00")
),
`Airway Device Placement Confirmed Method List (eAirway.04)` = rep("4004019", 5),
`Vitals Signs Taken Date Time (eVitals.01)` = c(
lubridate::as_datetime("2023-01-01 15:03:00"),
lubridate::as_datetime("2023-06-01 14:03:00"),
lubridate::as_datetime("2023-05-01 13:03:00"),
lubridate::as_datetime("2023-12-01 12:03:00"),
lubridate::as_datetime("2023-12-01 06:03:00")
),
`Vitals Carbon Dioxide CO2 (eVitals.16)` = rep(6, 5)
)
# all arguments correct
# expect success
result <- airway_18_population(
df = big_df,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
)
testthat::expect_type(result, "list")
testthat::expect_equal(nrow(result$filter_process), 12)
testthat::expect_equal(nrow(result$initial_population), 5)
})
testthat::test_that("Test for incorrectly formatted vitals/airway times", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
# get wrong data
wrong_data_vitals <- nemsqar_vitals_table
wrong_data_airway <- nemsqar_airway_table
wrong_data_proc <- nemsqar_procedures_table
wrong_data_vitals$`Vitals Signs Taken Date Time (eVitals.01)` <- as.character(nemsqar_vitals_table$`Vitals Signs Taken Date Time (eVitals.01)`)
wrong_data_proc$`Procedure Performed Date Time (eProcedures.01)` <- as.character(nemsqar_procedures_table$`Procedure Performed Date Time (eProcedures.01)`)
wrong_data_airway$`Airway Device Placement Confirmation Date Time (eAirway.02)` <- as.character(nemsqar_airway_table$`Airway Device Placement Confirmation Date Time (eAirway.02)`)
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(
df = NULL,
patient_scene_table = nemsqar_patient_scene_table,
procedures_table = wrong_data_proc,
vitals_table = wrong_data_vitals,
airway_table = wrong_data_airway,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "For the variables"
)
})
testthat::test_that("Test for incorrectly formatted table argument", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
# all NULL arguments to tables and df
# expect an error
testthat::expect_error(
airway_18_population(
df = NULL,
patient_scene_table = list(),
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
),
regexp = "One or more"
)
})
testthat::test_that("Test for missing column names", {
# Load necessary test data
data("nemsqar_airway_table")
data("nemsqar_patient_scene_table")
data("nemsqar_response_table")
data("nemsqar_vitals_table")
data("nemsqar_procedures_table")
testthat::expect_error(airway_18_population(
df = NULL,
patient_scene_table = nemsqar_patient_scene_table,
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`
), "arguments is missing")
})
testthat::test_that("Test for missing df and tables", {
testthat::expect_error(airway_18_population(
df = NULL,
patient_scene_table = NULL,
procedures_table = NULL,
vitals_table = NULL,
airway_table = NULL,
response_table = NULL,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
))
})
testthat::test_that("Test for correct input handling (table method)", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01 = 1:5,
incident_date = as.Date(c("2025-01-01", "2025-01-05", "2025-02-01", "2025-01-01", "2025-06-01")),
patient_dob = as.Date(c("2000-01-01", "2020-01-01", "2023-02-01", "2023-01-01", "1970-06-01")),
epatient_15 = c(25, 5, 2, 2, 55), # Ages
epatient_16 = rep("Years", 5)
)
procedures_table <- tibble::tibble(
erecord_01 = 1:5,
eprocedures_01 = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02 = rep("No", 5),
eprocedures_03 = rep("44738004", 5),
eprocedures_05 = c(1, 1, 1, 1, 1),
eprocedures_06 = rep("Yes", 5)
)
response_table <- tibble::tibble(
erecord_01 = 1:5,
eresponse_05 = rep("2205001", 5)
)
vitals_table <- tibble::tibble(
erecord_01 = 1:5,
evitals_01 = Sys.time() + c(0, 1, 2, 3, 4),
evitals_16 = c(6, 5, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01 = 1:5,
eairway_02 = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04 = rep("4004019", 5)
)
result <- airway_18_population(
df = NULL,
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01,
incident_date_col = incident_date,
patient_DOB_col = patient_dob,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05,
eprocedures_01_col = eprocedures_01,
eprocedures_02_col = eprocedures_02,
eprocedures_03_col = eprocedures_03,
eprocedures_06_col = eprocedures_06,
eairway_02_col = eairway_02,
eairway_04_col = eairway_04,
evitals_01_col = evitals_01,
evitals_16_col = evitals_16
)
testthat::expect_type(result, "list")
testthat::expect_true(all(names(result) %in% c("filter_process", "adults", "peds", "initial_population", "computing_population")))
})
testthat::test_that("Test for invalid column names", {
testthat::expect_error(airway_18_population(
df = nemsqar_airway_18_df,
patient_scene_table = NULL,
procedures_table = NULL,
vitals_table = NULL,
airway_table = NULL,
response_table = NULL,
erecord_01_col = `Invalid Column Name`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
))
})
testthat::test_that("Test for table and df input conflicts", {
df <- tibble::tibble()
testthat::expect_error(airway_18_population(
df = nemsqar_airway_18_df,
patient_scene_table = nemsqar_patient_scene_table,
procedures_table = nemsqar_procedures_table,
vitals_table = nemsqar_vitals_table,
airway_table = nemsqar_airway_table,
response_table = nemsqar_response_table,
erecord_01_col = `Incident Patient Care Report Number - PCR (eRecord.01)`,
incident_date_col = `Incident Date`,
patient_DOB_col = `Patient Date Of Birth (ePatient.17)`,
epatient_15_col = `Patient Age (ePatient.15)`,
epatient_16_col = `Patient Age Units (ePatient.16)`,
eresponse_05_col = `Response Type Of Service Requested With Code (eResponse.05)`,
eprocedures_01_col = `Procedure Performed Date Time (eProcedures.01)`,
eprocedures_02_col = `Procedure Performed Prior To EMS Care (eProcedures.02)`,
eprocedures_03_col = `Procedure Performed Description And Code (eProcedures.03)`,
eprocedures_06_col = `Procedure Successful (eProcedures.06)`,
eairway_02_col = `Airway Device Placement Confirmation Date Time (eAirway.02)`,
eairway_04_col = `Airway Device Placement Confirmed Method List (eAirway.04)`,
evitals_01_col = `Vitals Signs Taken Date Time (eVitals.01)`,
evitals_16_col = `Vitals Carbon Dioxide CO2 (eVitals.16)`
))
})
# Example test: Check if intubation data is correctly filtered
testthat::test_that("incident date is correctly validated", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01_col = 1:5,
incident_date_col = c(5, 10, 15, 20, 25),
patient_DOB_col = c(20, 25, 30, 35, 40),
epatient_15 = c(20, 30, 40, 50, 60),
epatient_16 = c("Years", "Months", "Days", "Years", "Months")
)
procedures_table <- tibble::tibble(
erecord_01_col = 1:5,
eprocedures_01_col = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02_col = c("Yes", "No", "Yes", "No", "Yes"),
eprocedures_03_col = c("endotracheal intubation", "other", "endotracheal intubation", "other", "endotracheal intubation"),
eprocedures_06_col = c("yes", "no", "yes", "no", "yes")
)
response_table <- tibble::tibble(
erecord_01_col = 1:5,
eresponse_05_col = c("911", "911", "other", "other", "911")
)
vitals_table <- tibble::tibble(
erecord_01_col = 1:5,
evitals_01_col = Sys.time() + c(0, 1, 2, 3, 4),
evitals_16_col = c(6, 4, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01_col = 1:5,
eairway_02_col = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04_col = c("waveform etco2", "other", "waveform etco2", "other", "waveform etco2")
)
testthat::expect_error(airway_18_population(
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01_col,
incident_date_col = incident_date_col,
patient_DOB_col = patient_DOB_col,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05_col,
eprocedures_01_col = eprocedures_01_col,
eprocedures_02_col = eprocedures_02_col,
eprocedures_03_col = eprocedures_03_col,
eprocedures_06_col = eprocedures_06_col,
eairway_02_col = eairway_02_col,
eairway_04_col = eairway_04_col,
evitals_01_col = evitals_01_col,
evitals_16_col = evitals_16_col
))
})
# Test case 1: Verify patient age calculation when both dates are provided
testthat::test_that("vitals times are correctly validated", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01_col = 1:5,
incident_date_col = Sys.time() - c(5, 10, 15, 20, 25),
patient_DOB_col = Sys.time() - c(1120, 1125, 1130, 1135, 1140),
epatient_15 = c(20, 30, 40, 50, 60),
epatient_16 = c("Years", "Months", "Days", "Years", "Months")
)
procedures_table <- tibble::tibble(
erecord_01_col = 1:5,
eprocedures_01_col = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02_col = c("Yes", "No", "Yes", "No", "Yes"),
eprocedures_03_col = c("endotracheal intubation", "other", "endotracheal intubation", "other", "endotracheal intubation"),
eprocedures_06_col = c("yes", "no", "yes", "no", "yes")
)
response_table <- tibble::tibble(
erecord_01_col = 1:5,
eresponse_05_col = c("911", "911", "other", "other", "911")
)
vitals_table <- tibble::tibble(
erecord_01_col = 1:5,
evitals_01_col = c(0, 1, 2, 3, 4),
evitals_16_col = c(6, 4, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01_col = 1:5,
eairway_02_col = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04_col = c("waveform etco2", "other", "waveform etco2", "other", "waveform etco2")
)
testthat::expect_error(airway_18_population(
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01_col,
incident_date_col = incident_date_col,
patient_DOB_col = patient_DOB_col,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05_col,
eprocedures_01_col = eprocedures_01_col,
eprocedures_02_col = eprocedures_02_col,
eprocedures_03_col = eprocedures_03_col,
eprocedures_06_col = eprocedures_06_col,
eairway_02_col = eairway_02_col,
eairway_04_col = eairway_04_col,
evitals_01_col = evitals_01_col,
evitals_16_col = evitals_16_col
))
})
# Test case 2: Check if the numerator data extraction works
testthat::test_that("denominator data is correctly extracted", {
# Mock data setup
patient_scene_table <- tibble::tibble(
erecord_01 = 1:5,
incident_date = as.Date(c("2025-01-01", "2025-01-05", "2025-02-01", "2025-01-01", "2025-06-01")),
patient_dob = as.Date(c("2000-01-01", "2020-01-01", "2023-02-01", "2023-01-01", "1970-06-01")),
epatient_15 = c(25, 5, 2, 2, 55), # Ages
epatient_16 = rep("Years", 5)
)
procedures_table <- tibble::tibble(
erecord_01 = 1:5,
eprocedures_01 = Sys.time() - c(1, 3, 5, 7, 9),
eprocedures_02 = rep("No", 5),
eprocedures_03 = rep("44738004", 5),
eprocedures_05 = c(1, 1, 1, 1, 1),
eprocedures_06 = rep("Yes", 5)
)
response_table <- tibble::tibble(
erecord_01 = 1:5,
eresponse_05 = rep("2205001", 5)
)
vitals_table <- tibble::tibble(
erecord_01 = 1:5,
evitals_01 = Sys.time() + c(0, 1, 2, 3, 4),
evitals_16 = c(6, 5, 8, 7, 9)
)
airway_table <- tibble::tibble(
erecord_01 = 1:5,
eairway_02 = Sys.time() + c(1, 3, 5, 7, 9),
eairway_04 = rep("4004019", 5)
)
result <- airway_18_population(
patient_scene_table = patient_scene_table,
procedures_table = procedures_table,
vitals_table = vitals_table,
airway_table = airway_table,
response_table = response_table,
erecord_01_col = erecord_01,
incident_date_col = incident_date,
patient_DOB_col = patient_dob,
epatient_15_col = epatient_15,
epatient_16_col = epatient_16,
eresponse_05_col = eresponse_05,
eprocedures_01_col = eprocedures_01,
eprocedures_02_col = eprocedures_02,
eprocedures_03_col = eprocedures_03,
eprocedures_06_col = eprocedures_06,
eairway_02_col = eairway_02,
eairway_04_col = eairway_04,
evitals_01_col = evitals_01,
evitals_16_col = evitals_16
)
filters <- result$filter_process
testthat::expect_equal(nrow(filters), 12)
})
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