testthat::test_that("trauma_14 produces expected results", { # Synthetic test data test_data <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), epatient_15 = c(34, 5, 45, 2, 60), # Ages epatient_16 = c("Years", "Years", "Years", "Months", "Years"), eresponse_05 = rep(2205001, 5), eresponse_10 = rep(2210011, 5), esituation_02 = rep("Yes", 5), evitals_06 = c(100, 90, 80, 70, 85), evitals_10 = c(110, 89, 88, 71, 85), evitals_12 = c(50, 60, 70, 80, 75), evitals_14 = c(30, 9, 8, 7, 31), evitals_15 = c("apneic", "labored", "rapid", "shallow", "weak/agonal"), evitals_21 = c(5, 4, 3, 2, 1), eexam_16 = c(3516043, 3516067, 3516043, 3516067, 3516067), eexam_20 = c(3520045, 3520043, 3520019, 3520017, 3520017), eexam_23 = c(3523011, 3523003, 3523001, 3523011, 3523003), eexam_25 = c(3525039, 3525023, 3525005, 3525039, 3525023), edisposition_24 = c(4224017, 4224003, 4224017, 4224003, 4224017), edisposition_30 = c(4230001, 4230003, 4230001, 4230007, 4230007), eprocedures_03 = c(424979004, 427753009, 429705000, 47545007, 243142003), einjury_01 = c("V20", "V36", "V86", "V39", "V32"), einjury_03 = c(2903011, 2903009, 2903005, 3903003, 2903001), einjury_04 = c(2904013, 2904011, 2904009, 2904007, 2904001), einjury_09 = c(11, 12, 13, 14, 15) ) # Run function with the first and last pain score columns result <- trauma_14( df = test_data, erecord_01_col = erecord_01, epatient_15_col = epatient_15, epatient_16_col = epatient_16, eresponse_05_col = eresponse_05, eresponse_10_col = eresponse_10, esituation_02_col = esituation_02, evitals_06_col = evitals_06, evitals_10_col = evitals_10, evitals_12_col = evitals_12, evitals_14_col = evitals_14, evitals_15_col = evitals_15, evitals_21_col = evitals_21, eexam_16_col = eexam_16, eexam_20_col = eexam_20, eexam_23_col = eexam_23, eexam_25_col = eexam_25, edisposition_24_col = edisposition_24, transport_disposition_col = edisposition_30, eprocedures_03_col = eprocedures_03, einjury_01_col = einjury_01, einjury_03_col = einjury_03, einjury_04_col = einjury_04, einjury_09_col = einjury_09 ) # Check structure testthat::expect_s3_class(result, "data.frame") testthat::expect_true(all(c("measure", "pop", "numerator", "denominator", "prop", "prop_label") %in% names(result))) # Check calculations testthat::expect_equal(sum(result$numerator), 5) testthat::expect_equal(sum(result$denominator), 5) testthat::expect_equal(result$prop[result$pop == "10-64 yrs"], 1) testthat::expect_equal(nrow(result), 3) # create tables to test correct functioning patient_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), 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 = c("Years", "Years", "Years", "Years", "Years") ) # response table response_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), eresponse_05 = rep(2205001, 5), eresponse_10 = rep(2210011, 5) ) # situation table situation_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), esituation_02 = rep("Yes", 5), ) # vitals table vitals_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), evitals_06 = c(100, 90, 80, 70, 85), evitals_10 = c(110, 89, 88, 71, 85), evitals_12 = c(50, 60, 70, 80, 75), evitals_14 = c(30, 9, 8, 7, 31), evitals_15 = c("apneic", "labored", "rapid", "shallow", "weak/agonal"), evitals_21 = c(5, 4, 3, 2, 1) ) # disposition table disposition_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), edisposition_24 = c(4224017, 4224003, 4224017, 4224003, 4224017), edisposition_30 = c(4230001, 4230003, 4230001, 4230007, 4230007) ) # injury table injury_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), einjury_01 = c("V20", "V36", "V86", "V39", "V32"), einjury_03 = c(2903011, 2903009, 2903005, 3903003, 2903001), einjury_04 = c(2904013, 2904011, 2904009, 2904007, 2904001), einjury_09 = c(11, 12, 13, 14, 15) ) # exam table exam_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), eexam_16 = c(3516043, 3516067, 3516043, 3516067, 3516067), eexam_20 = c(3520045, 3520043, 3520019, 3520017, 3520017), eexam_23 = c(3523011, 3523003, 3523001, 3523011, 3523003), eexam_25 = c(3525039, 3525023, 3525005, 3525039, 3525023) ) # procedures table procedures_table <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), eprocedures_03 = c(424979004, 427753009, 429705000, 47545007, 243142003) ) # test the success of the function result <- trauma_14(patient_scene_table = patient_table, response_table = response_table, situation_table = situation_table, vitals_table = vitals_table, disposition_table = disposition_table, exam_table = exam_table, injury_table = injury_table, procedures_table = procedures_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, eresponse_10_col = eresponse_10, esituation_02_col = esituation_02, evitals_06_col = evitals_06, evitals_10_col = evitals_10, evitals_12_col = evitals_12, evitals_14_col = evitals_14, evitals_15_col = evitals_15, evitals_21_col = evitals_21, eexam_16_col = eexam_16, eexam_20_col = eexam_20, eexam_23_col = eexam_23, eexam_25_col = eexam_25, edisposition_24_col = edisposition_24, transport_disposition_col = edisposition_30, eprocedures_03_col = eprocedures_03, einjury_01_col = einjury_01, einjury_03_col = einjury_03, einjury_04_col = einjury_04, einjury_09_col = einjury_09 ) # Check calculations testthat::expect_equal(sum(result$numerator), 5) testthat::expect_equal(sum(result$denominator),5) testthat::expect_equal(result$prop[result$pop == "10-64 yrs"], 1) testthat::expect_equal(nrow(result), 3) }) testthat::test_that("trauma_14 handles missing data correctly", { # Synthetic test data test_data <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), epatient_15 = c(34, 5, 45, 2, 60), # Ages epatient_16 = c("Years", "Years", "Years", "Months", "Years"), eresponse_05 = rep(2205001, 5), eresponse_10 = rep(2210011, 5), esituation_02 = c("Yes", "Yes", "Yes", NA, NA), evitals_06 = c(100, 90, 80, 70, 85), evitals_10 = c(110, 89, 88, 71, 85), evitals_12 = c(50, 60, 70, 80, 75), evitals_14 = c(30, 9, 8, 7, 31), evitals_15 = c("apneic", "labored", "rapid", "shallow", "weak/agonal"), evitals_21 = c(5, 4, 3, 2, 1), eexam_16 = c(3516043, 3516067, 3516043, 3516067, 3516067), eexam_20 = c(3520045, 3520043, 3520019, 3520017, 3520017), eexam_23 = c(3523011, 3523003, 3523001, 3523011, 3523003), eexam_25 = c(3525039, 3525023, 3525005, 3525039, 3525023), edisposition_24 = c(4224017, 4224003, 4224017, 4224003, 4224017), edisposition_30 = c(NA, NA, 4230001, 4230007, 4230007), eprocedures_03 = c(424979004, 427753009, 429705000, 47545007, 243142003), einjury_01 = c("V20", "V36", "V86", "V39", "V32"), einjury_03 = c(2903011, 2903009, 2903005, 3903003, 2903001), einjury_04 = c(2904013, 2904011, 2904009, 2904007, 2904001), einjury_09 = c(11, 12, 13, 14, 15) ) # run the function with first and last # pain scale columns result <- trauma_14( df = test_data, erecord_01_col = erecord_01, epatient_15_col = epatient_15, epatient_16_col = epatient_16, eresponse_05_col = eresponse_05, eresponse_10_col = eresponse_10, esituation_02_col = esituation_02, evitals_06_col = evitals_06, evitals_10_col = evitals_10, evitals_12_col = evitals_12, evitals_14_col = evitals_14, evitals_15_col = evitals_15, evitals_21_col = evitals_21, eexam_16_col = eexam_16, eexam_20_col = eexam_20, eexam_23_col = eexam_23, eexam_25_col = eexam_25, edisposition_24_col = edisposition_24, transport_disposition_col = edisposition_30, eprocedures_03_col = eprocedures_03, einjury_01_col = einjury_01, einjury_03_col = einjury_03, einjury_04_col = einjury_04, einjury_09_col = einjury_09 ) testthat::expect_true(nrow(result) > 0) testthat::expect_true(all(!is.na(result$denominator))) }) testthat::test_that("trauma_14 returns empty result for non-matching criteria", { # Synthetic test data test_data <- tibble::tibble( erecord_01 = c("R1", "R2", "R3", "R4", "R5"), epatient_15 = c(34, 5, 45, 2, 60), # Ages epatient_16 = c("Years", "Years", "Years", "Months", "Years"), eresponse_05 = rep(2205001, 5), eresponse_10 = rep(2210011, 5), esituation_02 = rep("No", 5), evitals_06 = c(100, 90, 80, 70, 85), evitals_10 = c(110, 89, 88, 71, 85), evitals_12 = c(50, 60, 70, 80, 75), evitals_14 = c(30, 9, 8, 7, 31), evitals_15 = c("apneic", "labored", "rapid", "shallow", "weak/agonal"), evitals_21 = c(5, 4, 3, 2, 1), eexam_16 = c(3516043, 3516067, 3516043, 3516067, 3516067), eexam_20 = c(3520045, 3520043, 3520019, 3520017, 3520017), eexam_23 = c(3523011, 3523003, 3523001, 3523011, 3523003), eexam_25 = c(3525039, 3525023, 3525005, 3525039, 3525023), edisposition_24 = c(4224017, 4224003, 4224017, 4224003, 4224017), edisposition_30 = c(4230001, 4230003, 4230001, 4230007, 4230007), eprocedures_03 = c(424979004, 427753009, 429705000, 47545007, 243142003), einjury_01 = c("V20", "V36", "V86", "V39", "V32"), einjury_03 = c(2903011, 2903009, 2903005, 3903003, 2903001), einjury_04 = c(2904013, 2904011, 2904009, 2904007, 2904001), einjury_09 = c(11, 12, 13, 14, 15) ) # run the function with the # initial and last pain scale # columns result <- trauma_14( df = test_data, erecord_01_col = erecord_01, epatient_15_col = epatient_15, epatient_16_col = epatient_16, eresponse_05_col = eresponse_05, eresponse_10_col = eresponse_10, esituation_02_col = esituation_02, evitals_06_col = evitals_06, evitals_10_col = evitals_10, evitals_12_col = evitals_12, evitals_14_col = evitals_14, evitals_15_col = evitals_15, evitals_21_col = evitals_21, eexam_16_col = eexam_16, eexam_20_col = eexam_20, eexam_23_col = eexam_23, eexam_25_col = eexam_25, edisposition_24_col = edisposition_24, transport_disposition_col = edisposition_30, eprocedures_03_col = eprocedures_03, einjury_01_col = einjury_01, einjury_03_col = einjury_03, einjury_04_col = einjury_04, einjury_09_col = einjury_09 ) testthat::expect_equal(sum(result$denominator), 0) })