tests/testthat/test-check_ae_aesdth_aedthdtc.R

In sdtmchecks: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets

test_that("function errors when given bad input", {
    # expect_error(check_ae_aesdth_aedthdtc(list()))
    expect_error(check_ae_aesdth_aedthdtc(data.frame(USUBJID = c(1:6), AEDTHDTC = c(1:2, NA, "NA", 3),
                                                           AESDTH = c("", rep("Y",2), rep("", 2)),
                                                           AEDECOD = letters[1:5], AETERM = letters[1:5], AESTDTC = c(1:5),
                                                           stringsAsFactors=FALSE)))

})

test_that("function returns true when no errors are present", {

    AE <- data.frame(USUBJID = c(1:5), AEDTHDTC = 1:5,
                     AESDTH = c("", rep("Y",2), rep("", 2)),
                     AEDECOD = letters[1:5], AETERM =letters[1:5], AESTDTC = c(1:5),
                     stringsAsFactors=FALSE)

    expect_true(check_ae_aesdth_aedthdtc(AE))

})

test_that("function returns false when errors are present", {

    AE <- data.frame(USUBJID = c(1:5), AEDTHDTC = c(1:2, NA, "NA", 3),
                     AESDTH = c("", rep("Y",2), rep("", 2)),
                     AEDECOD = letters[1:5], AESTDTC = c(1:5), AETERM =letters[1:5],
                     stringsAsFactors=FALSE)

    expect_false(check_ae_aesdth_aedthdtc(AE = AE))

})

test_that("Function returns true when no errors are present for an empty dataframe (zero rows)", {

    AE <- data.frame(USUBJID =integer(),
                     AEDTHDTC=integer(),
                     AESDTH=character(),
                     AEDECOD = character(),
                     AESTDTC = integer(),
                     AETERM = character(),
                     stringsAsFactors=FALSE)

    expect_true(check_ae_aesdth_aedthdtc(AE))
})

# test_that("Function returns false when errors are present for an empty dataframe (zero rows)", {
# 
#     AE <- data.frame(USUBJID =NA,
#                      AESEQ=NA,
#                      AESTDTC=NA,
#                      AETERM="",
#                      AEDECOD ="NA",
#                      stringsAsFactors=FALSE)
# 
#     expect_false(check_ae_aesdth_aedthdtc(AE))
# })

test_that("Function returns true when no errors are present for a single input (one row)", {

    AE <- data.frame(USUBJID = c(1), AEDTHDTC = 1,
                     AESDTH = c("Y"),
                     AEDECOD = letters[1], 
                     AETERM = letters[1],
                     AESTDTC = c(1),
                     stringsAsFactors=FALSE)

    expect_true(check_ae_aesdth_aedthdtc(AE))
})

test_that("Function returns false when errors are present for a single input (one row)", {

    AE <- data.frame(USUBJID = c(1), AEDTHDTC = "",
                     AESDTH = c("Y"),
                     AEDECOD = letters[1], 
                     AETERM = letters[1],
                     AESTDTC = c(1),
                     stringsAsFactors=FALSE)

    expect_false(check_ae_aesdth_aedthdtc(AE))
})

test_that("Function returns true when no errors are present for a multiple inputs (900 rows)", {

    USUBJID <- rep(unlist(lapply(X =list("MYSTUDY-S0001-1"), function(x) paste0(x,seq(from = 100, to = 999)))), times = 1)

    AE <- data.frame(USUBJID = USUBJID[order(nchar(USUBJID), USUBJID)],
                     # AESEQ = rep(x = seq(1, 60, by=1), times = 900),
                     AEDTHDTC = rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15),
                     AESDTH = rep("Y", times = 900),
                     AETERM = rep(x = c("UPPER RESPIRATORY INFECTION","HEADACHE",
                                         "WORSENING THROMBOCYTOPENIA","LOW POTASSIUM","ANEMIA", "TREMORS"), times = 150),
                     AEDECOD = rep(x = c("Upper Respiratory Tract Infection","Headache","Thrombocytopenia",
                                         "Blood Potassium Decreased","Anaemia","Tremor"), times = 150),
                     AESTDTC = rep(seq(as.Date('2010-01-01'), as.Date('2010-03-01'), by = 1), times = 15),
                     stringsAsFactors = FALSE)

    expect_true(check_ae_aesdth_aedthdtc(AE))
})

test_that("Function returns false when errors are present for a multiple inputs (900 rows)", {

    USUBJID <- rep(unlist(lapply(X =list("MYSTUDY-S0001-1"), function(x) paste0(x,seq(from = 100, to = 999)))), times = 1)

    AE <- data.frame(USUBJID = USUBJID[order(nchar(USUBJID), USUBJID)],
                     # AESEQ = rep(x = seq(1, 60, by=1), times = 900),
                     AEDTHDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1)), times = 15),
                     AESDTH = rep("Y", times = 900),
                     AETERM = rep(x = c("UPPER RESPIRATORY INFECTION","HEADACHE",
                                        "WORSENING THROMBOCYTOPENIA","LOW POTASSIUM","ANEMIA", "TREMORS"), times = 150),
                     AEDECOD = rep(x = c("Upper Respiratory Tract Infection","Headache","Thrombocytopenia",
                                         "Blood Potassium Decreased","Anaemia","Tremor"), times = 150),
                     AESTDTC = rep(seq(as.Date('2010-01-01'), as.Date('2010-03-01'), by = 1), times = 15),
                     stringsAsFactors = FALSE)

    AE$AEDTHDTC[1:60] <- ""


    expect_false(check_ae_aesdth_aedthdtc(AE))
})

test_that("Function returns the failed object in attr(data)", {

    AE <- data.frame(USUBJID = c(1:5), AEDTHDTC = c(1:2, NA, "NA", 3),
                     AESDTH = c("", rep("Y",2), rep("", 2)),
                     AEDECOD = letters[1:5], AESTDTC = c(1:5),
                     AETERM = letters[1:5],
                     stringsAsFactors=FALSE)

    check <- check_ae_aesdth_aedthdtc(AE)

    expect_true(!is.null(attr(check, "data")))
    # expect_equal(attr(check, "data"), filter(AE, !is.na(AEDTHDTC) & AESDTH != "Y"))

})