tests/testthat/test-check_vs_vsdtc_after_dd.R

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

test_that("function errors when given bad input", {
    expect_error(check_vs_vsdtc_after_dd(list()))

    # AE <- data.frame(STUDYID = 1:6, USUBJID = LETTERS[1:5],
    #                  AEDTHDTC = c(rep("", 4), "2016-01-01"),
    #                  AESTDTC = rep("2016-01-01", 5),
    #                  AEDECOD = LETTERS[1:5], AETERM = LETTERS[1:5],
    #                  stringsAsFactors = FALSE)
    #
    # DS <- data.frame(STUDYID = 1:6, USUBJID = LETTERS[1:5],
    #                  DSSTDTC = rep("2016-01-02", 5),
    #                  DSDECOD = c(LETTERS[1:4], "death"),
    #                  DSTERM = letters[1:5],
    #                  stringsAsFactors = FALSE)
    #
    # VS <- data.frame(STUDYID = 1:6, USUBJID = LETTERS[1:5],
    #                  VSDTC = rep("2015-12-31", 5),
    #                  VSTESTCD = letters[1:5],
    #                  VSORRES = 1:5,
    #                  stringsAsFactors = FALSE)


    # VS$VSDTC[1] <- "2016-01-03"
    # VS$USUBJID[1] <- VS$USUBJID[5]

    expect_error(check_vs_vsdtc_after_dd(data.frame(STUDYID = 1:6, USUBJID = LETTERS[1:5],
                                                          AEDTHDTC = c(rep("", 4), "2016-01-01"),
                                                          AESTDTC = rep("2016-01-01", 5),
                                                          AEDECOD = LETTERS[1:5], AETERM = LETTERS[1:5],
                                                          stringsAsFactors = FALSE), data.frame(STUDYID = 1:6, USUBJID = LETTERS[1:5],
                                                                                                DSSTDTC = rep("2016-01-02", 5),
                                                                                                DSDECOD = c(LETTERS[1:4], "death"),
                                                                                                DSTERM = letters[1:5],
                                                                                                stringsAsFactors = FALSE), data.frame(STUDYID = 1:6, USUBJID = LETTERS[1:5],
                                                                                                                                      VSDTC = rep("2015-12-31", 5),
                                                                                                                                      VSTESTCD = letters[1:5],
                                                                                                                                      VSORRES = 1:5,
                                                                                                                                      stringsAsFactors = FALSE)))

})

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

    AE <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     AEDTHDTC = c(rep("", 4), "2016-01-01"),
                     AESTDTC = rep("2016-01-01", 5),
                     AEDECOD = LETTERS[1:5], AETERM = LETTERS[1:5],
                     stringsAsFactors = FALSE)

    DS <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     DSSTDTC = rep("2016-01-02", 5),
                     DSDECOD = c(LETTERS[1:4], "death"),
                     DSTERM = letters[1:5],
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     VSDTC = rep("2015-12-31", 5),
                     VSTESTCD = letters[1:5],
                     VSORRES = 1:5,
                     stringsAsFactors = FALSE)


    #
    # VS$VSDTC[1] <- "2016-01-03"
    # VS$USUBJID[1] <- VS$USUBJID[5]

    expect_true(check_vs_vsdtc_after_dd(AE, DS, VS))

})

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

    AE <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     AEDTHDTC = c(rep("", 4), "2016-01-01"),
                     AESTDTC = rep("2016-01-01", 5),
                     AEDECOD = LETTERS[1:5], AETERM = LETTERS[1:5],
                     stringsAsFactors = FALSE)

    DS <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     DSSTDTC = rep("2016-01-02", 5),
                     DSDECOD = c(LETTERS[1:4], "death"),
                     DSTERM = letters[1:5],
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     VSDTC = rep("2015-12-31", 5),
                     VSTESTCD = letters[1:5],
                     VSORRES = 1:5,
                     stringsAsFactors = FALSE)


    VS$VSDTC[1] <- "2016-01-03"
    VS$USUBJID[1] <- VS$USUBJID[5]

    expect_false(check_vs_vsdtc_after_dd(AE, DS, VS))

})

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


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

    DS <- data.frame(STUDYID = integer(),
                     USUBJID = character(),
                     DSSTDTC = character(),
                     DSDECOD = character(),
                     DSTERM = character(),
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = integer(),
                     USUBJID = character(),
                     VSDTC = character(),
                     VSTESTCD = character(),
                     VSORRES = integer(),
                     stringsAsFactors = FALSE)


    expect_true(check_vs_vsdtc_after_dd(AE, DS, VS))

})

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

    AE <- data.frame(STUDYID = 1, USUBJID = LETTERS[1],
                     AEDTHDTC = "2016-01-01",
                     AESTDTC = "2016-01-01",
                     AEDECOD = LETTERS[1], AETERM = LETTERS[1],
                     stringsAsFactors = FALSE)

    DS <- data.frame(STUDYID = 1, USUBJID = LETTERS[1],
                     DSSTDTC = "2016-01-02",
                     DSDECOD = LETTERS[1],
                     DSTERM = letters[1],
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1, USUBJID = LETTERS[1],
                     VSDTC = "2015-12-31",
                     VSTESTCD = letters[1],
                     VSORRES = 1,
                     stringsAsFactors = FALSE)


    # VS$VSDTC[1] <- "2016-01-03"
    # VS$USUBJID[1] <- VS$USUBJID[5]

    expect_true(check_vs_vsdtc_after_dd(AE, DS, VS))
})

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

    AE <- data.frame(STUDYID = 1, USUBJID = LETTERS[1],
                     AEDTHDTC = "2016-01-01",
                     AESTDTC = "2016-01-01",
                     AEDECOD = LETTERS[1], AETERM = LETTERS[1],
                     stringsAsFactors = FALSE)

    DS <- data.frame(STUDYID = 1, USUBJID = LETTERS[1],
                     DSSTDTC = "2016-01-02",
                     DSDECOD = LETTERS[1],
                     DSTERM = letters[1],
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1, USUBJID = LETTERS[1],
                     VSDTC = "2015-12-31",
                     VSTESTCD = letters[1],
                     VSORRES = 1,
                     stringsAsFactors = FALSE)


    VS$VSDTC[1] <- "2016-01-03"


    expect_false(check_vs_vsdtc_after_dd(AE, DS, VS))
})

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(STUDYID = 1:900,
                     USUBJID = USUBJID[order(nchar(USUBJID), USUBJID)],
                     AEDTHDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15)),
                     AESTDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15)),
                     AEDECOD = rep(x = c("Upper Respiratory Tract Infection","Headache","Thrombocytopenia",
                                                    "Blood Potassium Decreased","Anaemia","Tremor"), times = 150),
                     AETERM = rep(x = c("UPPER RESPIRATORY INFECTION","HEADACHE",
                                        "WORSENING THROMBOCYTOPENIA","LOW POTASSIUM","ANEMIA", "TREMORS"), times = 9000),
                     stringsAsFactors = FALSE)

    DS <- data.frame(STUDYID = 1:900,
                     USUBJID = USUBJID[order(nchar(USUBJID), USUBJID)],
                     DSSTDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15)),
                     DSDECOD = c(rep("ALIVE", 300), rep("COMPLETED", 300), rep("ENROLLMENT", 300)),
                     DSTERM = c(rep("ALIVE", 300), rep("COMPLETED", 300), rep("ENROLLMENT", 300)),
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1:900, USUBJID =  USUBJID[order(nchar(USUBJID), USUBJID)],
                     VSDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15)),
                     VSTESTCD = c(rep("TEMPERATURE", 300), rep("VITAL SIGNS", 300), rep("PULSE RATE", 300)),
                     VSORRES = c(rep(36.9, 300), rep("", 300), rep(120, 300)),
                     stringsAsFactors = FALSE)

    #
    # VS$VSDTC[1] <- "2016-01-03"
    # VS$USUBJID[1] <- VS$USUBJID[5]


    expect_true(check_vs_vsdtc_after_dd(AE, DS, VS))

})

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

    DS <- data.frame(STUDYID = 1:900,
                     USUBJID = USUBJID[order(nchar(USUBJID), USUBJID)],
                     DSSTDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15)),
                     DSDECOD = c(rep("ALIVE", 300), rep("COMPLETED", 300), rep("ENROLLMENT", 300)),
                     DSTERM = c(rep("ALIVE", 300), rep("COMPLETED", 300), rep("ENROLLMENT", 300)),
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1:900, USUBJID =  USUBJID[order(nchar(USUBJID), USUBJID)],
                     VSDTC = as.character(rep(seq(as.Date('2011-01-01'), as.Date('2011-03-01'), by = 1), times = 15)),
                     VSTESTCD = c(rep("TEMPERATURE", 300), rep("VITAL SIGNS", 300), rep("PULSE RATE", 300)),
                     VSORRES = c(rep(36.9, 300), rep("", 300), rep(120, 300)),
                     stringsAsFactors = FALSE)


    VS$VSDTC[1] <- "2016-01-03"
    VS$USUBJID[1] <- VS$USUBJID[5]


    expect_false(check_vs_vsdtc_after_dd(AE, DS, VS))

})

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

    AE <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     AEDTHDTC = c(rep("", 4), "2016-01-01"),
                     AESTDTC = rep("2016-01-01", 5),
                     AEDECOD = LETTERS[1:5], AETERM = LETTERS[1:5],
                     stringsAsFactors = FALSE)

    DS <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     DSSTDTC = rep("2016-01-02", 5),
                     DSDECOD = c(LETTERS[1:4], "death"),
                     DSTERM = letters[1:5],
                     stringsAsFactors = FALSE)

    VS <- data.frame(STUDYID = 1:5, USUBJID = LETTERS[1:5],
                     VSDTC = rep("2015-12-31", 5),
                     VSTESTCD = letters[1:5],
                     VSORRES = 1:5,
                     stringsAsFactors = FALSE)


    VS$VSDTC[1] <- "2016-01-03"
    VS$USUBJID[1] <- VS$USUBJID[5]

    check <- check_vs_vsdtc_after_dd(AE, DS, VS)

    expect_true(!is.null(attr(check, "data")))
    # expect_equal(attr(check, "data"), )

})