Check for QS dates occurring after death date

Source: R/check_qs_qsdtc_after_dd.R

This check looks for QS dates that occur after death date

check_qs_qsdtc_after_dd(AE, DS, QS)

Arguments

AE

Adverse Event SDTM dataset with variables USUBJID, AEDTHDTC, AESTDTC, AEDECOD, and AETERM

DS

DS Disposition SDTM dataset with variables USUBJID, DSSTDTC, DSDECOD, and DSTERM

QS

Questionnaire Test Findings SDTM dataset with variables USUBJID, QSDTC, QSCAT, and QSORRES

Value

boolean value if check failed or passed with 'msg' attribute if the test failed

Author

Monarch Shah

Examples


AE <- data.frame(USUBJID = c(1,1,1,2,2,2),
                 AEDTHDTC = c("", "", "2016-01-01", "", "2016-01", "2016-01-01"),
                 AESTDTC = "2016-01-01",
                 AEDECOD = LETTERS[1:6],
                 AETERM = LETTERS[1:6],
                 stringsAsFactors = FALSE)

DS <- data.frame(USUBJID = c(1,1,1,2,2,2),
                 DSSTDTC = "2016-01-01",
                 DSDECOD = c("A", "B", "death", "AC", "BC", "death"),
                 DSTERM = letters[1:6],
                 stringsAsFactors = FALSE)

QS <- data.frame(USUBJID = c(1,1,1,2,2,2),
                 QSDTC   = c("2015-06-30", "2015-09-30", "2015-12-30",
                             "2015-06-30", "2015-09-30", "2015-12-30"),
                 QSCAT   = "A",
                 QSORRES =  LETTERS[1:6],
                 QSSTAT  = "",
                 VISIT  =  c("Week 1", "Week 12", "Week 24", "Week 1", "Week 12", "Week 24"),
                 QSSTRESC = LETTERS[1:6],
                 stringsAsFactors = FALSE)

check_qs_qsdtc_after_dd(AE, DS, QS)
#> [1] TRUE

QS$QSDTC[3:5] <- "2016-01-03"
check_qs_qsdtc_after_dd(AE, DS, QS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 unique patient(s) with 5 QS record(s) occurring after death date. "
#> attr(,"data")
#>   USUBJID      QSDTC   VISIT QSCAT   AEDTHDTC    DSSTDTC EARLIEST_DTHDTC
#> 1       1 2016-01-03 Week 24     A 2016-01-01 2016-01-01      2016-01-01
#> 2       2 2016-01-03  Week 1     A    2016-01 2016-01-01      2016-01-01
#> 3       2 2016-01-03  Week 1     A 2016-01-01 2016-01-01      2016-01-01
#> 4       2 2016-01-03 Week 12     A    2016-01 2016-01-01      2016-01-01
#> 5       2 2016-01-03 Week 12     A 2016-01-01 2016-01-01      2016-01-01

QS$QSSTAT[3] <- "Not Done"
check_qs_qsdtc_after_dd(AE, DS, QS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 4 QS record(s) occurring after death date. "
#> attr(,"data")
#>   USUBJID      QSDTC   VISIT QSCAT   AEDTHDTC    DSSTDTC EARLIEST_DTHDTC
#> 1       2 2016-01-03  Week 1     A    2016-01 2016-01-01      2016-01-01
#> 2       2 2016-01-03  Week 1     A 2016-01-01 2016-01-01      2016-01-01
#> 3       2 2016-01-03 Week 12     A    2016-01 2016-01-01      2016-01-01
#> 4       2 2016-01-03 Week 12     A 2016-01-01 2016-01-01      2016-01-01

DS$DSSTDTC <- NULL
check_qs_qsdtc_after_dd(AE, DS, QS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "DS is missing the variable: DSSTDTC"

AE1 <- data.frame(USUBJID = 1,
                  AEDTHDTC = "",
                  AESTDTC = c("2015-11-01", "2016-02-01"),
                  AEDECOD = "Rash",
                  AETERM = "RASH",
                  stringsAsFactors = FALSE)

DS1 <- data.frame(USUBJID = 1,
                  DSSTDTC = "2016-01",
                  DSCAT = c("DISPOSITION EVENT", "OTHER"),
                  DSSCAT = c('STUDY COMPLETION/EARLY DISCONTINUATION', ''),
                  DSDECOD = "DEATH",
                  DSTERM = c("DEATH", "DEATH DUE TO PROGRESSIVE DISEASE"),
                  stringsAsFactors = FALSE)

QS1 <- data.frame(USUBJID = 1,
                  QSDTC   = c("2015-06-30", "2016-01-15", "2016-01-15"),
                  QSCAT   = rep("EQ-5D-5L"),
                  QSORRES = "1",
                  QSSTAT  = "",
                  VISIT  =  c("Week 1", "Week 12", "Week 12"),
                  QSSTRESC = "1",
                  stringsAsFactors = FALSE)

check_qs_qsdtc_after_dd(AE=AE1, DS=DS1, QS=QS1)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 2 QS record(s) occurring after death date. "
#> attr(,"data")
#>   USUBJID      QSDTC   VISIT    QSCAT AEDTHDTC DSSTDTC EARLIEST_DTHDTC
#> 1       1 2016-01-15 Week 12 EQ-5D-5L     <NA> 2016-01         2016-01

AE1$AEDTHDTC[1:2] <- "2015-07-01"
check_qs_qsdtc_after_dd(AE=AE1, DS=DS1, QS=QS1)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 unique patient(s) with 2 QS record(s) occurring after death date. "
#> attr(,"data")
#>   USUBJID      QSDTC   VISIT    QSCAT   AEDTHDTC DSSTDTC EARLIEST_DTHDTC
#> 1       1 2016-01-15 Week 12 EQ-5D-5L 2015-07-01 2016-01      2015-07-01