R/check_qs_qsdtc_after_dd.R
check_qs_qsdtc_after_dd.RdThis check looks for QS dates that occur after death date
check_qs_qsdtc_after_dd(AE, DS, QS)Adverse Event SDTM dataset with variables USUBJID, AEDTHDTC, AESTDTC, AEDECOD, and AETERM
DS Disposition SDTM dataset with variables USUBJID, DSSTDTC, DSDECOD, and DSTERM
Questionnaire Test Findings SDTM dataset with variables USUBJID, QSDTC, QSCAT, and QSORRES
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