Check for missing SSTDTC (Study Start Date) in TS — check_ts_sstdtc_ds

This check looks for missing SSTDTC (Study Start Date) in TS; if it's present, check that the date matches the earliest informed consent among any subject enrolled in the study. The FDA Technical Rejection Criteria for Study Data - effective September 15, 2021 requires Study Start Date (https://www.fda.gov/media/100743/download). If missing, no data queries are needed - this would be updating the assignment in the TS domain.

check_ts_sstdtc_ds_consent(DS, TS)

Arguments

DS: Disposition SDTM dataset with variables DSCAT, DSSCAT, DSDECOD, DSSTDTC
TS: Trial Summary SDTM dataset with variables TSPARMCD, TSPARM, TSVAL

Value

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

Author

Sara Bodach

Examples


TS1 <- data.frame(
 STUDYID = 1,
 TSPARMCD = "SSTDTC",
 TSPARM = "Study Start Date",
 TSVAL = "2017-01-01",
 TSVAL1 = "",
 TSVAL2 = ""
)

TS2 <- data.frame(
 STUDYID = 2,
 TSPARMCD = "AEDICT",
 TSPARM = "Study Start Date",
 TSVAL = "MedDRA v23.0",
 TSVAL1 = ""
)

TS3 <- data.frame(
 STUDYID = 3,
 TSPARMCD = "SSTDTC",
 TSPARM = "Study Start Date",
 TSVAL = ""
)

TS4 <- data.frame(
 STUDYID = 1,
 TSPARMCD = "SSTDTC",
 TSPARM = "Study Start Date",
 TSVAL = "2020-01-02",
 TSVAL1 = "",
 TSVAL2 = ""
)

TS5 = rbind(TS1, TS4)

TS6 <- data.frame(
 STUDYID = 1,
 TSPARMCD = "SSTDTC",
 TSPARM = "Study Start Date",
 TSVAL = "2020-01",
 TSVAL1 = "",
 TSVAL2 = ""
)

DS1 <- data.frame(
 USUBJID = c(1,1,2,3,4),
 DSCAT   = rep("PROTOCOL MILESTONE", 5),
 DSSCAT   = rep("PROTOCOL MILESTONE", 5),
 DSDECOD = c("INFORMED CONSENT OBTAINED", "OTHER", "PHYSICIAN DECISION",
             "OTHER", "INFORMED CONSENT OBTAINED"),
 DSSTDTC = c("2021-01-01", "2021-01-02", "2021-01-02", "2021-01-02", "2020-01-02"),
 stringsAsFactors = FALSE
)

check_ts_sstdtc_ds_consent(DS=DS1, TS=TS1)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TS.TSPARMCD = 'SSTDTC' (Study Start Date) has TS.TSVAL that does not match earliest informed consent date based on DS. TS with Study Start Date required for FDA submissions. "
#> attr(,"data")
#>   TSPARMCD           TSPARM      TSVAL DS_FIRST_ICDATE
#> 1   SSTDTC Study Start Date 2017-01-01      2020-01-02
check_ts_sstdtc_ds_consent(DS=DS1, TS=TS2)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TS.TSPARMCD = 'SSTDTC' (Study Start Date), which is required for FDA submissions, not found. Date in TSVAL should correspond with earliest informed consent date of enrolled patient. "
check_ts_sstdtc_ds_consent(DS=DS1, TS=TS3)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TS.TSPARMCD = 'SSTDTC' (Study Start Date) has missing TS.TSVAL (yyyy-mm-dd) character date. TS with Study Start Date required for FDA submissions. "
#> attr(,"data")
#>   TSPARMCD           TSPARM TSVAL DS_FIRST_ICDATE
#> 1   SSTDTC Study Start Date            2020-01-02
check_ts_sstdtc_ds_consent(DS=DS1, TS=TS4)
#> [1] TRUE
check_ts_sstdtc_ds_consent(DS=DS1, TS=TS5)
#> [1] FALSE
#> attr(,"msg")
#> [1] "Multiple records with TS.TSPARMCD = 'SSTDTC' (Study Start Date) found when only one expected. TS with Study Start Date required for FDA submissions. "
#> attr(,"data")
#>   TSPARMCD           TSPARM      TSVAL DS_FIRST_ICDATE
#> 1   SSTDTC Study Start Date 2017-01-01      2020-01-02
#> 2   SSTDTC Study Start Date 2020-01-02      2020-01-02
check_ts_sstdtc_ds_consent(DS=DS1, TS=TS6)
#> [1] FALSE
#> attr(,"msg")
#> [1] "TS.TSPARMCD = 'SSTDTC' (Study Start Date) is missing complete TS.TSVAL (yyyy-mm-dd) character date. TS with Study Start Date required for FDA submissions. "
#> attr(,"data")
#>   TSPARMCD           TSPARM   TSVAL DS_FIRST_ICDATE
#> 1   SSTDTC Study Start Date 2020-01      2020-01-02