Check non-missing DEAD status date in SS and non-missing according DS record with death date where status date is greater or equal to death date

Source: R/check_ss_ssdtc_dead_ds.R

This check looks for missing death date in DS dataset if there is DEAD status date in SS dataset or if Subject Status Date/Time of Assessments is less than Start Date/Time of Disposition Event(SS.SSDTC < DS.DSSTDTC)

check_ss_ssdtc_dead_ds(SS, DS, preproc = identity, ...)

Arguments

SS

Subject Status SDTM dataset with variables USUBJID, SSDTC, SSSTRESC, VISIT

DS

Disposition SDTM dataset with variables USUBJID, DSSTDTC, DSDECOD, DSCAT

preproc

An optional company specific preprocessing script

...

Other arguments passed to methods

Value

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

Author

Vira Vrakina

Examples


SS <- data.frame(
 USUBJID = 1:5,
 SSDTC = "2020-01-02",
 SSSTRESC  = c("DEAD","DEAD","ALIVE","DEAD","ALIVE"),
 VISIT = "FOLLOW-UP",
 SSSPID = "FORMNAME-R:13/L:13XXXX"
)

DS <- data.frame(
 USUBJID = 1:5,
 DSSTDTC  = c("2020-01-02","2020-01-02", "2020-01-01", "2020-01-03", "2020-01-01"),
 DSDECOD = c(rep('DEATH', 5)),
 DSSPID = "FORMNAME-R:13/L:13XXXX",
 DSCAT   = c("OTHER EVENT", rep("DISPOSITION EVENT", 4))
)

check_ss_ssdtc_dead_ds(SS, DS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 patient(s) with death information in SS domain but no death information in DS domain or date with DEAD status in SS dataset is less than death date in DS dataset. "
#> attr(,"data")
#>   USUBJID      SSDTC SSSTRESC     VISIT    DSSTDTC DSDECOD             DSCAT
#> 1       1 2020-01-02     DEAD FOLLOW-UP       <NA>    <NA>              <NA>
#> 2       4 2020-01-02     DEAD FOLLOW-UP 2020-01-03   DEATH DISPOSITION EVENT
check_ss_ssdtc_dead_ds(SS, DS, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "2 patient(s) with death information in SS domain but no death information in DS domain or date with DEAD status in SS dataset is less than death date in DS dataset. "
#> attr(,"data")
#>   USUBJID      SSDTC SSSTRESC     VISIT       SS_RAVE    DSSTDTC DSDECOD
#> 1       1 2020-01-02     DEAD FOLLOW-UP FORMNAME-R:13       <NA>    <NA>
#> 2       4 2020-01-02     DEAD FOLLOW-UP FORMNAME-R:13 2020-01-03   DEATH
#>               DSCAT       DS_RAVE
#> 1              <NA>          <NA>
#> 2 DISPOSITION EVENT FORMNAME-R:13


SS <- data.frame(
 USUBJID = 1:5,
 SSDTC = "2020-01-02",
 SSSTRESC  = c( rep("DEAD", 5)),
 VISIT = "FOLLOW-UP",
 SSSPID = "FORMNAME-R:13/L:13XXXX"
)

DS <- data.frame(
 USUBJID = 1:5,
 DSSTDTC  = c("2020-01-02","2020-01-02", "2020-01-01", "2020-01-03", "2020-01-01"),
 DSDECOD = c(rep('DEATH', 5)),
 DSSPID = "FORMNAME-R:13/L:13XXXX",
 DSCAT   = c(rep("DISPOSITION EVENT", 5))
)

check_ss_ssdtc_dead_ds(SS, DS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 patient(s) with death information in SS domain but no death information in DS domain or date with DEAD status in SS dataset is less than death date in DS dataset. "
#> attr(,"data")
#>   USUBJID      SSDTC SSSTRESC     VISIT    DSSTDTC DSDECOD             DSCAT
#> 1       4 2020-01-02     DEAD FOLLOW-UP 2020-01-03   DEATH DISPOSITION EVENT
check_ss_ssdtc_dead_ds(SS, DS, preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 patient(s) with death information in SS domain but no death information in DS domain or date with DEAD status in SS dataset is less than death date in DS dataset. "
#> attr(,"data")
#>   USUBJID      SSDTC SSSTRESC     VISIT       SS_RAVE    DSSTDTC DSDECOD
#> 1       4 2020-01-02     DEAD FOLLOW-UP FORMNAME-R:13 2020-01-03   DEATH
#>               DSCAT       DS_RAVE
#> 1 DISPOSITION EVENT FORMNAME-R:13


SS <- data.frame(
 USUBJID = 1:5,
 SSDTC = "2020-01-02",
 SSSTRESC  = c(rep("DEAD", 5)),
 VISIT = "FOLLOW-UP",
 SSSPID = "FORMNAME-R:13/L:13XXXX"
)

DS <- data.frame(
 USUBJID = 1:5,
 DSSTDTC  = 2,
 DSDECOD = c(rep('DEATH', 5)),
 DSSPID = "FORMNAME-R:13/L:13XXXX",
 DSCAT   = c(rep("DISPOSITION EVENT", 5))
)

check_ss_ssdtc_dead_ds(SS, DS)
#> [1] TRUE