R/check_ae_withdr_ds_discon.R
check_ae_withdr_ds_discon.Rd
This checks that if there is an AE with AEACN="DRUG WITHDRAWN" then there should be a treatment discontinuation record indicated by DS.DSSCAT
check_ae_withdr_ds_discon(AE, DS, TS, preproc = identity, ...)
Adverse Events SDTM dataset with variables USUBJID, AEACN
Disposition SDTM dataset with variables USUBJID, DSCAT, DSSCAT
Trial Summary SDTM dataset with variables TSPARMCD, TSVAL
An optional company specific preprocessing script
Other arguments passed to methods
boolean value if check failed or passed with 'msg' attribute if the test failed
AE <- data.frame(
USUBJID = 1:6,
AEACN = c("DRUG WITHDRAWN",NA,NA,NA,NA,NA),
AETOXGR = c(NA,NA,NA,NA,"5",NA),
AEDECOD=c("NAUSEA","HEADACHE"),
AESPID = "FORMNAME-R:5/L:5XXXX"
)
DS <- data.frame(
USUBJID = 1:3,
DSCAT="DISPOSITION EVENT",
DSSCAT="STUDY TREATMENT",
DSDECOD=c("COMPLETED","ADVERSE EVENT","DEATH")
)
TS <- data.frame(
TSPARMCD="TRT",
TSVAL="CHECK"
)
check_ae_withdr_ds_discon(AE,DS,TS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 1 patient(s) where AE data treatment discontinuation but no treatment discontinuation record in DS. "
#> attr(,"data")
#> USUBJID DSSCAT DSCAT AEACN AEDECOD
#> 1 1 <NA> <NA> DRUG WITHDRAWN NAUSEA
check_ae_withdr_ds_discon(AE,DS,TS,preproc=roche_derive_rave_row)
#> [1] FALSE
#> attr(,"msg")
#> [1] "There are 1 patient(s) where AE data treatment discontinuation but no treatment discontinuation record in DS. "
#> attr(,"data")
#> USUBJID DSSCAT DSCAT AEACN AEDECOD RAVE
#> 1 1 <NA> <NA> DRUG WITHDRAWN NAUSEA FORMNAME-R:5
DS$DSSCAT = NULL
check_ae_withdr_ds_discon(AE,DS,TS)
#> [1] FALSE
#> attr(,"msg")
#> [1] "DS is missing the variable: DSSCAT"