Check for treatment discontinuation consistency between DS and AE

This check looks for consistency when DS.DSSPID=DISCTX* then there should be AE.AEACNn=DRUG WITHDRAWN

check_ds_ae_discon(DS, AE)

Arguments

DS

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

AE

Adverse Events SDTM dataset with variables USUBJID, AEDECOD, AESTDTC, AEACNn

Value

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

Author

Sarwan Singh

Examples

AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = "01JAN2017",
 AETERM  = c("AE1","AE2","AE3","AE4","AE5"),
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEACN = c("DOSE REDUCED", "DOSE REDUCED", "DOSE NOT CHANGED",
 "DOSE NOT CHANGED", "NOT APPLICABLE"),
 stringsAsFactors = FALSE
)


DS <- data.frame(
 USUBJID = 1:5,
 DSSPID  = c('XXXDISCTXXXXX'),
 DSSTDTC = '01JAN2017',
 DSCAT   = rep("DISPOSITION EVENT", 5),
 DSSCAT   = rep("TX FORM", 5),
 DSDECOD = c("PHYSICIAN DECISION", "OTHER", "PHYSICIAN DECISION", "OTHER", "DEATH"),
 stringsAsFactors = FALSE
)

# no case
check_ds_ae_discon(DS, AE)
#> [1] TRUE

# 1 case
DS[3, "DSDECOD"] <- 'ADVERSE EVENT'
check_ds_ae_discon(DS, AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 patient(s) with Treatment Discon due to AE but no AE record indicating drug withdrawn. "
#> attr(,"data")
#>   USUBJID  DSSCAT       DSDECOD   DSSTDTC
#> 1       3 TX FORM ADVERSE EVENT 01JAN2017

# mutliple AEACNx
AE <- data.frame(
 USUBJID = 1:5,
 AESTDTC = c("01JAN2017"),
 AETERM  = c("AE1","AE2","AE3","AE4","AE5"),
 AEDECOD = c("AE1","AE2","AE3","AE4","AE5"),
 AEACN   = rep("MULTIPLE", 5),
 AEACN1  = c("DOSE REDUCED", "DOSE NOT CHANGED", "DOSE NOT CHANGED",
 "DOSE NOT CHANGED", "NOT APPLICABLE"),
 stringsAsFactors = FALSE
)

check_ds_ae_discon(DS, AE)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 patient(s) with Treatment Discon due to AE but no AE record indicating drug withdrawn. "
#> attr(,"data")
#>   USUBJID  DSSCAT       DSDECOD   DSSTDTC
#> 1       3 TX FORM ADVERSE EVENT 01JAN2017