Check for COVID-19 AE with DRUG WITHDRAWN action without DS Trt Discon

This checks for a COVID-19 AE reported with Action Taken (AEACN*==DRUG WITHDRAWN) but without a corresponding DS record indicating DS.DSDECOD with "ADVERSE EVENT" on any Treatment Discontinuation form. This relies on DSSPID with the string "DISCTX" when DSCAT == "DISPOSITION EVENT" to select Treatment Discontinuation records in DS, as DSSCAT typically includes a text string referring to specific study drug(s).

check_ae_aeacn_ds_disctx_covid(AE, DS, covid_df = NULL)

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AETERM, AEDECOD, AESTDTC, AEACNx

DS

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

covid_df

Dataframe of AE preferred terms for COVID-19, containing the variable REFTERM

Value

boolean value if check returns 0 obs, otherwise return subset dataframe.

See also

Other COVID: check_ae_aeacnoth_ds_stddisc_covid(), check_dv_ae_aedecod_covid(), check_dv_covid()

Author

Sarwan Singh

Examples

covid_df = data.frame(REFTERM = c("COVID-19",
                                  "CORONAVIRUS POSITIVE"
                                  )
                     )
AE <- data.frame(
    STUDYID = 1,
    USUBJID = c(1,2,3,1,2,3),
    AESTDTC = '2020-05-05',
    AETERM  = c("abc Covid-19", "covid TEST POSITIVE",rep("other AE",4)),
    AEDECOD = c("COVID-19", "CORONAVIRUS POSITIVE", rep("OTHER AE",4)),
    AEACN = c("DRUG WITHDRAWN", rep("DOSE NOT CHANGED",5)),
    stringsAsFactors = FALSE
)

DS <- data.frame(
 USUBJID = c(1,1,2,3,4),
 DSSPID  = 'XXX-DISCTX-XXX',
 DSCAT   = "DISPOSITION EVENT",
 DSDECOD = "REASON",
 stringsAsFactors = FALSE
)

check_ae_aeacn_ds_disctx_covid(AE, DS, covid_df)
#> [1] FALSE
#> attr(,"msg")
#> [1] "1 patient(s) with COVID-19 AE indicating drug withdrawn but no Treatment Discon form indicating AE. "
#> attr(,"data")
#>   USUBJID  AEDECOD    AESTDTC          AEACN
#> 1       1 COVID-19 2020-05-05 DRUG WITHDRAWN

DS[1, "DSDECOD"] <- 'ADVERSE EVENT'
check_ae_aeacn_ds_disctx_covid(AE, DS, covid_df)
#> [1] TRUE