Check for COVID-19 AE leading to Study Discon without DS Study Discon

Flag if patient has a COVID-19 AE where AE.AEDECOD matches a COVID-19 preferred term event action of Study Discontinuation (AE.AEACNOT* includes "DISCONTINUED FROM STUDY") but missing Study Discontinuation record in DS (DS.DSSCAT includes "STUDY" and "DISCON" and excludes "DRUG" and "TREATMENT")

check_ae_aeacnoth_ds_stddisc_covid(AE, DS, covid_df = NULL)

Arguments

AE

Adverse Events SDTM dataset with variables USUBJID, AEDECOD, AEACNOT* (can be multiple variables)

DS

Disposition SDTM dataset with variables USUBJID, DSSCAT, DSDECOD

covid_df

dataframe of AE terms identify COVID-19, contains variable REFTERM

Value

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

See also

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

Author

Natalie Springfield

Examples

covid_df = data.frame(REFTERM = c("COVID-19",
                                  "CORONAVIRUS POSITIVE"
                                  )
                     )

AE <- data.frame(
 USUBJID = 1:5,
 AEDECOD = c("covid-19", "covid-19", "covid-19","Some AE", "CORONAVIRUS POSITIVE" ),
 AEACNOTH=c("SUBJECT DISCONTINUED FROM STUDY",
            "NONE",
            "NONE", 
            "SUBJECT DISCONTINUED FROM STUDY",
            "NONE"),
 AEACNOTH1=c("SUBJECT DISCONTINUED FROM STUDY", 
             "NONE",
             "SUBJECT DISCONTINUED FROM STUDY",
             "NONE", 
             "SUBJECT DISCONTINUED FROM STUDY"),
 AEACNOTH2=c("SUBJECT DISCONTINUED FROM STUDY", 
             "NONE",
             "NONE",
             "SUBJECT DISCONTINUED FROM STUDY",
             "NONE")
)

DS <- data.frame(
 USUBJID = 1:3,
 DSSCAT=c("TREATMENT DISCONTINUATION", 
 "STUDY DISCONTINUATION",
 "STUDY DISCONTINUATION"),
 DSDECOD="DISCON REASON"
)

check_ae_aeacnoth_ds_stddisc_covid(AE,DS,covid_df = covid_df)
#> [1] FALSE
#> attr(,"msg")
#> [1] "Found 2 patient(s) with COVID-related AE(s) leading to Study Discon, but no corresponding Study Discon in DS. "
#> attr(,"data")
#>   USUBJID              AEDECOD DSDECOD DSSCAT                        AEACNOTH
#> 1       1             COVID-19    <NA>   <NA> SUBJECT DISCONTINUED FROM STUDY
#> 3       5 CORONAVIRUS POSITIVE    <NA>   <NA>                            NONE
#>                         AEACNOTH1                       AEACNOTH2
#> 1 SUBJECT DISCONTINUED FROM STUDY SUBJECT DISCONTINUED FROM STUDY
#> 3 SUBJECT DISCONTINUED FROM STUDY                            NONE