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

In sdtmchecks: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets

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

Description

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")

Usage

check_ae_aeacnoth_ds_stddisc_covid(
  AE,
  DS,
  covid_terms = c("COVID-19", "CORONAVIRUS POSITIVE")
)

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_terms	A length >=1 vector of AE terms identifying COVID-19 (case does not matter)

Value

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

Author(s)

Natalie Springfield

See Also

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

Examples

AE <- data.frame(
 USUBJID = 1:5,
 AEDECOD = c("This is a covid AE", "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"
)

#expect fail
check_ae_aeacnoth_ds_stddisc_covid(AE,DS)

#use custom terms for identifying covid AEs
check_ae_aeacnoth_ds_stddisc_covid(
  AE,
  DS,
  covid_terms=c("COVID-19", "CORONAVIRUS POSITIVE","THIS IS A COVID AE")
  )

sdtmchecks documentation built on Sept. 11, 2024, 9:34 p.m.