R/check_ae_aedthdtc_ds_death.R

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

#' @title Check for missing AEDTHDTC where DS indicates death due to AE
#'
#' @description This check looks for missing AEDTHDTC values if a patient has a
#'   DS record where DSDECOD=DEATH and DSTERM contains ADVERSE EVENT
#'
#' @param AE Adverse Events SDTM dataset with variables USUBJID, AEDTHDTC
#' @param DS Disposition SDTM dataset with variables USUBJID, DSDECOD, DSTERM, DSSTDTC
#'
#' @return boolean value if check failed or passed with 'msg' attribute if the
#'   test failed
#'
#' @export
#'
#' @author Aldrich Salva
#'
#' @examples
#'
#' AE <- data.frame(
#'  USUBJID = 1:3,
#'  AEDTHDTC = c(NA,NA,1)
#' )
#'
#'
#' # older mapping 
#' DS <- data.frame(
#'  USUBJID = 1:4,
#'  DSTERM = c("DEATH DUE TO ADVERSE EVENT","DEATH DUE TO PROGRESSIVE DISEASE",
#'             "DEATH DUE TO ADVERSE EVENT","DEATH DUE TO ADVERSE EVENT")
#'             ,
#'  DSDECOD = rep("DEATH",4),
#'  DSSTDTC = "2020-01-01"
#' )
#'
#' check_ae_aedthdtc_ds_death(AE,DS)
#'
#' DS$DSSTDTC = NULL
#'
#' check_ae_aedthdtc_ds_death(AE,DS)
#'
#' # newer mapping that  
#' DS <- data.frame(
#'  USUBJID = 1:4,
#'  DSTERM = c("DEATH DUE TO MYOCARDIAL INFARCTION","DEATH DUE TO PROGRESSIVE DISEASE",
#'             "DEATH DUE TO COVID-19","DEATH")
#'             ,
#'  DSDECOD = rep("DEATH",4),
#'  DSSTDTC = "2020-01-01"
#'  )
#'  
#' # pass for study with newer mapping, as another function (check_dd_death_date.R) covers this
#' check_ae_aedthdtc_ds_death(AE,DS)
#' 
#' 


check_ae_aedthdtc_ds_death <- function(AE,DS){
  
  ###First check that required variables exist and return a message if they don't
  if (AE %lacks_any% c("USUBJID", "AEDTHDTC")) {
    
    fail(lacks_msg(AE, c("USUBJID", "AEDTHDTC")))
    
  } else if (DS %lacks_any% c("USUBJID", "DSDECOD", "DSTERM","DSSTDTC")) {
    
    fail(lacks_msg(DS, c("USUBJID", "DSDECOD", "DSTERM", "DSSTDTC")))
    
  } else{
    
    
    ######### Check if study has older mapping where "DEATH DUE TO ADVERSE EVENT" used,
    #########  based on an instance of the particular text string in DSTERM 
    if('DEATH DUE TO ADVERSE EVENT' %in% DS$DSTERM){
      
      ### if yes - then use existing function ###
      
      ######### Only consider DS records from patients who have a record with DEATH and ADVERSE EVENT
      ds0a  <- subset(DS,(regexpr("DEATH", DS$DSDECOD, ignore.case = TRUE) != -1) &
                        (regexpr("ADVERSE EVENT", DS$DSTERM, ignore.case = TRUE) != -1),)
      
      ######### If there are no DS records that qualify for the check ###########
      if(nrow(ds0a)==0){
        
        pass()
        
        ######### If there are DS records that qualify ###########
      }else if(nrow(ds0a)>0){
        
        # Look for all records in AE where the death date is populated
        ae0a <- subset(AE,!is_sas_na(AE$AEDTHDTC),)
        
        # Check for subjects in ds0a that do not have a matching record in ae0a
        ds11 <- subset(ds0a,!(ds0a$USUBJID %in% ae0a$USUBJID),c('USUBJID','DSTERM','DSSTDTC'))
        rownames(ds11)=NULL
        
        # If all all subjects in ds0a have a matching record in ae0a
        if(nrow(ds11)==0){
          pass()
          
          ### Return subset dataframe if there are records with inconsistency
        }else if(nrow(ds11)>0){
          
          fail(
            msg = paste(length(unique(ds11$USUBJID)),
                        "patient(s) where DS.DSDECOD contains 'DEATH' and DS.DSTERM contains 'ADVERSE EVENT'",
                        "but with no death date in AE.AEDTHDTC (DSTERM mapping only applicable to older studies). "
            ),
            data = ds11
          )
        }
      }
      
    }
    
    ######### If study has newer mapping where DSDECOD = DEATH 
    else{ 
      
      ## assign pass, based on the idea this check being covered via check_dd_death_date.R
      ## consider consolidating those that check and this one 
      
      pass()
       
      
    }
    
  }
  
}