Generate subdistribution hazard time values

subdistn.R

subdistn <- function(survData){
  ## substitute in later times to change risk sets
  ## time representation appropriate for subdistribution hazards
  ## 
  ## Accounts for administrative censoring
  ## note that within a specific organism subset the maximum time
  ## may be from a patient infected by a different organism
  
  ## default entries
  survData$time2disch <- survData$time2death <- survData$time
  
  ## event times of INFECTED database, DISCHARGE alive (censored at death)
  mtime1 <- max(survData[survData$infstatus==1, "time"], na.rm=TRUE)   # maximum infected database time, Dead=TRUE
                                                                      # not actually the administritive censoring time which is bigger than this
  survData$time2disch[survData$infstatus==1 & survData$event & survData$missingType] <- mtime1+1
  
  ## event times of INFECTED database, DEATH (censored at discharge alive)
  survData$time2death[survData$infstatus==1 & !survData$event & survData$missingType] <- mtime1+1
  
  ## event times of UNINFECTED, DISCHARGE alive (censored at death)
  mtime0 <- max(survData[survData$infstatus==0, "time"], na.rm=TRUE)  # maximum uninfected database time, Dead=TRUE
  
  survData$time2disch[survData$infstatus==0 & survData$event & survData$missingType] <- mtime0+1
                            
  ## event times of UNINFECTED, DEATH (censored at discharge alive)
  survData$time2death[survData$infstatus==0 & !survData$event & survData$missingType] <- mtime0+1

survData
}
## END FUNCTION ##