R/va_lag.R

In princeofbrit/Biosensequlaty_BZ: A Data Quality Report Generator for NSSP BioSense Platform

 ## this function computes the average time difference between Record and Visit, Message and Record, Arrival and Message, Arrival and Visit
 ## for each visit.
 ## Record: the time that the first message is entered into system; Message: the time that the first message was sent;
 ## Arrival: the time that the first message arraived at CDC; Visit: patient visit time
 
va_lag <- function(data) {
    LagTime=data %>% 
      select(C_Biosense_Facility_ID, Arrived_Date_Time, C_Visit_Date_Time, Message_Date_Time, Recorded_Date_Time)%>% 
      mutate(Arrived=as.POSIXct(Arrived_Date_Time,format="%Y-%m-%d %H:%M:%S"),
             Visit=as.POSIXct(C_Visit_Date_Time,format="%Y-%m-%d %H:%M:%S"),
             Message=as.POSIXct(Message_Date_Time,format="%Y-%m-%d %H:%M:%S"),
             Record=as.POSIXct(Recorded_Date_Time,format="%Y-%m-%d %H:%M:%S")
      )
    
    Time_Diff=LagTime%>%
      transmute(C_Biosense_Facility_ID,
                lag_Record_Visit=as.numeric(difftime(Record,Visit,units="hours")),
                lag_Message_Record=as.numeric(difftime(Message,Record,units="hours")),
                lag_Arrival_Message=as.numeric(difftime(Arrived,Message,units="hours")),
                lag_Arrival_Visit=as.numeric(difftime(Arrived,Visit,units="hours"))         
      )
    
  
     Lag_Summary=Time_Diff %>%
       group_by(C_Biosense_Facility_ID)%>%
       summarise(Record_Visit=round(mean(lag_Record_Visit,na.rm=TRUE),2),
                 Message_Record=round(mean(lag_Message_Record,na.rm=TRUE),2),
                 Arrival_Message=round(mean(lag_Arrival_Message,na.rm=TRUE),2),
                 Arrival_Visit=round(mean(lag_Arrival_Visit,na.rm=TRUE),2)
                 )
    
   return(Lag_Summary)
}