if(m==1||m==2||m==4){
  if(adv_id<=6){
    all.var.keep = c("sname",
                     "age_start_yrs", "age_end_yrs",
                     "age_class",
                     "grp","hydroyear","failure_1eqdead",covariate.collect.index,
                     mediator.name[m],adverse.name[1:6])
    Complete.data= DSI_data[, all.var.keep]
  }else{
    all.var.keep = c("sname",
                     "age_start_yrs", "age_end_yrs",
                     "age_class",
                     "grp","hydroyear","failure_1eqdead",covariate.collect.index,
                     mediator.name[m],adverse.name[adv_id])
    Complete.data= DSI_data[, all.var.keep]
  }
}else{
  if(adv_id<=6){
    all.var.keep = c("sname",
                     "age_start_time","age_end_time","status",
                     "state","season","age_sample","age_group",
                     "grp","hydroyear","gc",covariate.collect.index,adverse.name[1:6])
    Complete.data= GC_survival_data[, all.var.keep]
  }else{
    all.var.keep = c("sname",
                     "age_start_time","age_end_time","status",
                     "state","season","age_sample","age_group",
                     "grp","hydroyear","gc",
                     covariate.collect.index,adverse.name[adv_id])
    
    Complete.data= GC_survival_data[, all.var.keep]
  }
  Complete.data$gc=log(Complete.data$gc)
  # Complete.data$cycling = as.integer(Complete.data$state=="Cycling")
  # Complete.data$pregnany = as.integer(Complete.data$state=="Pregnant")
  # Complete.data$dry  = as.integer(Complete.data$season=="Dry")
}

##Standardize
Complete.data[, covariate.collect.index] =
  scale(Complete.data[, covariate.collect.index] )
if(m==3){
  # add categorical variables
  covariate.index.dsi = c("state","season",covariate.index.dsi)
  covariate.collect.index=union(covariate.index.dsi,covariate.index)
}


if(adv_id<=6){
  Complete.data$adv_rain = as.integer(Complete.data$adv_rain)
  Complete.data$adv_density = as.integer(Complete.data$adv_density)
  Complete.data$adv_sib = as.integer(Complete.data$adv_sib)
  Complete.data$adv_mom = as.integer(Complete.data$adv_mom)
  Complete.data$adv_mom_sci = as.integer(Complete.data$adv_mom_sci)
  Complete.data$adv_mom_rank = as.integer(Complete.data$adv_mom_rank)
}

Complete.data$adv_use=Complete.data[,adverse.name[adv_id]]
Complete.data$m_use=Complete.data[,mediator.name[m]]

complete_id=which(!apply(Complete.data,1,FUN=function(x){any(is.na(x))}))
Complete.data=Complete.data[complete_id,]
Complete.data$hydroyear = as.factor(Complete.data$hydroyear)

#Normalize the time to [0,1] Interval
if(m==3){
  range.y=range(Complete.data$age_sample)
  Complete.data$t=(Complete.data$age_sample-range.y[1]+0.0001)/(range.y[2]-range.y[1]+0.0002)
}else{
  range.y=range(Complete.data$age_class)
  Complete.data$t=(Complete.data$age_class-range.y[1]+0.0001)/(range.y[2]-range.y[1]+0.0002)
}

Complete.data$treatment_factor=
  as.factor(Complete.data[,adverse.name[adv_id]])

delete.sname = unique(Complete.data$sname)[which(table(Complete.data$sname)<=2)]
Complete.data = subset(Complete.data,!sname%in%delete.sname)