R/popperadm2.R

In arranhamlet/popvac_package: Generate population level vaccination data from a csv template.

#' Populates a cleaned UN WPP interpolated csv at adm2
#' @param popage Cleaned UN WPP interpolated csv
#' @examples
#' popperadm2(WPPintAGO)
#' @keywords internal


popperadm2<-function(popage){

  #Subset populations to country
  popcountryISO<-poptab[as.character(poptab$ISO) %in% as.character(popage$ISO),]
  
  #Calculate the population at adm2 for all ages
  adm2popages<-sapply(1:dim(popage)[1], function(x){
    popcountrylevel<-popage[x,-which(names(popage) %in% c("LocID","Location","VarID","Variant","Time","SexID","Sex","ISO"))]
    eachadm2<-sapply(1:length(popcountryISO$prop_pop), function(y){
      as.numeric(unlist(popcountrylevel*popcountryISO$prop_pop[y]))
    })
    eachadm2<-t(eachadm2)
    df<-cbind(popage[x,c("Location","LocID","Time","ISO")],"adm1_name"=as.character(popcountryISO$adm1_name),"adm1_id"=as.character(popcountryISO$adm1_id),
              "adm2_name"=as.character(popcountryISO$adm2_name),"adm2_id"=popcountryISO$adm2_id,eachadm2)
    for(z in which((names(df) %in% c("Location","LocID","Time","ISO","adm1_name","adm1_id","adm2_name","adm2_id"))==FALSE)){
      df[,z]<-as.numeric(df[,z])
    }
    df$adm1_name<-as.character(df$adm1_name)
    df$adm2_name<-as.character(df$adm2_name)
    df$ISO<-as.character(df$ISO)
    print(x)
    df
  })
  
  #Save as dataframe and fix names
  df2<-data.frame(matrix(unlist(t(adm2popages)), ncol = 109, byrow = FALSE),stringsAsFactors=FALSE)
  colnames(df2)<-c("Country","Country.code","Date","ISO","adm1_name","adm1_id","adm2_name","adm2_id",
                   paste("X",0:100,sep=""))
  
  #Remove NA's as 0
  df2[is.na(df2)]<-0
  #Translate to numbers not characters
  for(x in 9:length(df2)){
    df2[,x]<-as.numeric(df2[,x])*1000
  }
  
  df2
  
  
}