R/imputeVariable.R

In SWS-Methodology/faoswsImputation: Package to perform ensemble imputation for various FAO domains

##' Function to impute production or yield
##'
##' This is a wrapper of the ensemble imputation for the production domain.
##'
##' @param data The data.table object containing the data.
##' @param imputationParameters A list of the parameters for the imputation
##'   algorithms.  See defaultImputationParameters() for a starting point.

##'
##' @return This function doesn't return any objects but modifies the underlying
##'   data.table that it was passed.
##'
##' @export
##'
##' @import data.table
##'

imputeVariable = function(data, imputationParameters){

    ### Data Quality Checks
        if(!exists("ensuredImputationData") || !ensuredImputationData)
        ensureImputationInputs(data = data,
                              imputationParameters = imputationParameters)
    ## Define which columns should store the imputation and flags, and create
  ## those columns if they don't currently exist.
    if(imputationParameters$newImputationColumn == ""){
        newValueColumn = imputationParameters$imputationValueColumn
        newObsFlagColumn = imputationParameters$imputationFlagColumn
        newMethodFlagColumn = imputationParameters$imputationMethodColumn
    } else {
        newValueColumn = paste0("Value_",
                                imputationParameters$newImputationColumn)
        newObsFlagColumn = paste0("flagObservationStatus_",
                                imputationParameters$newImputationColumn)
        newMethodFlagColumn = paste0("flagMethod_",
                                imputationParameters$newImputationColumn)
    }

    ## NOTE (Michael): We impute variables which has only single
    ##                 observation with the only observed
    ##                 value. Although not a good practice but
    ##                 explaination is offered in issue 8.
   
  
    imputeSingleObservation(data, imputationParameters)
    
    missingIndex = data[[imputationParameters$imputationFlagColumn]]=="M" & 
                   data[[imputationParameters$imputationMethodColumn]]=="u"
    
    
    ensemble = ensembleImpute(data = data,
                                imputationParameters = imputationParameters)
    
    if(!is.null(nrow(ensemble))){
        
      
        data=cbind(data, ensemble)
        
        data[missingIndex & !is.na(ensemble),
             c(newValueColumn) := ensemble]
 
        data=data[,ensemble:=NULL]
        
        
        
    } 
    
   
    imputedIndex = missingIndex & !is.na(data[[newValueColumn]])
    invisible(data[imputedIndex,
                   c(newObsFlagColumn, newMethodFlagColumn) :=
                       list(imputationParameters$imputationFlag,
                            imputationParameters$newMethodFlag)])
    
    
}