extra/PRM Functions/AssignNearestSpeciesCategory_CIWG.R

In datalimited/datalimited: Stock Assessment Methods for Data-limited Fisheries

AssignNearestSpeciesCategory<- function(Data,AvailableCategories,AllCategories)
{
  
  
#   Data<- FaoSpeciesLevel
# 
#    AvailableCategories<- TempLevel
#   
# AllCategories<- AllPossible

  
  PossibleNumbers<- (AllCategories$SpeciesCatNames  %in% AvailableCategories)
  
  PossibleCats<- AllCategories[PossibleNumbers,]
  
  AllCats<- unique(Data$SpeciesCatName)
  
  OriginalSpeciesCatName<- Data$SpeciesCatName
  
  for (s in 1:length(AllCats))
  {
    
    IsAvailable<- any(AllCats[s] %in% PossibleCats$SpeciesCatNames)
    
    if (IsAvailable==F)
    {
      
      Where<- Data$SpeciesCatName==AllCats[s] & is.na(Data$SpeciesCatName)==F
      
      Group<- floor(Data$SpeciesCat[Where][1]/10) #Find taxonomic group that it is in
      
      Possible<- floor(PossibleCats$SpeciesCat/10)
      
      if (any(Possible==Group))
      {
        
       SpeciesCat<- Data$SpeciesCat[Where][1]
       
       GroupDistance<- (abs(PossibleCats$SpeciesCat-SpeciesCat)) # Find the closest match within the group
      
       ClosestGroupNumber<- PossibleCats$SpeciesCat[GroupDistance==min(GroupDistance)[1]][1]
       
       ClosestGroup<- PossibleCats$SpeciesCatNames[PossibleCats$SpeciesCat==ClosestGroupNumber]
       
       Data$SpeciesCatName[Where]<- ClosestGroup
       
      } #Close if 
      else
      {
        
        GroupDistance<- ((abs(Possible-Group)))
      
        ClosestCategories<- PossibleCats[GroupDistance==min(GroupDistance)[1],]
        
        ClosestGroup<- ClosestCategories[ClosestCategories$SpeciesCat==max(ClosestCategories$SpeciesCat),]
        
        Data$SpeciesCatName[Where]<- ClosestGroup$SpeciesCatNames
                
      } #Close else loop
      
    } #Close if IsAvailable statement
  } #Close species category loop
  
  
  return(list(Data=Data,OriginalSpeciesCatName=OriginalSpeciesCatName))
  
}# Close function