R/get_taxa_missing_1_infos.R

In Eliot-RUIZ/eDNAevaluation: Metabarcodes Evaluation

# Info: This function search for taxa with NA and returning previous rank with missing informations in order to search informations easily.

# Note: The names of the list are those of the columns missing taxonomic infos

get_taxa_missing_1_infos = function(data){
  
  output = list()
  
  missing_rows = data[rowSums(is.na(data)) == 1, ]
  
  missing_columns = colSums(is.na(missing_rows))[colSums(is.na(missing_rows)) > 0]
  
  for(i in length(names(missing_columns)):1){
    
    missing_taxa = names(missing_columns)[i]
    
    missing_data = missing_rows[is.na(missing_rows[[missing_taxa]]), ]
    
    last_taxa = unique(missing_data[, which(colnames(missing_rows) == missing_taxa) - 1][[1]])
    
    output[[missing_taxa]] = last_taxa
    
  }
  
  output
  
}