1 files changed, 0 insertions, 63 deletions
diff --git a/paper/rmse.rb b/paper/rmse.rb
deleted file mode 100644
index 90245eb..0000000
--- a/paper/rmse.rb
+++ /dev/null
@@ -1,63 +0,0 @@
-require_relative '../../lazar/lib/lazar'
-include OpenTox
-
-old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression","LOAEL_mg_corrected_smiles_mmol.csv")
-new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"..","regression","swissRat_chron_LOAEL_mmol.csv")
-
-File.open("rmse.R","w+") do |result|
-
-  names = {old => "mazzatorta",new  => "swiss"} 
-
-  [old,new].each do |dataset|
-    rmse = 0
-    nr = 0
-    dataset.compound_ids.each do |cid|
-      c = Compound.find cid
-      values = dataset.values(c,dataset.features.first)
-      if values.size > 1
-        median = -Math.log(values.mean) 
-        values.each do |v|
-          rmse += (-Math.log(v) - median)**2
-          nr += 1
-        end
-      end
-    end
-    rmse = Math.sqrt(rmse/nr)
-    result.puts "#{names[dataset]}.rmse <- #{rmse}"
-  end
-
-  rmse = 0
-  nr = 0
-  (old.compound_ids & new.compound_ids).each do |cid|
-    c = Compound.find cid
-    values = old.values(c,old.features.first) + new.values(c,new.features.first)
-    if values.size > 1
-      median = -Math.log(values.mean) 
-      values.each do |v|
-        rmse += (-Math.log(v) - median)**2
-        nr += 1
-      end
-    end
-  end
-  rmse = Math.sqrt(rmse/nr)
-  result.puts "common.rmse <- #{rmse}"
-
-  rmse = 0
-  nr = 0
-  (old.compound_ids + new.compound_ids).uniq.each do |cid|
-    c = Compound.find cid
-    values = old.values(c,old.features.first) + new.values(c,new.features.first)
-    if values.size > 1
-      median = -Math.log(values.mean) 
-      values.each do |v|
-        rmse += (-Math.log(v) - median)**2
-        nr += 1
-      end
-    end
-  end
-  rmse = Math.sqrt(rmse/nr)
-  result.puts "combined.rmse <- #{rmse}"
-end
-
-#combined_rmse = Math.sqrt(combined_rmse/combined_nr)
-#p "combined: #{combined_rmse}"