1 files changed, 0 insertions, 75 deletions
diff --git a/paper/loael-dataset-comparison.rb b/paper/loael-dataset-comparison.rb
deleted file mode 100644
index 5850236..0000000
--- a/paper/loael-dataset-comparison.rb
+++ /dev/null
@@ -1,75 +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")
-
-combined_compounds = old.compound_ids & new.compound_ids
-
-compound_vector = []
-value_vector = []
-dataset_vector = []
-
-old_median = []
-new_median = []
-
-errors = []
-combined_compounds.each do |cid|
-  c = Compound.find cid
-  old_values = old.values(c,old.features.first)
-  old_median << -Math.log(old_values.mean) 
-  old_values.each do |v|
-    compound_vector << c.smiles
-    value_vector << -Math.log(v.to_f)
-    dataset_vector << old.name
-  end
-  new_values = new.values(c,new.features.first)
-  new_median << -Math.log(new_values.mean)
-  new_values.each do |v|
-    compound_vector << c.smiles
-    value_vector << -Math.log(v)
-    dataset_vector << new.name
-  end
-end
-old_median.each_index do |i|
-  errors[i] = (old_median[i] - new_median[i]).abs unless old_median[i] == new_median[i]
-end
-rmse = 0
-mae = 0
-errors.compact.each do |e|
-  rmse += e**2
-  mae += e
-end
-rmse = Math.sqrt(rmse/errors.size)
-mae = mae/errors.size
-
-=begin
-R.assign "smi", compound_vector
-R.assign "values", value_vector
-R.assign "dataset", dataset_vector
-R.eval "df <- data.frame(factor(smi),values,factor(dataset))"
-R.eval "df$smi <- reorder(df$factor.smi,df$values)"
-R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))"
-R.eval "img <- img + ylab('-log(LOAEL mg/kg_bw/day)') + xlab('Compound') + theme(axis.text.x = element_blank())"
-R.eval "img <- img + geom_point()"
-
-R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-dataset-comparison-mmol_kg_day.svg', plot=img,width=12, height=8)"
-=end
-#img <- ggplot(data, aes(SMILES,LOAEL,ymin = min(LOAEL), ymax=max(LOAEL),color=Dataset))
-
-#img <- img + ylab('-log(LOAEL mg/kg_bw/day)') + xlab('Compound') + theme(axis.text.x = element_blank())
-
-#img <- img + geom_point()
-
-#print(img)
-
-R.assign "Mazzatorta", old_median
-R.assign "SwissFederalOffice", new_median
-R.eval "df <- data.frame(Mazzatorta,SwissFederalOffice)"
-R.eval "ggplot(df, aes(Mazzatorta,SwissFederalOffice)) + geom_point() + geom_abline(intercept=0.0) "
-R.eval "ggsave(file='/home/ch/src/lazar-nestec-data/paper/loael-dataset-correlation.pdf')"
-
-puts "Correlation Mazzatorta/SwissFederalOffice:"
-puts "\tr^2: #{R.eval("cor(Mazzatorta,SwissFederalOffice,use='complete')").to_f**2}"
-puts "\tRMSE: #{rmse}"
-puts "\tMAE: #{mae}"