From 280f81dcffb3b8b929ff9cbe92ba17403f5a9dd3 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 28 Oct 2016 12:31:53 +0200
Subject: adjusted r^2 removed (does not apply well to local models)

---
 lib/crossvalidation.rb          | 2 --
 lib/validation-statistics.rb    | 1 +
 test/validation-nanoparticle.rb | 1 +
 3 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index 4f779a2..be680ae 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -95,7 +95,6 @@ module OpenTox
         crossvalidation_ids.collect{|id| CrossValidation.find(id)}
       end
 
-=begin
       def correlation_plot format: "png"
         #unless correlation_plot_id
           feature = Feature.find(crossvalidations.first.model.prediction_feature)
@@ -129,7 +128,6 @@ module OpenTox
         #end
       $gridfs.find_one(_id: correlation_plot_id).data
       end
-=end
     end
   end
 
diff --git a/lib/validation-statistics.rb b/lib/validation-statistics.rb
index b251bdb..799bb34 100644
--- a/lib/validation-statistics.rb
+++ b/lib/validation-statistics.rb
@@ -139,6 +139,7 @@ module OpenTox
           :mae => mae,
           :rmse => rmse,
           :r_squared => r_squared,
+          :r_squared_adjusted => r_squared_adjusted,
           :within_prediction_interval => within_prediction_interval,
           :out_of_prediction_interval => out_of_prediction_interval,
         }
diff --git a/test/validation-nanoparticle.rb b/test/validation-nanoparticle.rb
index c0f2f92..1742ef2 100644
--- a/test/validation-nanoparticle.rb
+++ b/test/validation-nanoparticle.rb
@@ -15,6 +15,7 @@ class NanoparticleValidationTest  < MiniTest::Test
   def test_validate_default_nanoparticle_model
     model = Model::Lazar.create training_dataset: @training_dataset, prediction_feature: @prediction_feature
     cv = CrossValidation.create model
+    p cv
     p cv.rmse
     p cv.r_squared
     #File.open("tmp.pdf","w+"){|f| f.puts cv.correlation_plot}
-- 
cgit v1.2.3


From c6e86fc1bfee7cb91782dd7067408d78a8e48ed9 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 8 Nov 2016 16:04:49 +0100
Subject: probability plot for classification

---
 lib/validation-statistics.rb      | 12 ++++++++----
 test/descriptor.rb                |  4 +++-
 test/validation-classification.rb |  6 ++++--
 3 files changed, 15 insertions(+), 7 deletions(-)

diff --git a/lib/validation-statistics.rb b/lib/validation-statistics.rb
index 799bb34..b6f8a60 100644
--- a/lib/validation-statistics.rb
+++ b/lib/validation-statistics.rb
@@ -66,8 +66,13 @@ module OpenTox
       end
 
       def probability_plot format: "pdf"
-        unless probability_plot_id
-          tmpfile = "/tmp/#{id.to_s}_probability.#{format}"
+        #unless probability_plot_id
+
+          #tmpdir = File.join(ENV["HOME"], "tmp")
+          tmpdir = "/tmp"
+          #p tmpdir
+          FileUtils.mkdir_p tmpdir
+          tmpfile = File.join(tmpdir,"#{id.to_s}_probability.#{format}")
           accuracies = []
           probabilities = []
           correct_predictions = 0
@@ -91,7 +96,7 @@ module OpenTox
           file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_probability_plot.svg")
           plot_id = $gridfs.insert_one(file)
           update(:probability_plot_id => plot_id)
-        end
+        #end
         $gridfs.find_one(_id: probability_plot_id).data
       end
     end
@@ -139,7 +144,6 @@ module OpenTox
           :mae => mae,
           :rmse => rmse,
           :r_squared => r_squared,
-          :r_squared_adjusted => r_squared_adjusted,
           :within_prediction_interval => within_prediction_interval,
           :out_of_prediction_interval => out_of_prediction_interval,
         }
diff --git a/test/descriptor.rb b/test/descriptor.rb
index e5d8ff9..42d4661 100644
--- a/test/descriptor.rb
+++ b/test/descriptor.rb
@@ -12,7 +12,9 @@ class DescriptorTest < MiniTest::Test
 
   def test_smarts
     c = OpenTox::Compound.from_smiles "N=C=C1CCC(=F=FO)C1"
-    File.open("tmp.png","w+"){|f| f.puts c.png}
+    File.open("/tmp/tmp.png","w+"){|f| f.puts c.png}
+    assert_match /^PNG/,`file -b /tmp/tmp.png`
+    File.delete "/tmp/tmp.png"
     s = Smarts.find_or_create_by(:smarts => "F=F")
     result = c.smarts_match [s]
     assert_equal [1], result
diff --git a/test/validation-classification.rb b/test/validation-classification.rb
index c93e71f..fb4c3e7 100644
--- a/test/validation-classification.rb
+++ b/test/validation-classification.rb
@@ -11,8 +11,10 @@ class ValidationClassificationTest < MiniTest::Test
     cv = ClassificationCrossValidation.create model
     assert cv.accuracy > 0.7, "Accuracy (#{cv.accuracy}) should be larger than 0.7, this may occur due to an unfavorable training/test set split"
     assert cv.weighted_accuracy > cv.accuracy, "Weighted accuracy (#{cv.weighted_accuracy}) should be larger than accuracy (#{cv.accuracy})."
-    #p cv
-    #File.open("tmp.pdf","w+"){|f| f.puts cv.probability_plot}
+    File.open("/tmp/tmp.pdf","w+"){|f| f.puts cv.probability_plot(format:"pdf")}
+    p `file -b /tmp/tmp.pdf`
+    File.open("/tmp/tmp.png","w+"){|f| f.puts cv.probability_plot(format:"png")}
+    p `file -b /tmp/tmp.png`
   end
 
   # parameters
-- 
cgit v1.2.3