From 003332ad95dd4c63d0b7c00d22c73f460b163139 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 29 Feb 2016 14:11:30 +0100
Subject: modular regression algorithms

---
 test/lazar-regression.rb | 51 ------------------------------------------------
 test/regression.rb       | 42 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 51 deletions(-)
 delete mode 100644 test/lazar-regression.rb
 create mode 100644 test/regression.rb

(limited to 'test')

diff --git a/test/lazar-regression.rb b/test/lazar-regression.rb
deleted file mode 100644
index ae8f725..0000000
--- a/test/lazar-regression.rb
+++ /dev/null
@@ -1,51 +0,0 @@
-require_relative "setup.rb"
-
-class LazarRegressionTest < MiniTest::Test
-
-  def test_weighted_average
-    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.weighted_average"}
-    compound = Compound.from_smiles "CC(C)(C)CN"
-    prediction = model.predict compound
-    assert_equal 7.2, prediction[:value].round(1)
-    assert_equal 88, prediction[:neighbors].size
-  end
-
-  def test_mpd_fingerprints
-    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create training_dataset
-    model.neighbor_algorithm_parameters[:type] = "MP2D"
-    compound = Compound.from_smiles "CCCSCCSCC"
-    prediction = model.predict compound
-    assert_equal 0.04, prediction[:value].round(2)
-    assert_equal 3, prediction[:neighbors].size
-  end
-
-  def test_local_pls_regression
-    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create training_dataset
-    compound = Compound.from_smiles "NC(=O)OCCC"
-    prediction = model.predict compound
-    p prediction
-    model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.local_pls_regression")
-    prediction = model.predict compound
-    p prediction
-    #assert_equal 13.6, prediction[:value].round(1)
-    #assert_equal 0.83, prediction[:confidence].round(2)
-    #assert_equal 1, prediction[:neighbors].size
-  end
-
-  def test_local_physchem_regression
-    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
-    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
-    compound = Compound.from_smiles "NC(=O)OCCC"
-    prediction = model.predict compound
-    model.update(:prediction_algorithm => "OpenTox::Algorithm::Regression.local_pls_regression")
-    prediction = model.predict compound
-    # TODO assertions
-    #assert_equal 13.6, prediction[:value].round(1)
-    #assert_equal 0.83, prediction[:confidence].round(2)
-    #assert_equal 1, prediction[:neighbors].size
-  end
-
-end
diff --git a/test/regression.rb b/test/regression.rb
new file mode 100644
index 0000000..fa3b7fb
--- /dev/null
+++ b/test/regression.rb
@@ -0,0 +1,42 @@
+require_relative "setup.rb"
+
+class LazarRegressionTest < MiniTest::Test
+
+  def test_weighted_average
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create training_dataset, {:neighbor_algorithm_parameters => {:min_sim => 0}, :prediction_algorithm => "OpenTox::Algorithm::Regression.weighted_average"}
+    compound = Compound.from_smiles "CC(C)(C)CN"
+    prediction = model.predict compound
+    assert_equal 7.2, prediction[:value].round(1)
+    assert_equal 88, prediction[:neighbors].size
+  end
+
+  def test_mpd_fingerprints
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create training_dataset
+    model.neighbor_algorithm_parameters[:type] = "MP2D"
+    compound = Compound.from_smiles "CCCSCCSCC"
+    prediction = model.predict compound
+    assert_equal 0.04, prediction[:value].round(2)
+    assert_equal 3, prediction[:neighbors].size
+  end
+
+  def test_local_fingerprint_regression
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_fingerprint_regression")
+    compound = Compound.from_smiles "NC(=O)OCCC"
+    prediction = model.predict compound
+    p prediction[:value]
+    refute_nil prediction[:value]
+  end
+
+  def test_local_physchem_regression
+    training_dataset = Dataset.from_csv_file "#{DATA_DIR}/EPAFHM.medi.csv"
+    model = Model::LazarRegression.create(training_dataset, :prediction_algorithm => "OpenTox::Algorithm::Regression.local_physchem_regression")
+    compound = Compound.from_smiles "NC(=O)OCCC"
+    prediction = model.predict compound
+    p prediction[:value]
+    refute_nil prediction[:value]
+  end
+
+end
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