nimbus 0.10 → 1.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/lib/nimbus/application.rb +2 -1
- data/lib/nimbus/configuration.rb +15 -6
- data/lib/nimbus/tree.rb +1 -1
- data/spec/configuration_spec.rb +92 -0
- data/spec/fixtures/regression_config.yml +12 -0
- data/spec/fixtures/regression_random_forest.yml +1741 -0
- data/spec/fixtures/regression_snp_importances.txt +200 -0
- data/spec/fixtures/{testing_regression.data → regression_testing.data} +0 -0
- data/spec/fixtures/regression_testing_file_predictions.txt +200 -0
- data/spec/fixtures/{training_regression.data → regression_training.data} +0 -0
- data/spec/fixtures/regression_training_file_predictions.txt +758 -0
- data/spec/forest_spec.rb +57 -0
- data/spec/individual_spec.rb +13 -0
- data/spec/nimbus_spec.rb +17 -1
- data/spec/spec_helper.rb +7 -1
- data/spec/training_set_spec.rb +25 -0
- data/spec/tree_spec.rb +130 -0
- metadata +27 -10
- data/README.rdoc +0 -1
- data/spec/fixtures/config.yml +0 -11
data/spec/forest_spec.rb
ADDED
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# encoding: UTF-8
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require File.dirname(__FILE__) + '/spec_helper'
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describe Nimbus::Forest do
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before(:each) do
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@config = Nimbus::Configuration.new
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@config.load fixture_file('regression_config.yml')
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@config.load_training_data
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@forest = ::Nimbus::Forest.new @config
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end
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it 'grows a forest of N trees' do
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@forest.trees.should == []
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@config.forest_size.should == 3
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@forest.grow
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@forest.trees.size.should == @config.forest_size
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@forest.trees.each{|t| t.should be_kind_of Hash}
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end
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it 'creates averaged predictions for individuals in the training set' do
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@forest.predictions.should == {}
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@forest.grow
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(@forest.predictions.keys - (1..800).to_a ).should == []
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@forest.predictions.values.each{|v| v.should be_kind_of Numeric}
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end
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it 'computes averaged SNP importances for every SNP' do
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@forest.snp_importances.should == {}
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@forest.grow
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@forest.snp_importances.keys.sort.should == (1..200).to_a
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@forest.snp_importances.values.each{|v| v.should be_kind_of Numeric}
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end
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it 'traverses a set of testing individuals through every tree in the forest and return predictions' do
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@forest = @config.load_forest
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@forest.predictions.should == {}
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tree_structure = YAML.load(File.open fixture_file('regression_random_forest.yml'))
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expected_predictions = {}
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@config.read_testing_data{|individual|
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individual_prediction = 0.0
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tree_structure.each do |t|
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individual_prediction = (individual_prediction + Nimbus::Tree.traverse(t, individual.snp_list)).round(5)
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end
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expected_predictions[individual.id] = (individual_prediction / 3).round(5)
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}
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@forest.traverse
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@forest.predictions.should == expected_predictions
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end
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it 'can output forest structure in YAML format' do
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@forest = @config.load_forest
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YAML.load(File.open fixture_file('regression_random_forest.yml')) == YAML.load(@forest.to_yaml)
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end
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end
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# encoding: UTF-8
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require File.dirname(__FILE__) + '/spec_helper'
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describe Nimbus::Individual do
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it "stores id, fenotype and SNPs information for an individual" do
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@individual = Nimbus::Individual.new(11, 33.275, [1,0,2,1])
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@individual.id.should == 11
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@individual.fenotype.should == 33.275
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@individual.snp_list.should == [1,0,2,1]
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end
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end
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data/spec/nimbus_spec.rb
CHANGED
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@@ -1,2 +1,18 @@
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# encoding: UTF-8
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require File.dirname(__FILE__) + '/spec_helper'
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require File.dirname(__FILE__) + '/spec_helper'
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describe 'Nimbus module' do
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it "manages a Nimbus::Application object" do
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app = Nimbus.application
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app.should be_kind_of Nimbus::Application
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end
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it "accepts setting an external Nimbus::Application" do
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app = Nimbus::Application.new
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Nimbus.application = app
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Nimbus.application.should == app
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end
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end
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data/spec/spec_helper.rb
CHANGED
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@@ -1,2 +1,8 @@
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# encoding: UTF-8
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require File.dirname(__FILE__) + '/../lib/nimbus'
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require File.dirname(__FILE__) + '/../lib/nimbus'
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$fixtures_path = File.dirname(__FILE__) + '/fixtures'
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ENV['nimbus_test'] = 'running_nimbus_tests'
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def fixture_file(filename) #:nodoc:
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return "#{$fixtures_path}/#{filename}"
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end
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# encoding: UTF-8
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require File.dirname(__FILE__) + '/spec_helper'
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describe Nimbus::TrainingSet do
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it "stores individuals list and fenotype data for them" do
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i1 = Nimbus::Individual.new 1, 11.0, [1,0,2,1]
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i2 = Nimbus::Individual.new 2, 22.0, [2,1,2,2]
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i3 = Nimbus::Individual.new 3, 33.0, [0,2,1,0]
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@training_set = Nimbus::TrainingSet.new [i1, i3], {i1.id => 11.0, i3.id => 33.0}
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@training_set.individuals.should == [i1, i3]
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@training_set.ids_fenotypes.should == {i1.id => 11.0, i3.id => 33.0}
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end
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it "keeps track of ids of all individuals in the training set" do
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i1 = Nimbus::Individual.new 1, 11.0, [1,0,2,1]
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i2 = Nimbus::Individual.new 2, 22.0, [2,1,2,2]
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i3 = Nimbus::Individual.new 3, 33.0, [0,2,1,0]
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@training_set = Nimbus::TrainingSet.new [i1, i3], {i1.id => 11.0, i3.id => 33.0}
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@training_set.all_ids.should == [1,3]
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end
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end
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data/spec/tree_spec.rb
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# encoding: UTF-8
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require File.dirname(__FILE__) + '/spec_helper'
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describe Nimbus::Tree do
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before(:each) do
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@config = Nimbus::Configuration.new
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@config.load fixture_file('regression_config.yml')
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@tree = Nimbus::Tree.new @config.tree
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end
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it "is initialized with tree config info" do
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@tree.snp_total_count.should == 200
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@tree.snp_sample_size.should == 60
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@tree.node_min_size.should == 5
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end
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it "creates a tree structure when seeded with training data" do
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@config.load_training_data
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@tree.structure.should be_nil
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@tree.seed(@config.training_set.individuals, @config.training_set.all_ids, @config.training_set.ids_fenotypes)
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@tree.structure.should_not be_nil
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@tree.structure.should be_kind_of Hash
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@tree.structure.keys.first.should == @tree.used_snps.last
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@tree.used_snps.should_not be_empty
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end
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it "split node in three when building a node and finds a suitable split" do
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@config.load_training_data
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@tree.stub!(:snps_random_sample).and_return((141..200).to_a) #189 is best split
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@tree.individuals = @config.training_set.individuals
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@tree.id_to_fenotype = @config.training_set.ids_fenotypes
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@tree.used_snps = []
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@tree.predictions = {}
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branch = @tree.build_node @config.training_set.all_ids, Nimbus::LossFunctions.average(@config.training_set.all_ids, @config.training_set.ids_fenotypes)
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branch.keys.size.should == 1
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branch.keys.first.should == 189
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branch[189].size.should == 3
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branch[189][0].should be_kind_of Hash
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branch[189][1].should be_kind_of Hash
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branch[189][2].should be_kind_of Hash
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end
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it "keeps track of all SNPs used for the tree" do
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@config.load_training_data
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snps = (131..190).to_a
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@tree.stub!(:snps_random_sample).and_return(snps)
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@tree.used_snps.should be_nil
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@tree.seed(@config.training_set.individuals, @config.training_set.all_ids, @config.training_set.ids_fenotypes)
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@tree.used_snps.size.should > 4
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@tree.used_snps.each{|snp|
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snps.include?(snp).should be_true
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}
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end
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it "labels node when building a node and there is not a suitable split" do
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@config.load_training_data
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@tree.stub!(:snps_random_sample).and_return([33])
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@tree.individuals = @config.training_set.individuals
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@tree.id_to_fenotype = @config.training_set.ids_fenotypes
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@tree.used_snps = []
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@tree.predictions = {}
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branch = @tree.build_node @config.training_set.all_ids, Nimbus::LossFunctions.average(@config.training_set.all_ids, @config.training_set.ids_fenotypes)
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branch[33][0].should be_kind_of Numeric
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branch[33][1].should be_kind_of Numeric
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branch[33][2].should be_kind_of Numeric
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end
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it "labels node when building a node with less individuals than the minimum node size" do
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@config.load_training_data
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@tree.individuals = @config.training_set.individuals
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@tree.id_to_fenotype = @config.training_set.ids_fenotypes
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@tree.used_snps = []
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@tree.predictions = {}
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label = @tree.build_node [1, 10, 33], Nimbus::LossFunctions.average(@config.training_set.all_ids, @config.training_set.ids_fenotypes)
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label.should be_kind_of Numeric
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label = @tree.build_node [2, 10], Nimbus::LossFunctions.average(@config.training_set.all_ids, @config.training_set.ids_fenotypes)
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label.should be_kind_of Numeric
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label = @tree.build_node [1, 10, 33], Nimbus::LossFunctions.average(@config.training_set.all_ids, @config.training_set.ids_fenotypes)
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label.should be_kind_of Numeric
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label = @tree.build_node [108, 22, 10, 33], Nimbus::LossFunctions.average(@config.training_set.all_ids, @config.training_set.ids_fenotypes)
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label.should be_kind_of Numeric
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end
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it 'computes generalization error for the tree' do
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@config.load_training_data
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@tree.seed(@config.training_set.individuals, @config.training_set.all_ids, @config.training_set.ids_fenotypes)
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@tree.generalization_error.should be_nil
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@tree.generalization_error_from_oob((2..200).to_a)
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@tree.generalization_error.should be_kind_of Numeric
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@tree.generalization_error.should > 0.0
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@tree.generalization_error.should < 100.0
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end
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it 'estimates importance for all SNPs' do
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@config.load_training_data
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@tree.seed(@config.training_set.individuals, @config.training_set.all_ids, @config.training_set.ids_fenotypes)
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@tree.importances.should be_nil
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@tree.estimate_importances((300..533).to_a)
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@tree.importances.should be_kind_of Hash
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@tree.importances.keys.should_not be_empty
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(@tree.importances.keys - (1..200).to_a).should be_empty
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end
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it 'get prediction for an individual pushing it down a tree structure' do
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tree_structure = YAML.load(File.open fixture_file('regression_random_forest.yml')).first
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individual_data = [0]*200
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prediction = Nimbus::Tree.traverse tree_structure, individual_data
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prediction.should == 0.25043
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individual_data[189-1] = 1
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individual_data[4-1] = 1
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individual_data[62-1] = 2
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individual_data[146-1] = 2
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prediction = Nimbus::Tree.traverse tree_structure, individual_data
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prediction.should == -0.9854
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end
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end
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metadata
CHANGED
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name: nimbus
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version: !ruby/object:Gem::Version
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prerelease:
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version: "0
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version: "1.0"
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platform: ruby
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authors:
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- "Juanjo Baz\xC3\xA1n"
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bindir: bin
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cert_chain: []
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date: 2011-08-
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date: 2011-08-25 00:00:00 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: rspec
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files:
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- MIT-LICENSE.txt
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-
- README.rdoc
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- lib/nimbus/application.rb
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- lib/nimbus/configuration.rb
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- lib/nimbus/exceptions.rb
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@@ -45,13 +44,22 @@ files:
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45
44
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- lib/nimbus/training_set.rb
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46
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- lib/nimbus/tree.rb
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46
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- lib/nimbus.rb
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48
|
-
- spec/
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|
-
- spec/fixtures/
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-
- spec/fixtures/
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+
- spec/configuration_spec.rb
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48
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+
- spec/fixtures/regression_config.yml
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49
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+
- spec/fixtures/regression_random_forest.yml
|
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50
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+
- spec/fixtures/regression_snp_importances.txt
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51
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+
- spec/fixtures/regression_testing.data
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+
- spec/fixtures/regression_testing_file_predictions.txt
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53
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+
- spec/fixtures/regression_training.data
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54
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+
- spec/fixtures/regression_training_file_predictions.txt
|
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55
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+
- spec/forest_spec.rb
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|
56
|
+
- spec/individual_spec.rb
|
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51
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|
- spec/nimbus_spec.rb
|
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52
58
|
- spec/spec_helper.rb
|
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59
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+
- spec/training_set_spec.rb
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+
- spec/tree_spec.rb
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53
61
|
- bin/nimbus
|
|
54
|
-
homepage: http://
|
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62
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+
homepage: http://nimbusgem.org
|
|
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|
licenses: []
|
|
56
64
|
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57
65
|
post_install_message:
|
|
@@ -81,8 +89,17 @@ signing_key:
|
|
|
81
89
|
specification_version: 3
|
|
82
90
|
summary: Random Forest algorithm for Genomics
|
|
83
91
|
test_files:
|
|
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|
-
- spec/
|
|
85
|
-
- spec/fixtures/
|
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|
-
- spec/fixtures/
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|
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+
- spec/configuration_spec.rb
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93
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- spec/fixtures/regression_config.yml
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- spec/fixtures/regression_random_forest.yml
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+
- spec/fixtures/regression_snp_importances.txt
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+
- spec/fixtures/regression_testing.data
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+
- spec/fixtures/regression_testing_file_predictions.txt
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+
- spec/fixtures/regression_training.data
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99
|
+
- spec/fixtures/regression_training_file_predictions.txt
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|
100
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+
- spec/forest_spec.rb
|
|
101
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+
- spec/individual_spec.rb
|
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87
102
|
- spec/nimbus_spec.rb
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|
88
103
|
- spec/spec_helper.rb
|
|
104
|
+
- spec/training_set_spec.rb
|
|
105
|
+
- spec/tree_spec.rb
|
data/README.rdoc
DELETED
|
@@ -1 +0,0 @@
|
|
|
1
|
-
= Nimbus
|
data/spec/fixtures/config.yml
DELETED