pest 0.0.0

data/spec/pest/data_set_spec.rb

@@ -0,0 +1,95 @@
+require 'spec_helper'
+
+class TestClass
+  include Pest::DataSet
+end
+
+describe Pest::DataSet do
+  before(:each) { @instance = TestClass.new }
+
+  describe Pest::DataSet::ClassMethods do
+    before(:each) { @class = TestClass }
+
+    describe "::from" do
+      before(:each) do
+        @class.stub(:translators).and_return(Hash => :from_hash)
+        @class.stub(:from_hash).and_return(Hash.new)
+        @class.stub(:send).with(:from_hash, kind_of(Hash)).and_return(true)
+
+        @hash_source = {:foo => :bar}
+        @unknown_source = double("Unknown Instance")
+        @unknown_source.stub(:to_hash).and_return(@hash_source)
+      end
+
+      it "checks for translator with passed class" do
+        @class.translators.should_receive(:[]).with(Hash).and_return(:from_hash)
+        @class.from({:foo => :bar})
+      end
+
+      it "passes to translator if found" do
+        @class.should_receive(:send).with(:from_hash, @hash_source)
+        @class.from(@hash_source)
+      end
+
+      it "calls to_hash if unrecognized class" do
+        @unknown_source.should_receive(:to_hash)
+        @class.from(@unknown_source)
+      end
+
+      it "passes to translator after converting to hash" do
+        @class.should_receive(:send).with(:from_hash, @hash_source)
+        @class.from(@unknown_source)
+      end
+    end
+
+    describe "::translators" do
+      # Required
+      it "raises an error if called from module" do
+        lambda { @class.translators }.should raise_error(NotImplementedError)
+      end
+    end
+    
+    describe "::from_file" do
+      # Required
+      it "raises an error if called from module" do
+        lambda { @class.from_file }.should raise_error(NotImplementedError)
+      end
+    end
+    
+    describe "::from_hash" do
+      # Required
+      it "raises an error if called from module" do
+        lambda { @class.from_hash }.should raise_error(NotImplementedError)
+      end
+    end
+  end
+
+  describe "#variables" do
+    it "defaults to an empty list" do
+      @instance.variables.should == {}
+    end
+  end
+
+  describe "#to_hash" do
+    # Required
+    it "raises an error if called from module" do
+      lambda { @instance.to_hash }.should raise_error(NotImplementedError)
+    end
+  end
+
+  describe "#save" do
+    # Required
+    it "raises an error if called from module" do
+      lambda { @instance.save }.should raise_error(NotImplementedError)
+    end
+  end
+
+  describe "#length" do
+    # Required
+    it "raises an error if called from module" do
+      lambda { @instance.length }.should raise_error(NotImplementedError)
+    end
+  end
+
+  # Enumerable interface?
+end

data/spec/pest/estimator/bernoulli_spec.rb

@@ -0,0 +1,21 @@
+# require 'spec_helper'
+# 
+# describe Pest::Estimator::Bernoulli do
+#   it "inherits from set"
+# 
+#   describe "estimate_class" do
+#     before(:each) { @instance = Pest::Estimator::Bernoulli.new }
+# 
+#     it "returns class" do
+#       @instance.estimate_class.should == Pest::Estimate::Bernoulli
+#     end
+#   end
+# 
+#   describe Distribution do
+#     describe "cache" do
+#     end
+# 
+#     describe "evaluate" do
+#     end
+#   end
+# end

data/spec/pest/estimator/frequency_spec.rb

@@ -0,0 +1,85 @@
+require 'spec_helper'
+
+describe Pest::Estimator::Frequency do
+  before(:each) do
+    @class = Pest::Estimator::Frequency
+    @v1 = Pest::Variable.new(:name => :foo)
+    @v2 = Pest::Variable.new(:name => :bar)
+    @data = Pest::DataSet::NArray.from_hash @v1 => [1,1,2,3], @v2 => [1,1,1,1]
+    @test = Pest::DataSet::NArray.from_hash @v1 => [1,2,4], @v2 => [1,1,1]
+    @instance = @class.new(@data)
+  end
+
+  it "inherits from set" do
+    @instance.should be_a(Pest::Estimator)
+  end
+
+  it "generates marginal probabilities" do
+    @instance.p(@v2).in(@test).should === NArray[[1.0, 1.0, 1.0]]
+  end
+
+  it "generates joint probability" do
+    @instance.p(@v1, @v2).in(@test).should == NArray[[0.5, 0.25, 0]]
+  end
+
+  it "generates conditional probability" do
+    @instance.p(@v1).given(@v2).in(@test).should == NArray[[0.5, 0.25, 0]]
+  end
+
+  describe Pest::Estimator::Frequency::Distribution do
+    before(:each) do
+      @dist = @instance.distributions[@data.variables.values.to_set]
+    end
+
+    describe "#cache_model" do
+      context "with unrecognized checksum" do
+        it "determines vector frequency" do
+          @dist.cache_model
+          @dist.frequencies[[1,1]].should == 2
+        end
+
+        it "defaults to 0" do
+          @dist.cache_model
+          @dist.frequencies[[4,1]].should == 0
+        end
+      end
+
+      context "with recognized checksum but no file" do
+        it "determines vector frequency" do
+          @data.should_receive(:data_vectors).and_return @data
+          @dist.cache_model
+        end
+      end
+
+      context "with recognized checksum and cache file" do
+        before(:each) do
+          @file = @dist.cache_model
+        end
+      end
+    end
+
+    describe "#probability" do
+      it "returns an NArray" do
+        @dist.probability(@test).should be_a(NArray)
+      end
+
+      it "calculates vector frequency / dataset length"  do
+        @dist.probability(@test).should == NArray[[0.5,0.25,0]]        
+      end
+    end
+    
+    describe "#entropy" do
+      it "returns a Float" do
+        @dist.entropy.should be_a(Float)
+      end
+
+      it "calculates -sum(PlogP)" do
+        # Outcomes = ([1,1]: 2, [2,1]: 1, [3,1]: 1)
+        # P = (0.5, 0.25, 0.25)
+        # logP = (-1, -2, -2) (log base 2 for bits)
+        # -sum(PlogP) = (0.5, 0.5, 0.5).sum
+        @dist.entropy.should == 1.5
+      end
+    end
+  end
+end

data/spec/pest/estimator/gaussian_spec.rb

@@ -0,0 +1,21 @@
+# require 'spec_helper'
+# 
+# describe Pest::Estimator::Gaussian do
+#   it "inherits from discrete"
+# 
+#   describe "estimate_class" do
+#     before(:each) { @instance = Pest::Extimator::Gaussian.new }
+# 
+#     it "returns class" do
+#       @instance.estimate_class.should == Pest::Estimate::Gaussian
+#     end
+#   end
+# 
+#   describe Distribution do
+#     describe "cache" do
+#     end
+# 
+#     describe "evaluate" do
+#     end
+#   end
+# end

data/spec/pest/estimator/multinomial_spec.rb

@@ -0,0 +1,21 @@
+# require 'spec_helper'
+# 
+# describe Pest::Estimator::Multinomial do
+#   it "inherits from set"
+# 
+#   describe "estimate_class" do
+#     before(:each) { @instance = Pest::Estimator::Multinomial.new }
+# 
+#     it "returns class" do
+#       @instance.estimate_class.should == Pest::Estimate::Multinomial
+#     end
+#   end
+# 
+#   describe Distribution do
+#     describe "cache" do
+#     end
+# 
+#     describe "evaluate" do
+#     end
+#   end
+# end

data/spec/pest/estimator/parzen_spec.rb

@@ -0,0 +1,21 @@
+# require 'spec_helper'
+# 
+# describe Pest::Estimator::Parzen do
+#   it "inherits from continuous"
+# 
+#   describe "estimate_class" do
+#     before(:each) { @instance = Pest::Estimator::Parzen.new }
+# 
+#     it "returns class" do
+#       @instance.estimate_class.should == Pest::Estimate::Parzen
+#     end
+#   end
+# 
+#   describe Distribution do
+#     describe "cache" do
+#     end
+# 
+#     describe "evaluate" do
+#     end
+#   end
+# end

data/spec/pest/estimator/svd_spec.rb

@@ -0,0 +1,21 @@
+# require 'spec_helper'
+# 
+# describe Pest::Estimator::SVD do
+#   it "inherits from continuous"
+# 
+#   describe "estimate_class" do
+#     before(:each) { @instance = Pest::Estimator::SVD.new }
+# 
+#     it "returns class" do
+#       @instance.estimate_class.should == Pest::Estimate::SVD
+#     end
+#   end
+# 
+#   describe Distribution do
+#     describe "cache" do
+#     end
+# 
+#     describe "evaluate" do
+#     end
+#   end
+# end

data/spec/pest/estimator_spec.rb

@@ -0,0 +1,74 @@
+require 'spec_helper'
+
+class TestClass
+  include Pest::Estimator
+  def distribution_class; Distribution end
+  class Distribution
+    include Pest::Estimator::Distribution
+  end
+end
+
+describe Pest::Estimator do
+  before(:each) do
+    @data = Pest::DataSet::NArray.from_hash :foo => [1,1,2,3], :bar => [1,1,1,1]
+    @class = TestClass
+  end
+
+  describe "::new" do
+    it "accepts a dataset" do
+      @class.new(@data).data.should == @data
+    end
+  end
+
+  describe "#variables" do
+    it "proxies data set" do
+      @class.new(@data).variables.should == @data.variables
+    end
+  end
+
+  describe "#estimates" do
+    before(:each) do
+      @v1 = Pest::Variable.new(:name => :foo)
+      @v2 = Pest::Variable.new(:name => :bar)
+      @v3 = Pest::Variable.new(:name => :baz)
+
+      @instance = TestClass.new
+      @instance.stub(:variables).and_return({:foo => @v1, :bar => @v2})
+    end
+
+    it "accepts a set of variables" do
+      @instance.distributions[@v1, @v2].should be_a(Pest::Estimator::Distribution)
+    end
+
+    it "returns an estimator for the passed variables" do
+      @instance.distributions[@v1, @v2].variables.should == [@v1, @v2].to_set
+    end
+
+    it "returns an estimator for the passed strings" do
+      @instance.distributions[:foo, :bar].variables.should == [@v1, @v2].to_set
+    end
+
+    it "is variable order agnostic" do
+      @instance.distributions[@v1, @v2].should == @instance.distributions[@v2, @v1]
+    end
+
+    it "fails if a set variable isn't defined" do
+      lambda { @instance.distributions[@v1, @v3] }.should raise_error(ArgumentError)
+    end
+  end
+
+  describe Pest::Estimator::Distribution do
+    before(:each) do
+      @class = TestClass::Distribution
+      @estimator = TestClass.new
+      @estimator.stub(:variables).and_return({:foo => @v1, :bar => @v2})
+      @instance = @class.new(@estimator, @estimator.variables) 
+    end
+
+    describe "#probability" do
+      it "raises no implemented" do
+        expect { @instance.probability }.to raise_error(NotImplementedError)
+      end
+    end
+  end
+end

data/spec/pest/function/entropy_spec.rb

@@ -0,0 +1,105 @@
+require 'spec_helper'
+
+class EntropyTestClass
+  include Pest::Estimator
+  include Pest::Function::Entropy
+end
+
+describe Pest::Function::Entropy do
+  before(:each) do
+    @v1 = Pest::Variable.new(:name => :foo)
+    @v2 = Pest::Variable.new(:name => :bar)
+    @v3 = Pest::Variable.new(:name => :baz)
+    @instance = EntropyTestClass.new
+    @instance.stub(:variables).and_return({:foo => @v1, :bar => @v2})
+  end
+
+  describe "#entropy" do
+    it "returns a Builder" do
+      @instance.entropy.should be_a(Pest::Function::Entropy::Builder)
+    end
+
+    it "is aliased as h" do
+      @instance.h.should be_a(Pest::Function::Entropy::Builder)
+    end
+  end
+
+  describe Pest::Function::Entropy::Builder do
+    describe "::new" do
+      before(:each) { @builder = EntropyTestClass::Builder.new(@instance, [@v1, :bar]) }
+
+      it "sets estimator" do
+        @builder.estimator.should == @instance
+      end
+
+      it "sets event" do
+        @builder.event.should == [@v1, @v2].to_set
+      end
+
+      it "fails if variable undefined for estimator" do
+        lambda { EntropyTestClass::Builder.new(@instance, [@v1, @v3]) }.should raise_error(ArgumentError)
+      end
+
+      it "constructs dataset if passed hash"
+    end
+
+    describe "#given" do
+      before(:each) { @builder = EntropyTestClass::Builder.new(@instance, [:foo]) }
+
+      it "sets givens" do
+        @builder.given(:bar)
+        @builder.givens.should include(@v2)
+      end
+
+      it "returns self" do
+        @builder.given(:bar).should be_a(EntropyTestClass::Builder)
+      end
+
+      it "fails if variables aren't variables on the estimator" do
+        lambda { @builder.given(:baz) }.should raise_error(ArgumentError)
+      end
+
+      it "adds to dataset if passed hash"
+
+      it "raises error if passed hash with existing (non hash) dataset"
+    end
+
+    describe "#evaluate" do
+      it "generates dataset if not specified"
+
+      it "gets entropy of event" do
+        event = double('EntropyEventDist')
+        @instance.distributions.stub(:[]).with([@v1].to_set).and_return(event)
+        event.should_receive(:entropy).and_return 0.5
+
+        EntropyTestClass::Builder.new(@instance,[:foo]).evaluate
+      end
+
+      it "gets entropy of givens" do
+        event = double("EntropyEventDist", :entropy => 0.5)
+        given = double("EntropyGivenDist", :entropy => 0.25)
+        @instance.distributions.stub(:[]).with([@v1].to_set).and_return(event)
+        @instance.distributions.stub(:[]).with([@v2].to_set).and_return(given)
+        given.should_receive(:entropy).and_return 0.25
+
+        EntropyTestClass::Builder.new(@instance,[:foo]).given(:bar).evaluate
+      end
+
+      it "returns H event - givens (if givens)" do
+        event = double("EntropyEventDist", :entropy => 0.5)
+        given = double("EntropyGivenDist", :entropy => 0.1)
+        @instance.distributions.stub(:[]).with([@v1].to_set).and_return(event)
+        @instance.distributions.stub(:[]).with([@v2].to_set).and_return(given)
+
+        EntropyTestClass::Builder.new(@instance,[:foo]).given(:bar).evaluate.should == 0.4
+      end
+
+      it "returns H event (if no givens)" do
+        event = double("EntropyEventDist", :entropy => 0.5)
+        @instance.distributions.stub(:[]).with([@v1].to_set).and_return(event)
+
+        EntropyTestClass::Builder.new(@instance,[:foo]).evaluate.should == 0.5
+      end
+    end
+  end
+end