distribution 0.6.0 → 0.8.0

data/spec/normal_spec.rb

@@ -1,109 +1,116 @@
-require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
-  
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper.rb')
+
 describe Distribution::Normal do
-  shared_examples_for "gaussian engine(with rng)" do
-  it "should return correct rng" do
-      samples=100
-      sum=0
-      ss=0
-      exp_mean=rand(10)-5
-      exp_sd=1
-      rng=@engine.rng(exp_mean,exp_sd)
-      
-      samples.times do 
-        v=rng.call
-        sum+=v
-        ss+=(v-exp_mean)**2
+  shared_examples_for 'gaussian engine(with rng)' do
+    it 'should return correct rng' do
+      samples = 100
+      sum = 0
+      ss = 0
+      exp_mean = rand(10) - 5
+      exp_sd = 1
+      rng = @engine.rng(exp_mean, exp_sd)
+
+      samples.times do
+        v = rng.call
+        sum += v
+        ss += (v - exp_mean)**2
       end
-      
-      
-      mean=sum.to_f/samples
-      sd=Math::sqrt(ss.to_f/samples)
-      mean.should be_within(0.5).of(exp_mean)
-      sd.should be_within(0.3).of(exp_sd)
+
+      mean = sum.to_f / samples
+      sd = Math.sqrt(ss.to_f / samples)
+      expect(mean).to be_within(0.5).of(exp_mean)
+      expect(sd).to be_within(0.3).of(exp_sd)
+    end
   end
-end
 
-shared_examples_for "gaussian engine(with pdf)" do
-  it "should return correct pdf" do
-    if @engine.respond_to? :pdf
-      10.times do |i|
-        x=(i-5)/2.0
-        pdf=(1.0 / Distribution::SQ2PI)*Math::exp(-(x**2/2.0))
-        @engine.pdf(x).should be_within(1e-10).of(pdf)
-      end
-    else
-      pending("No #{@engine}.pdf")
+  shared_examples_for 'gaussian engine(with rng)' do
+    it 'rng with a specified seed should be reproducible' do
+      seed = rand(10)
+      rng1 = @engine.rng(0, 1, seed)
+      rng2 = @engine.rng(0, 1, seed)
+      expect((rng1.call)).to eq(rng2.call)
     end
   end
-end
 
-shared_examples_for "gaussian engine" do
-  it "should return correct cdf" do
-    if @engine.respond_to? :cdf
-      @engine.cdf(1.96).should be_within(1e-10).of(0.97500210485178)
-      @engine.cdf(0).should be_within(1e-10).of(0.5)
-    else
-      pending("No #{@engine}.cdf")
+  shared_examples_for 'gaussian engine(with pdf)' do
+    it 'should return correct pdf' do
+      if @engine.respond_to? :pdf
+        10.times do |i|
+          x = (i - 5) / 2.0
+          pdf = (1.0 / Distribution::SQ2PI) * Math.exp(-(x**2 / 2.0))
+          expect(@engine.pdf(x)).to be_within(1e-10).of(pdf)
+        end
+      else
+        pending("No #{@engine}.pdf")
+      end
     end
   end
-  it "should return correct p_value" do
-    if @engine.respond_to? :p_value
-      @engine.p_value(0.5).should be_within(1e-3).of(0)
-      10.times do |i|
-        x=(i-5) / 2.0
-        cdf=@engine.cdf(x)
-        @engine.p_value(cdf).should be_within(1e-6).of(x)
+
+  shared_examples_for 'gaussian engine' do
+    it 'should return correct cdf' do
+      if @engine.respond_to? :cdf
+        expect(@engine.cdf(1.96)).to be_within(1e-10).of(0.97500210485178)
+        expect(@engine.cdf(0)).to be_within(1e-10).of(0.5)
+      else
+        pending("No #{@engine}.cdf")
+      end
+    end
+    it 'should return correct p_value' do
+      if @engine.respond_to? :p_value
+        expect(@engine.p_value(0.5)).to be_within(1e-3).of(0)
+        10.times do |i|
+          x = (i - 5) / 2.0
+          cdf = @engine.cdf(x)
+          expect(@engine.p_value(cdf)).to be_within(1e-6).of(x)
+        end
+      else
+        pending("No #{@engine}.p_value")
       end
-    else
-      pending("No #{@engine}.p_value")
     end
   end
-end
 
-  describe "singleton" do
+  describe 'singleton' do
     before do
-      @engine=Distribution::Normal
+      @engine = Distribution::Normal
     end
-    it_should_behave_like "gaussian engine"    
-    it_should_behave_like "gaussian engine(with rng)"    
-    it_should_behave_like "gaussian engine(with pdf)"    
+    it_should_behave_like 'gaussian engine'
+    it_should_behave_like 'gaussian engine(with rng)'
+    it_should_behave_like 'gaussian engine(with pdf)'
   end
-  
+
   describe Distribution::Normal::Ruby_ do
     before do
-      @engine=Distribution::Normal::Ruby_
+      @engine = Distribution::Normal::Ruby_
     end
-    it_should_behave_like "gaussian engine"    
-    it_should_behave_like "gaussian engine(with rng)"    
-    it_should_behave_like "gaussian engine(with pdf)"    
+    it_should_behave_like 'gaussian engine'
+    it_should_behave_like 'gaussian engine(with rng)'
+    it_should_behave_like 'gaussian engine(with pdf)'
   end
   if Distribution.has_gsl?
     describe Distribution::Normal::GSL_ do
       before do
-        @engine=Distribution::Normal::GSL_
+        @engine = Distribution::Normal::GSL_
       end
-    it_should_behave_like "gaussian engine"    
-    it_should_behave_like "gaussian engine(with rng)"    
-    it_should_behave_like "gaussian engine(with pdf)"    
+      it_should_behave_like 'gaussian engine'
+      it_should_behave_like 'gaussian engine(with rng)'
+      it_should_behave_like 'gaussian engine(with pdf)'
     end
-  end  
+  end
   if Distribution.has_statistics2?
     describe Distribution::Normal::Statistics2_ do
       before do
-        @engine=Distribution::Normal::Statistics2_
+        @engine = Distribution::Normal::Statistics2_
       end
-    it_should_behave_like "gaussian engine"    
-    end  
+      it_should_behave_like 'gaussian engine'
+    end
   end
-  
+
   if Distribution.has_java?
     describe Distribution::Normal::Java_ do
       before do
-        @engine=Distribution::Normal::Java_
+        @engine = Distribution::Normal::Java_
       end
-    it_should_behave_like "gaussian engine"    
-    end  
+      it_should_behave_like 'gaussian engine'
+    end
   end
-  
 end

data/spec/poisson_spec.rb

@@ -1,72 +1,114 @@
-require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
-  include ExampleWithGSL
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper.rb')
+include ExampleWithGSL
 describe Distribution::Poisson do
-    
-  shared_examples_for "poisson engine" do
-    it "should return correct pdf" do
+  shared_examples_for 'poisson engine(with rng)' do
+    it 'should return correct rng' do
+      # The expected rng output when 1 is set as the seed value
+      exp_means = [1, 2, 2, 3, 4, 5, 6, 7, 8, 9]
+
+      lambda_val = rand(10) + 1
+      exp_mean = exp_means[lambda_val - 1]
+      seed = 1
+
+      rng = @engine.rng(lambda_val, seed)
+
+      samples = 100
+      sum = 0
+      samples.times do
+        v = rng.call
+        sum += v
+      end
+      mean = sum / samples
+      expect(mean.to_i).to be_within(1e-10).of(exp_mean)
+    end
+  end
+
+  shared_examples_for 'poisson engine(with rng)' do
+    it 'rng with a specified seed should be reproducible' do
+      seed = 1
+      rng1 = @engine.rng(3, seed)
+      rng2 = @engine.rng(3, seed)
+      expect((rng1.call)).to eq(rng2.call)
+    end
+  end
+
+
+  shared_examples_for 'poisson engine' do
+    it 'should return correct pdf' do
       if @engine.respond_to? :pdf
-        [0.5,1,1.5].each {|l|
+        [0.5, 1, 1.5].each {|l|
           1.upto(5) {|k|
-            @engine.pdf(k,l).should be_within(1e-10).of((l**k*Math.exp(-l)).quo(Math.factorial(k)))
+            expect(@engine.pdf(k, l)).to be_within(1e-10).of((l**k * Math.exp(-l)).quo(Math.factorial(k)))
           }
         }
       else
         pending("No #{@engine}.pdf")
       end
     end
-    
-    it_only_with_gsl "should return correct cdf" do
+
+    it_only_with_gsl 'should return correct cdf' do
       if @engine.respond_to? :cdf
-        [0.5,1,1.5,4,10].each {|l|
+        [0.5, 1, 1.5, 4, 10].each {|l|
           1.upto(5) {|k|
-            @engine.cdf(k,l).should be_within(1e-10).of(GSL::Cdf.poisson_P(k,l))
+            expect(@engine.cdf(k, l)).to be_within(1e-10).of(GSL::Cdf.poisson_P(k, l))
           }
         }
-        
+
       else
         pending("No #{@engine}.cdf")
       end
     end
-  
-    
-    it "should return correct p_value" do
-      pending("No exact p_value")
+
+    it 'should return correct p_value' do
+      pending('No exact p_value')
       if @engine.respond_to? :p_value
-         [0.1,1,5,10].each {|l|
+        [0.1, 1, 5, 10].each {|l|
           1.upto(20) {|k|
-            pr=@engine.cdf(k,l)
-            @engine.p_value(pr,l).should eq(k)
+            pr = @engine.cdf(k, l)
+            expect(@engine.p_value(pr, l)).to eq(k)
           }
         }
       else
-        pending("No #{@engine}.p_value")
+        skip("No #{@engine}.p_value")
       end
     end
   end
-  
 
-  describe "singleton" do
+  describe 'singleton' do
     before do
-      @engine=Distribution::Poisson
+      @engine = Distribution::Poisson
     end
-    it_should_behave_like "poisson engine"
+    it_should_behave_like 'poisson engine'
   end
-  
+
   describe Distribution::Poisson::Ruby_ do
     before do
-      @engine=Distribution::Poisson::Ruby_
+      @engine = Distribution::Poisson::Ruby_
     end
-    it_should_behave_like "poisson engine"
-    
+    it_should_behave_like 'poisson engine'
   end
-    
-  describe Distribution::Poisson::GSL_ do
-    before do
-      @engine=Distribution::Poisson::GSL_
+  if Distribution.has_gsl?
+    describe Distribution::Poisson::GSL_ do
+      before do
+        @engine = Distribution::Poisson::GSL_
+      end
+      it_should_behave_like 'poisson engine'
+    end
+  end
+  if Distribution.has_java?
+    describe Distribution::Poisson::Java_ do
+      before do
+        @engine = Distribution::Poisson::Java_
+      end
+      it_should_behave_like 'poisson engine'
+
+      it 'should return correct cdf' do
+        [0.5, 1, 1.5, 4, 10].each {|l|
+          1.upto(5) {|k|
+            expect(@engine.cdf(k, l)).to be_within(1e-10).of(Distribution::Poisson::Ruby_.cdf(k, l))
+          }
+        }
+      end
     end
-    it_should_behave_like "poisson engine"
-    
   end
-  
-  
 end

data/spec/shorthand_spec.rb

@@ -1,34 +1,31 @@
-require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper.rb')
 describe Distribution::Shorthand do
   include Distribution::Shorthand
-  it "should have basic methods for all distributions" do
-    [:Normal,:ChiSquare, :F, :Hypergeometric, :Binomial, :T].each do |d|
-      klass=Distribution.const_get(d)
-      shortname=klass::SHORTHAND
-      methods=[:pdf, :cdf, :p_value].map {|m| "#{shortname}_#{m}".to_sym}
-      methods.each do |m| 
-        Distribution::Shorthand.instance_methods.map {|v| v.to_sym}.should include(m)
+  it 'should have basic methods for all distributions' do
+    [:Normal, :ChiSquare, :F, :Hypergeometric, :Binomial, :T].each do |d|
+      klass = Distribution.const_get(d)
+      shortname = klass::SHORTHAND
+      methods = [:pdf, :cdf, :p_value].map { |m| "#{shortname}_#{m}".to_sym }
+      methods.each do |m|
+        expect(Distribution::Shorthand.instance_methods.map(&:to_sym)).to include(m)
       end
     end
-    
   end
-  it "should have exact methods discrete distributions" do
+  it 'should have exact methods discrete distributions' do
     [:Hypergeometric, :Binomial].each do |d|
-      klass=Distribution.const_get(d)
-      shortname=klass::SHORTHAND
-      methods=[:epdf, :ecdf].map {|m| "#{shortname}_#{m}".to_sym}
-      methods.each do |m| 
-        Distribution::Shorthand.instance_methods.map {|v| v.to_sym}.should include(m)
+      klass = Distribution.const_get(d)
+      shortname = klass::SHORTHAND
+      methods = [:epdf, :ecdf].map { |m| "#{shortname}_#{m}".to_sym }
+      methods.each do |m|
+        expect(Distribution::Shorthand.instance_methods.map(&:to_sym)).to include(m)
       end
     end
-    
   end
 
-
-  it "returns same values as long form" do
-    x=rand()
-    norm_cdf(x).should eql(Distribution::Normal.cdf(x))
-    norm_pdf(x).should eql(Distribution::Normal.pdf(x))
-    norm_p_value(x).should eql(Distribution::Normal.p_value(x))
+  it 'returns same values as long form' do
+    x = rand
+    expect(norm_cdf(x)).to eql(Distribution::Normal.cdf(x))
+    expect(norm_pdf(x)).to eql(Distribution::Normal.pdf(x))
+    expect(norm_p_value(x)).to eql(Distribution::Normal.p_value(x))
   end
 end

data/spec/spec_helper.rb

@@ -1,22 +1,47 @@
-$:.unshift(File.dirname(__FILE__)+"/../lib")
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../lib')
 begin
   require 'simplecov'
   SimpleCov.start do
-    add_filter "/spec/"
-    add_group "Libraries", "lib"
+    add_filter '/spec/'
+    add_group 'Libraries', 'lib'
   end
 rescue LoadError
 end
 require 'rspec'
 require 'distribution'
 
+RSpec.configure do |config|
+  config.expect_with :rspec do |c|
+    c.syntax = [:should, :expect]
+  end
+
+  # Use color in STDOUT
+  config.color = true
+
+  # Use color not only in STDOUT but also in pagers and files
+  config.tty = true
+
+  # Use the specified formatter
+  config.formatter = :documentation # :progress, :html, :textmate
+end
+
 module ExampleWithGSL
-  def it_only_with_gsl(name,&block)
-    it(name) do
+  def it_only_with_gsl(name, opts = {}, &block)
+    it(name, opts) do
       if Distribution.has_gsl?
         instance_eval(&block)
       else
-        pending("Requires GSL")  
+        skip('Requires GSL')
+      end
+    end
+  end
+
+  def it_only_with_java(name, &block)
+    it(name) do
+      if Distribution.has_java?
+        instance_eval(&block)
+      else
+        skip('Requires Java')
       end
     end
   end

data/spec/t_spec.rb

@@ -1,111 +1,97 @@
-require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
+require File.expand_path(File.dirname(__FILE__) + '/spec_helper.rb')
 
 include ExampleWithGSL
 
 describe Distribution::T do
-shared_examples_for "T engine(with rng)" do
-  it "should return correct rng" do
-  pending()
+  shared_examples_for 'T engine(with rng)' do
+    it 'should return correct rng' do
+      pending
+    end
   end
-end
 
-shared_examples_for "T engine(cdf with fractional df)" do
-  it "should return correct cdf with fractional df" do
-    @engine.cdf(1,2.5).should be_within(1e-6).of(0.7979695)
-    @engine.cdf(2,3.5).should be_within(1e-6).of(0.9369307)
-    @engine.cdf(3,4.5).should be_within(1e-6).of(0.9828096)
-    
+  shared_examples_for 'T engine(cdf with fractional df)' do
+    it 'should return correct cdf with fractional df' do
+      expect(@engine.cdf(1, 2.5)).to be_within(1e-6).of(0.7979695)
+      expect(@engine.cdf(2, 3.5)).to be_within(1e-6).of(0.9369307)
+      expect(@engine.cdf(3, 4.5)).to be_within(1e-6).of(0.9828096)
+    end
   end
-end
-
-shared_examples_for "T engine" do
-  it_only_with_gsl "should return correct pdf" do
-    if @engine.respond_to? :pdf
-      [-2,0.1,0.5,1,2].each{|t|
-        [2,5,10].each{|n|
-          @engine.pdf(t,n).should be_within(1e-6).of(GSL::Ran.tdist_pdf(t,n))
-          @engine.pdf(t,n.to_f).should be_within(1e-6).of(@engine.pdf(t,n))
 
+  shared_examples_for 'T engine' do
+    it_only_with_gsl 'should return correct pdf' do
+      if @engine.respond_to? :pdf
+        [-2, 0.1, 0.5, 1, 2].each{|t|
+          [2, 5, 10].each{|n|
+            expect(@engine.pdf(t, n)).to be_within(1e-6).of(GSL::Ran.tdist_pdf(t, n))
+            expect(@engine.pdf(t, n.to_f)).to be_within(1e-6).of(@engine.pdf(t, n))
+          }
         }
-      }
-    else
-      pending("No #{@engine}.pdf")
+      else
+        pending("No #{@engine}.pdf")
+      end
     end
-  end
-  it_only_with_gsl "should return correct cdf" do
-    if @engine.respond_to? :cdf
-      # Testing with R values
-      @engine.cdf(1,2).should be_within(1e-7).of(0.7886751)
-      @engine.cdf(1,2.0).should be_within(1e-7).of(0.7886751)
-      @engine.cdf(1,3.0).should be_within(1e-7).of(0.8044989)
-      
-      [-2,0.1,0.5,1,2].each{|t|
-        [2,5,10].each{|n|
-          @engine.cdf(t,n).should be_within(1e-4).of(GSL::Cdf.tdist_P(t,n))
-          @engine.cdf(t,n).should be_within(1e-4).of(@engine.cdf(t,n.to_f))
-          
+    it_only_with_gsl 'should return correct cdf' do
+      if @engine.respond_to? :cdf
+        # Testing with R values
+        expect(@engine.cdf(1, 2)).to be_within(1e-7).of(0.7886751)
+        expect(@engine.cdf(1, 2.0)).to be_within(1e-7).of(0.7886751)
+        expect(@engine.cdf(1, 3.0)).to be_within(1e-7).of(0.8044989)
+
+        [-2, 0.1, 0.5, 1, 2].each{|t|
+          [2, 5, 10].each{|n|
+            expect(@engine.cdf(t, n)).to be_within(1e-4).of(GSL::Cdf.tdist_P(t, n))
+            expect(@engine.cdf(t, n)).to be_within(1e-4).of(@engine.cdf(t, n.to_f))
+          }
         }
-      }
-    else
-      pending("No #{@engine}.cdf")
+      else
+        pending("No #{@engine}.cdf")
+      end
     end
-  
-  end
-  it_only_with_gsl "should return correct p_value" do
-    if @engine.respond_to? :p_value
-   [-2,0.1,0.5,1,2].each{|t|
-        [2,5,10].each{|n|
-          area=Distribution::T.cdf(t,n)
-          @engine.p_value(area,n).should be_within(1e-4).of(GSL::Cdf.tdist_Pinv(area,n))
-    }
-    }
-    else
-      pending("No #{@engine}.p_value")
+    it_only_with_gsl 'should return correct p_value' do
+      if @engine.respond_to? :p_value
+        [-2, 0.1, 0.5, 1, 2].each{|t|
+          [2, 5, 10].each{|n|
+            area = Distribution::T.cdf(t, n)
+            expect(@engine.p_value(area, n)).to be_within(1e-4).of(GSL::Cdf.tdist_Pinv(area, n))
+          }
+        }
+      else
+        pending("No #{@engine}.p_value")
+      end
     end
   end
-end
 
-  describe "singleton" do
+  describe 'singleton' do
     before do
-      @engine=Distribution::T
+      @engine = Distribution::T
     end
-    it_should_behave_like "T engine"    
+    it_should_behave_like 'T engine'
   end
-  
+
   describe Distribution::T::Ruby_ do
     before do
-      @engine=Distribution::T::Ruby_
+      @engine = Distribution::T::Ruby_
     end
-    it_should_behave_like "T engine"    
-    it_should_behave_like "T engine(cdf with fractional df)"
-    
+    it_should_behave_like 'T engine'
+    it_should_behave_like 'T engine(cdf with fractional df)'
   end
+
   if Distribution.has_gsl?
     describe Distribution::T::GSL_ do
       before do
-        @engine=Distribution::T::GSL_
+        @engine = Distribution::T::GSL_
       end
-    it_should_behave_like "T engine"    
-    it_should_behave_like "T engine(cdf with fractional df)"    
+      it_should_behave_like 'T engine'
+      it_should_behave_like 'T engine(cdf with fractional df)'
     end
   end
-=begin
-  if Distribution.has_statistics2?
-    describe Distribution::T::Statistics2_ do
-      before do
-        @engine=Distribution::T::Statistics2_
-      end
-    it_should_behave_like "T engine"    
-    end  
-  end
-=end  
+
   if Distribution.has_java?
     describe Distribution::T::Java_ do
       before do
-        @engine=Distribution::T::Java_
+        @engine = Distribution::T::Java_
       end
-    it_should_behave_like "T engine"    
-    end  
+      it_should_behave_like 'T engine'
+    end
   end
-  
 end