distribution 0.7.1 → 0.7.2

data/lib/distribution/version.rb

@@ -1,3 +1,3 @@
 module Distribution
-  VERSION = "0.7.1"
+  VERSION = '0.7.2'
 end

data/spec/beta_spec.rb

@@ -9,10 +9,10 @@ describe Distribution::Beta do
           a=rand * x
           b=1 + rand * 5
           g=GSL::Ran.beta_pdf(x,a,b)
-          @engine.pdf(x,a,b).should be_within(1e-10).of(g)
+          @engine.pdf(x,a,b).should be_within(1e-09).of(g)
         end
       else
-        pending("No #{@engine}.pdf")
+        skip("No #{@engine}.pdf")
       end
     end
 
@@ -32,7 +32,7 @@ describe Distribution::Beta do
       @engine.cdf(0.999, 1.2, 1.3).should be_within(tol).of(9.99843792833067634e-1)
       @engine.cdf(1.0, 1.2, 1.3).should be_within(tol).of(1.0)
     else
-      pending("No #{@engine}.cdf")
+      skip("No #{@engine}.cdf")
     end
   end
   it "should return correct p_value" do
@@ -41,10 +41,10 @@ describe Distribution::Beta do
         a=rand() * x
         b=1 + rand() * 5
         pr=@engine.cdf(x/100.0,a,b)
-        @engine.p_value(pr,a, b).should be_within(1e-10).of(x/100.0)
+        @engine.p_value(pr,a, b).should be_within(1e-09).of(x/100.0)
        end
     else
-      pending("No #{@engine}.p_value")
+      skip("No #{@engine}.p_value")
     end
   end
 end
@@ -55,7 +55,7 @@ end
     end
     it_should_behave_like "Beta engine"
   end
-  
+
   describe Distribution::Beta::Ruby_ do
     before do
       @engine=Distribution::Beta::Ruby_
@@ -76,7 +76,7 @@ end
         @engine=Distribution::Beta::Java_
       end
     it_should_behave_like "Beta engine"
-    end  
+    end
   end
-  
+
 end

data/spec/binomial_spec.rb

@@ -16,7 +16,7 @@ shared_examples_for "binomial engine" do
         end
       end
     else
-      pending("No #{@engine}.pdf")
+      skip("No #{@engine}.pdf")
     end
   end
   it_only_with_gsl "should return correct cdf for n<=100" do
@@ -31,7 +31,7 @@ shared_examples_for "binomial engine" do
           end
         end
       else
-        pending("No #{@engine}.cdf")
+        skip("No #{@engine}.cdf")
       end
   end
 
@@ -44,8 +44,6 @@ end
       @engine=Distribution::Binomial
     end
     it_should_behave_like "binomial engine"
-    
-    
     it {@engine.should respond_to(:exact_pdf) }
     it {
       pending("No exact_p_value")
@@ -64,9 +62,6 @@ end
       @engine.exact_pdf(1,1,1).should_not be_a(Float)
       @engine.exact_pdf(16, 80, 1.quo(2)).should_not be_a(Float)
     end
-
-    
-    
     
   end
   
@@ -76,8 +71,17 @@ end
     end
     it_should_behave_like "binomial engine"
     
-    it "should return correct cdf for n>100" do
-      pending("incomplete beta function is slow. Should be replaced for a faster one")
+    it "should return correct cdf for n>100" do      
+    [500,1000].each do |n|
+      [0.5,0.6].each do |pr|
+        [n/2].each do |x| 
+          cdf=@engine.exact_cdf(x,n,pr)
+          p_value=@engine.p_value(cdf,n,pr)
+          p_value.should eq(x), "For p_value(#{cdf},#{n},#{pr}) expected #{x}, obtained #{p_value}"
+        end
+      end
+    end
+      
     end
     
     it "should return correct p_value for n<=100" do

data/spec/chisquare_spec.rb

@@ -11,7 +11,7 @@ shared_examples_for "Chi-square engine(with pdf)" do
           @engine.pdf(v,k).should be_within(10e-10).of(chi)
         end
       else
-        pending("No #{@engine}.pdf")
+        skip("No #{@engine}.pdf")
       end
     end
 
@@ -27,7 +27,7 @@ shared_examples_for "Chi-square engine" do
         @engine.cdf(v,k).should be_within(10e-10).of(chi)
       end
     else
-      pending("No #{@engine}.cdf")
+      skip("No #{@engine}.cdf")
     end  
   end
   it "should return correct p_value" do
@@ -38,7 +38,7 @@ shared_examples_for "Chi-square engine" do
         @engine.p_value(pr,k).should be_within(10e-4).of(v)
        end
     else
-      pending("No #{@engine}.p_value")
+      skip("No #{@engine}.p_value")
     end
   end
 end

data/spec/distribution_spec.rb

@@ -3,17 +3,17 @@ describe Distribution do
   it "should respond to has_gsl?" do
     lambda {Distribution.has_gsl?}.should_not raise_exception
     if Distribution.has_gsl?
-      expect(defined?(GSL)).to be true
+      expect(defined?(GSL)).to be
     else
-      defined?(GSL).should be_false
+      defined?(GSL).should be_nil
     end 
   end
   it "should respond to has_statistics2?" do
     lambda {Distribution.has_statistics2?}.should_not raise_exception
     if Distribution.has_statistics2?
-      defined?(Statistics2).should be_true
+      defined?(Statistics2).should be
     else
-      defined?(Statistics2).should be_false
+      defined?(Statistics2).should be_nil
     end 
   end
 end

data/spec/exponential_spec.rb

@@ -1,7 +1,7 @@
 require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
   
 describe Distribution::Exponential do
-    
+  
   shared_examples_for "exponential engine" do
     it "should return correct pdf" do
       if @engine.respond_to? :pdf

data/spec/gamma_spec.rb

@@ -47,7 +47,7 @@ shared_examples_for "Gamma engine" do
         @engine.p_value(pr,a,b).should be_within(1e-3).of(x)
        end
     else
-      pending("No #{@engine}.p_value")
+      skip("No #{@engine}.p_value")
     end
   end
 end

data/spec/math_extension_spec.rb

@@ -2,10 +2,9 @@ require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 include ExampleWithGSL
 describe Distribution::MathExtension do
   it "binomial coefficient should be correctly calculated" do
-    
     n=50
     n.times do |k|
-      Math.binomial_coefficient(n,k).should eq(Math.factorial(n).quo(Math.factorial(k)*Math.factorial(n-k)))
+      Math.binomial_coefficient(n,k).should eq(Math.factorial(n).quo(Math.factorial(k)*Math.factorial(n-k))),"not correct for k=#{k}"
     end
   end
 

data/spec/poisson_spec.rb

@@ -41,7 +41,7 @@ describe Distribution::Poisson do
           }
         }
       else
-        pending("No #{@engine}.p_value")
+        skip("No #{@engine}.p_value")
       end
     end
   end

data/spec/spec_helper.rb

@@ -10,13 +10,28 @@ 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
       if Distribution.has_gsl?
         instance_eval(&block)
       else
-        pending("Requires GSL")  
+        skip("Requires GSL")  
       end
     end
   end
@@ -26,7 +41,7 @@ module ExampleWithGSL
       if Distribution.has_java?
         instance_eval(&block)
       else
-        pending("Requires Java")  
+        skip("Requires Java")  
       end
     end
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: distribution
 version: !ruby/object:Gem::Version
-  version: 0.7.1
+  version: 0.7.2
 platform: ruby
 authors:
 - Claudio Bustos
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-06 00:00:00.000000000 Z
+date: 2015-04-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -16,16 +16,16 @@ dependencies:
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.0
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: rspec
+  name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -38,8 +38,23 @@ dependencies:
     - - ">="
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.2'
 description: Distribution
-email: []
+email:
+- clbustos@gmail.com
 executables:
 - distribution
 extensions: []
@@ -50,7 +65,6 @@ files:
 - Gemfile
 - History.txt
 - LICENCE.md
-- Manifest.txt
 - README.md
 - Rakefile
 - benchmark/binomial_coefficient.rb
@@ -155,7 +169,7 @@ files:
 - spec/t_spec.rb
 - spec/weibull_spec.rb
 - vendor/java/commons-math-2.2.jar
-homepage: http://rubygems.org/gems/foodie
+homepage: https://github.com/sciruby/distribution
 licenses: []
 metadata: {}
 post_install_message: 
@@ -171,7 +185,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
   - - ">="
     - !ruby/object:Gem::Version
-      version: 1.3.6
+      version: '0'
 requirements: []
 rubyforge_project: 
 rubygems_version: 2.2.2

data/Manifest.txt

@@ -1,105 +0,0 @@
-Gemfile
-History.txt
-Manifest.txt
-README.txt
-Rakefile
-benchmark/binomial_coefficient.rb
-benchmark/binomial_coefficient/binomial_coefficient.ds
-benchmark/binomial_coefficient/binomial_coefficient.xls
-benchmark/binomial_coefficient/experiment.rb
-benchmark/factorial_hash.rb
-benchmark/factorial_method.rb
-benchmark/odd.rb
-benchmark/power.rb
-bin/distribution
-data/template/distribution.erb
-data/template/distribution/gsl.erb
-data/template/distribution/ruby.erb
-data/template/spec.erb
-lib/distribution.rb
-lib/distribution/beta.rb
-lib/distribution/beta/gsl.rb
-lib/distribution/beta/java.rb
-lib/distribution/beta/ruby.rb
-lib/distribution/binomial.rb
-lib/distribution/binomial/gsl.rb
-lib/distribution/binomial/java.rb
-lib/distribution/binomial/ruby.rb
-lib/distribution/bivariatenormal.rb
-lib/distribution/bivariatenormal/gsl.rb
-lib/distribution/bivariatenormal/java.rb
-lib/distribution/bivariatenormal/ruby.rb
-lib/distribution/bivariatenormal/statistics2.rb
-lib/distribution/chisquare.rb
-lib/distribution/chisquare/gsl.rb
-lib/distribution/chisquare/java.rb
-lib/distribution/chisquare/ruby.rb
-lib/distribution/chisquare/statistics2.rb
-lib/distribution/exponential.rb
-lib/distribution/exponential/gsl.rb
-lib/distribution/exponential/ruby.rb
-lib/distribution/f.rb
-lib/distribution/f/gsl.rb
-lib/distribution/f/java.rb
-lib/distribution/f/ruby.rb
-lib/distribution/f/statistics2.rb
-lib/distribution/gamma.rb
-lib/distribution/gamma/gsl.rb
-lib/distribution/gamma/java.rb
-lib/distribution/gamma/ruby.rb
-lib/distribution/hypergeometric.rb
-lib/distribution/hypergeometric/gsl.rb
-lib/distribution/hypergeometric/java.rb
-lib/distribution/hypergeometric/ruby.rb
-lib/distribution/logistic.rb
-lib/distribution/logistic/ruby.rb
-lib/distribution/lognormal.rb
-lib/distribution/lognormal/gsl.rb
-lib/distribution/lognormal/ruby.rb
-lib/distribution/math_extension.rb
-lib/distribution/math_extension/chebyshev_series.rb
-lib/distribution/math_extension/erfc.rb
-lib/distribution/math_extension/exponential_integral.rb
-lib/distribution/math_extension/gammastar.rb
-lib/distribution/math_extension/gsl_utilities.rb
-lib/distribution/math_extension/incomplete_beta.rb
-lib/distribution/math_extension/incomplete_gamma.rb
-lib/distribution/math_extension/log_utilities.rb
-lib/distribution/normal.rb
-lib/distribution/normal/gsl.rb
-lib/distribution/normal/java.rb
-lib/distribution/normal/ruby.rb
-lib/distribution/normal/statistics2.rb
-lib/distribution/normalmultivariate.rb
-lib/distribution/poisson.rb
-lib/distribution/poisson/gsl.rb
-lib/distribution/poisson/java.rb
-lib/distribution/poisson/ruby.rb
-lib/distribution/t.rb
-lib/distribution/t/gsl.rb
-lib/distribution/t/java.rb
-lib/distribution/t/ruby.rb
-lib/distribution/t/statistics2.rb
-lib/distribution/weibull.rb
-lib/distribution/weibull/gsl.rb
-lib/distribution/weibull/ruby.rb
-spec/beta_spec.rb
-spec/binomial_spec.rb
-spec/bivariatenormal_spec.rb
-spec/chisquare_spec.rb
-spec/distribution_spec.rb
-spec/exponential_spec.rb
-spec/f_spec.rb
-spec/gamma_spec.rb
-spec/hypergeometric_spec.rb
-spec/logistic_spec.rb
-spec/lognormal_spec.rb
-spec/math_extension_spec.rb
-spec/normal_spec.rb
-spec/poisson_spec.rb
-spec/shorthand_spec.rb
-spec/spec.opts
-spec/spec_helper.rb
-spec/t_spec.rb
-spec/weibull_spec.rb
-vendor/java/commons-math-2.2.jar