distribution 0.2.0 → 0.3.0

data/spec/distribution_spec.rb

@@ -13,7 +13,7 @@ describe Distribution do
     if Distribution.has_statistics2?
       defined?(Statistics2).should be_true
     else
-      defined?(Statistics2).should be_true
+      defined?(Statistics2).should be_false
     end 
   end
 end

data/spec/f_spec.rb

@@ -42,7 +42,7 @@ shared_examples_for "F engine" do
     end
   
   end
-  it "should return correct p_value" do
+  it_only_with_gsl "should return correct p_value" do
     if @engine.respond_to? :p_value
   
     [0.1,0.5,1,2,10,20,30].each{|f|

data/spec/hypergeometric_spec.rb

@@ -1,6 +1,6 @@
 require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 include ExampleWithGSL
-require 'ruby-prof'
+#require 'ruby-prof'
 
 # Need to test:
 # * that Fixnum fast_choose returns same as choose
@@ -8,30 +8,55 @@ require 'ruby-prof'
 # * that cdf in Ruby_ returns the same value as cdf in GSL_
 
 describe Distribution::Hypergeometric do
+  describe Distribution::Hypergeometric::GSL_ do
+     before do
+      @ruby=Distribution::Hypergeometric::Ruby_
+      @engine=Distribution::Hypergeometric::GSL_
+    end
+    it_only_with_gsl "cdf should return values near to exact Ruby calculations" do
+     #RubyProf.start
+      
+      if @engine.respond_to? :cdf
+        #[2].each do |k|
+         [0,1,2,4,8,16].each do |k|
+          @engine.cdf(k, 80, 100, 10000).should be_within(1e-10).of(@ruby.cdf(k, 80, 100, 10000))
+      end
+      #result = RubyProf.stop
+      
+      # Print a flat profile to text
+      #printer = RubyProf::FlatPrinter.new(result)
+      #printer.print(STDOUT)
+        
+      else
+        pending("No #{@engine}.pdf")
+      end
+    end
+    
+  end
   describe Distribution::Hypergeometric::Ruby_ do
+    
     before do
       @engine=Distribution::Hypergeometric::Ruby_
     end
     it_only_with_gsl "pdf_fast should return same as pdf" do
-      pending("Not working yet")
+      pending("Aprox. factorial doesn't work right")
       if @engine.respond_to? :pdf
         [0,1,2,4,8,16].each do |k|
-          
           @engine.pdf_aprox(k, 80, 100, 1000).should be_within(1e-8).of(GSL::Ran::hypergeometric_pdf(k, 80, 920, 100))
         end
       else
         pending("No #{@engine}.pdf")
       end
     end
-    
-    
+  
     it_only_with_gsl "should return correct pdf" do
       #RubyProf.start
       
       if @engine.respond_to? :pdf
         #[2].each do |k|
         [0,1,2,4,8,16].each do |k|
-          @engine.pdf(k, 80, 100, 10000).should be_within(1e-8).of(GSL::Ran::hypergeometric_pdf(k, 80, 9920, 100))
+          #puts "k:#{k}->#{@engine.pdf(k, 80, 100, 10000).to_f}"
+          @engine.pdf(k, 80, 100, 10000).to_f.should be_within(1e-8).of(GSL::Ran::hypergeometric_pdf(k, 80, 9920, 100))
       end
       #result = RubyProf.stop
       
@@ -44,24 +69,25 @@ describe Distribution::Hypergeometric do
       end
     end
     
+    
+    
+    
     it "should return correct cdf" do
-      total=rand(5)+30
+      total=rand(5)+3000
       n=rand(10)+15
       m=rand(10)+5
       ac=0
       0.upto(m) do |i| 
         ac+=@engine.pdf(i,m,n,total)
         @engine.cdf(i,m,n,total).should eq(ac)
-        
       end
     end
     
     it "should return correct p_value" do
-      
       #0.upto(10) do |i|
       #  puts "#{i}:#{@engine.pdf(i,5,7,10)}"
       #end
-      total=rand(5)+30
+      total=rand(5)+3000
       n=rand(10)+15
       m=rand(10)+5
       ac=0
@@ -69,9 +95,19 @@ describe Distribution::Hypergeometric do
         ac+=@engine.pdf(k,m,n,total)
         @engine.p_value(ac, m, n, total).should eq(k)
       end
-    end
-    
-    
+    end    
   end
+  describe Distribution::Hypergeometric do
+    before do
+      @engine=Distribution::Hypergeometric
+    end
+    it {@engine.should respond_to(:exact_pdf) }
+    it {@engine.should respond_to(:exact_cdf) }
+    it {@engine.should respond_to(:exact_p_value) }
+    it "exact pdf should return a Rational" do
+      @engine.exact_pdf(1,1,1,1).should_not be_a(Float)
+      @engine.exact_pdf(16, 80, 100, 10000).should_not be_a(Float)
+    end
 
+  end
 end

data/spec/math_extension_spec.rb

@@ -1,17 +1,63 @@
 require File.expand_path(File.dirname(__FILE__)+"/spec_helper.rb")
 describe Distribution::MathExtension do
-  it "fast_factorial should return 11 valid digits" do
-    pending("Doesn't worth the effort")
-    valid=11
-    (2..10).each {|i|
-      n=2**i
-      aprox=Math.fast_factorial(n).round.to_s[0,valid]
-      exact=Math.factorial(n).to_s[0,valid]
-      aprox.should eq exact
-      
+  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)))
+    end
+  end
+  
+  it "binomial coefficient(gamma) with n<=48 should be correct " do
+    
+    [1,5,10,25,48].each {|n|
+      k=(n/2).to_i
+      Math.binomial_coefficient_gamma(n,k).round.should eq(Math.binomial_coefficient(n,k))
+    }
+  end
+  it "rising_factorial should return correct values" do
+    
+    x=rand(10)+1
+    Math.rising_factorial(x,0).should eq 1
+    Math.rising_factorial(x,1).should eq x
+    Math.rising_factorial(x,2).should eq x**2+x
+    Math.rising_factorial(x,3).should eq x**3+3*x**2+2*x
+    Math.rising_factorial(x,4).should eq x**4+6*x**3+11*x**2+6*x
+
+  end
+  it "incomplete beta function should return similar results to R" do
+    pending("Not working yet")
+    Math.incomplete_beta(0.5,5,6).should be_within(1e-6).of(Math.beta(5,6)*0.6230469)
+    Math.incomplete_beta(0.6,5,6).should be_within(1e-6).of(Math.beta(5,6)*0.0006617154)
+  end
+  it "regularized incomplete beta should behave properly" do
+
+    Math.regularized_beta_function(0.5,5,5).should eq 0.5
+    Math.regularized_beta_function(0.5,5,6).should be_within(1e-6).of(0.6230469)
+    Math.regularized_beta_function(0.5,5,7).should  be_within(1e-6).of(0.725586)
+    
+    a=5
+    b=5
+    Math.regularized_beta_function(0,a,b).should eq 0
+    Math.regularized_beta_function(1,a,b).should eq 1
+    x=rand()
+    
+    Math.regularized_beta_function(x,a,b).should be_within(1e-6). of(1-Math.regularized_beta_function(1-x,b,a))
+    
+    
+  end
+  it "binomial coefficient(gamma) with 48<n<1000 should have 12 correct digits" do 
+    
+    [50,100,1000].each {|n|
+      k=n/2.to_i
+      obs=Math.binomial_coefficient_gamma(n,k).to_i.to_s[0,12]
+      exp=Math.binomial_coefficient(n,k).to_i.to_s[0,12]
+      obs.should eq(exp)
     }
   end
+  
   describe Distribution::MathExtension::SwingFactorial do
+
     it "Math.factorial should return correct values x<20" do
       ac=3628800 # 10!
       11.upto(19).each do |i|
@@ -21,6 +67,7 @@ describe Distribution::MathExtension do
     end
     
     it "Math.factorial should return correct values for values 21<x<33" do
+      
       ac=2432902008176640000 # 20!
       21.upto(33).each do |i|
         ac*=i
@@ -30,6 +77,7 @@ describe Distribution::MathExtension do
     end
     
     it "Math.factorial should return correct values for values x>33" do
+      
       ac=8683317618811886495518194401280000000 # 33!
       Math.factorial(33).should eq ac
       34.upto(40).each do |i|

data/spec/normal_spec.rb

@@ -40,8 +40,12 @@ end
 
 shared_examples_for "gaussian engine" do
   it "should return correct cdf" do
-    @engine.cdf(1.96).should be_within(1e-10).of(0.97500210485178)
-    @engine.cdf(0).should be_within(1e-10).of(0.5)
+    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")
+    end
   end
   it "should return correct p_value" do
     if @engine.respond_to? :p_value
@@ -98,7 +102,7 @@ end
       before do
         @engine=Distribution::Normal::Java_
       end
-      it_should_behave_like "all gaussian engines"
+    it_should_behave_like "gaussian engine"    
     end  
   end
   

data/spec/shorthand_spec.rb

@@ -2,15 +2,29 @@ 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, :T].each do |d|
+    [: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.should include(m)
+        Distribution::Shorthand.instance_methods.map {|v| v.to_sym}.should include(m)
       end
     end
+    
   end
+  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)
+      end
+    end
+    
+  end
+
+
   it "returns same values as long form" do
     x=rand()
     norm_cdf(x).should eql(Distribution::Normal.cdf(x))

data/spec/t_spec.rb

@@ -38,7 +38,7 @@ shared_examples_for "T engine" do
     end
   
   end
-  it "should return correct p_value" do
+  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|

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 2
+  - 3
   - 0
-  version: 0.2.0
+  version: 0.3.0
 platform: ruby
 authors: 
 - Claudio Bustos
@@ -35,7 +35,7 @@ cert_chain:
   rpP0jjs0
   -----END CERTIFICATE-----
 
-date: 2011-01-27 00:00:00 -03:00
+date: 2011-01-28 00:00:00 -03:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -54,9 +54,36 @@ dependencies:
   type: :development
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: hoe
+  name: rspec
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 2
+        - 0
+        version: "2.0"
+  type: :development
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: rubyforge
+  prerelease: false
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: hoe
+  prerelease: false
+  requirement: &id004 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
@@ -67,7 +94,7 @@ dependencies:
         - 0
         version: 2.8.0
   type: :development
-  version_requirements: *id002
+  version_requirements: *id004
 description: |-
   Statistical Distributions multi library wrapper.
   Uses Ruby by default and C (statistics2/GSL) or Java extensions where available.
@@ -89,35 +116,47 @@ files:
 - Manifest.txt
 - README.txt
 - Rakefile
+- benchmark/binomial_coefficient.rb
 - benchmark/factorial_method.rb
+- benchmark/odd.rb
 - bin/distribution
 - lib/distribution.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/f.rb
 - lib/distribution/f/gsl.rb
+- lib/distribution/f/java.rb
 - lib/distribution/f/ruby.rb
 - lib/distribution/f/statistics2.rb
 - lib/distribution/hypergeometric.rb
 - lib/distribution/hypergeometric/gsl.rb
+- lib/distribution/hypergeometric/java.rb
 - lib/distribution/hypergeometric/ruby.rb
 - lib/distribution/math_extension.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/t.rb
 - lib/distribution/t/gsl.rb
+- lib/distribution/t/java.rb
 - lib/distribution/t/ruby.rb
 - lib/distribution/t/statistics2.rb
+- spec/binomial_spec.rb
 - spec/bivariatenormal_spec.rb
 - spec/chisquare_spec.rb
 - spec/distribution_spec.rb