statsample-bivariate-extension 0.16.0 → 0.16.1

data/History.txt

@@ -1,3 +1,7 @@
+=== 0.16.1 / 2010-12-22
+
+* Added support for optimized tetrachoric correlation calculation. Update statsample-optimization before report any error, please.
+
 === 0.16.0 / 2010-11-14
 * Bug fix: Specs work without gsl. Counts iterations when using only ruby
 * Updated specs to rspec 2

data/Manifest.txt

@@ -10,8 +10,8 @@ lib/statsample/bivariate/polychoric.rb
 lib/statsample/bivariate/polychoric/processor.rb
 lib/statsample/bivariate/tetrachoric.rb
 references.txt
+spec/polychoric_processor_spec.rb
+spec/polychoric_spec.rb
 spec/spec.opts
 spec/spec_helper.rb
-spec/statsample/bivariate/polychoric_processor_spec.rb
-spec/statsample/bivariate/polychoric_spec.rb
-spec/statsample/bivariate/tetrachoric_spec.rb
+spec/tetrachoric_spec.rb

data/Rakefile

@@ -17,15 +17,4 @@ Hoe.spec 'statsample-bivariate-extension' do
   self.developer('Claudio Bustos', 'clbustos_at_gmail.com')
 end
 
-
-
-desc "Run all spec with RCov"
-RSpec::Core::RakeTask.new do |t|
-  t.rspec_opts = ["-c", "-f progress", "-r ./spec/spec_helper.rb"]
-  t.pattern = 'spec/**/*_spec.rb'
-  #t.rcov = true
-  #t.rcov_opts = ['--exclude', 'spec']
-
-end
-
 # vim: syntax=ruby

data/lib/statsample/bivariate/extension_version.rb

@@ -1,7 +1,7 @@
 module Statsample
   module Bivariate
     # Version  of bivariate extension
-    EXTENSION_VERSION="0.16.0" 
+    EXTENSION_VERSION="0.16.1" 
   end
 end
 

data/lib/statsample/bivariate/tetrachoric.rb

@@ -67,11 +67,16 @@ module Statsample
     # * Uebersax, J.S. (2006). The tetrachoric and polychoric correlation coefficients. Statistical Methods for Rater Agreement web site. 2006. Available at: http://john-uebersax.com/stat/tetra.htm . Accessed February, 11, 2010
 
     class Tetrachoric
-       RequerimentNotMeet=Class.new(Exception)
+      RequerimentNotMeet=Class.new(Exception)
       include Summarizable
+      # Value for tethrachoric correlation
       attr_reader :r
+      # Name on the analysis
       attr_accessor :name
-      
+      # Use ruby version of algorithm.
+      # By default, this attribute is set to false,
+      # and C version of algorithm is used
+      attr_accessor :ruby_engine
       TWOPI=Math::PI*2
       SQT2PI= 2.50662827
       RLIMIT = 0.9999
@@ -85,12 +90,12 @@ module Statsample
       X=[0,0.9972638618,  0.9856115115,  0.9647622556, 0.9349060759,  0.8963211558, 0.8493676137, 0.7944837960, 0.7321821187, 0.6630442669, 0.5877157572, 0.5068999089, 0.4213512761, 0.3318686023, 0.2392873623, 0.1444719616, 0.0483076657]
       W=[0, 0.0070186100,  0.0162743947,  0.0253920653, 0.0342738629,  0.0428358980,  0.0509980593, 0.0586840935,  0.0658222228,  0.0723457941, 0.0781938958, 0.0833119242, 0.0876520930, 0.0911738787, 0.0938443991, 0.0956387201, 0.0965400885]
       # Creates a Tetrachoric object based on a 2x2 Matrix.
-      def self.new_with_matrix(m)
-        Tetrachoric.new(m[0,0], m[0,1], m[1,0],m[1,1])
+      def self.new_with_matrix(m, opts=Hash.new)
+        Tetrachoric.new(m[0,0], m[0,1], m[1,0],m[1,1], opts)
       end
       # Creates a Tetrachoric object based on two vectors.
       # The vectors are dichotomized previously.
-      def self.new_with_vectors(v1,v2)
+      def self.new_with_vectors(v1,v2, opts=Hash.new)
         v1a, v2a=Statsample.only_valid(v1,v2)
         v1a=v1a.dichotomize
         v2a=v2a.dichotomize
@@ -104,7 +109,7 @@ module Statsample
           c+=1 if x==1 and y==0
           d+=1 if x==1 and y==1
         }
-        Tetrachoric.new(a,b,c,d)
+        Tetrachoric.new(a,b,c,d, opts)
       end
       # Standard error
       def se
@@ -138,34 +143,42 @@ module Statsample
       end
 
       # Creates a new tetrachoric object for analysis
-      def initialize(a,b,c,d)
+      def initialize(a,b,c,d, opts=Hash.new)
         @a,@b,@c,@d=a,b,c,d
-        @name=_("Tetrachoric correlation")
+        
+        opts_default={
+          :name=>_("Tetrachoric correlation"),
+          :ruby_engine=>false
+        }
+        
+        @opts=opts_default.merge opts
+        @opts.each{|k,v| self.send("#{k}=",v) if self.respond_to? k}
         #
         #       CHECK IF ANY CELL FREQUENCY IS NEGATIVE
         #
         raise "All frequencies should be positive" if  (@a < 0 or @b < 0 or @c < 0  or @d < 0)
         compute
       end
-      # Compute the tetrachoric correlation.
-      # Called on object creation.
-      #
       def compute
-
-        #
-        # INITIALIZATION
-        #
-        @r = 0
-        sdzero = 0
-        @sdr = 0
-        @itype = 0
-        @ifault = 0
-
+        if !ruby_engine and Statsample::OPTIMIZED and Statsample::STATSAMPLE__.respond_to? :tetrachoric
+          compute_optimized
+        else
+          compute_ruby
+        end
+      end
+      # Compute the tetrachoric correlation 
+      def compute_optimized
+        check_frequencies        
+        t=Statsample::STATSAMPLE__.tetrachoric(@a,@b,@c,@d)
+        raise "Error on calculation of tetrachoric correlation: #{t['ifault']}" if t['ifault']>0
+        @r,@sdr,@itype,@ifault,@zab, @zac = t['r'],t['sdr'],t['itype'],t['ifault'], t['threshold_x'], t['threshold_y']
+      end
+      def check_frequencies
         #
         #       CHECK IF ANY FREQUENCY IS 0.0 AND SET kdelta
         #
         @kdelta = 1
-        delta  = 0
+       
         @kdelta  = 2 if (@a == 0 or @d == 0)
         @kdelta += 2 if (@b == 0 or @c == 0)
         #
@@ -173,6 +186,22 @@ module Statsample
         #
 
         raise RequerimentNotMeet, "Rows and columns should have more than 0 items" if @kdelta==4
+      end
+      # Compute the tetrachoric correlation using ruby
+      # Called on object creation.
+      #
+      def compute_ruby
+        check_frequencies
+        #
+        # INITIALIZATION
+        #
+        @r = 0
+        sdzero = 0
+        @sdr = 0
+        @itype = 0
+        @ifault = 0
+        delta  = 0
+        
 
         #      GOTO (4, 1, 2 , 92), kdelta
         #

data/spec/{statsample/bivariate/polychoric_processor_spec.rb → polychoric_processor_spec.rb}

@@ -9,16 +9,17 @@ describe Statsample::Bivariate::Polychoric::Processor do
      @processor=Statsample::Bivariate::Polychoric::Processor.new(@alpha,@beta,@rho,@matrix)
   end
   it "im_function  method should return correct values according to index" do
-    @processor.im_function(0,0,0).should==@processor.fd_loglike_cell_rho(0,0)
-    @processor.im_function(1,0,0).should==@processor.fd_loglike_cell_a(0,0,0)
-    @processor.im_function(2,0,0).should==@processor.fd_loglike_cell_a(0,0,1)
-    @processor.im_function(3,1,0).should==@processor.fd_loglike_cell_b(1,0,0)
-    @processor.im_function(4,0,1).should==@processor.fd_loglike_cell_b(0,1,1)
+    @processor.im_function(0,0,0).should eq @processor.fd_loglike_cell_rho(0,0)
+    @processor.im_function(1,0,0).should eq @processor.fd_loglike_cell_a(0,0,0)
+    @processor.im_function(2,0,0).should eq @processor.fd_loglike_cell_a(0,0,1)
+    @processor.im_function(3,1,0).should eq @processor.fd_loglike_cell_b(1,0,0)
+    @processor.im_function(4,0,1).should eq @processor.fd_loglike_cell_b(0,1,1)
     lambda {@processor.im_function(5)}.should raise_error
     
   end
   it "should return informacion matrix" do
-    @processor.information_matrix.inverse.should be_instance_of(::Matrix)
+    im=@processor.information_matrix
+    im.should be_instance_of(::Matrix)    
   end
   it "fd a loglike should be equal usign eq.6 and eq.13" do
     2.times {|k|

data/spec/spec_helper.rb

@@ -1,8 +1,12 @@
 # encoding: utf-8
 
+
+
+
 $:.unshift File.join(File.dirname(__FILE__), '..', 'lib') 
 require "rubygems"
 require 'rspec'
 require 'statsample'
 require 'statsample/bivariate/tetrachoric'
 require 'statsample/bivariate/polychoric'
+

data/spec/{statsample/bivariate/tetrachoric_spec.rb → tetrachoric_spec.rb}

@@ -6,9 +6,9 @@ describe "Statsample::Bivariate tetrachoric extensions" do
     Statsample::Bivariate.should respond_to(:tetrachoric)
   end
   it "should return correct tetrachoric_matrix"do
-    ds=Statsample::PlainText.read(File.dirname(__FILE__)+"/../../../data/tetmat_test.txt", %w{a b c d e})
+    ds=Statsample::PlainText.read(File.dirname(__FILE__)+"/../data/tetmat_test.txt", %w{a b c d e})
     tcm_obs=Statsample::Bivariate.tetrachoric_correlation_matrix(ds)
-    tcm_exp=Statsample::PlainText.read(File.dirname(__FILE__)+"/../../../data/tetmat_matrix.txt", %w{a b c d e}).to_matrix
+    tcm_exp=Statsample::PlainText.read(File.dirname(__FILE__)+"/../data/tetmat_matrix.txt", %w{a b c d e}).to_matrix
     tcm_obs.row_size.times do |i|
       tcm_obs.column_size do |j|
         tcm_obs[i,j].should be_within( 0.00001).of(tcm_exp[i,k])
@@ -18,11 +18,11 @@ describe "Statsample::Bivariate tetrachoric extensions" do
   
 end
 
-describe Statsample::Bivariate::Tetrachoric do
+shared_examples_for "tetrachoric implementation" do
   context "Polychoric 2x2 vs tetrachoric" do
     before do
       @matrix=Matrix[[150+rand(10),1000+rand(20)],[1000+rand(20),200+rand(20)]]
-      @tetra = Statsample::Bivariate::Tetrachoric.new_with_matrix(@matrix)
+      @tetra = Statsample::Bivariate::Tetrachoric.new_with_matrix(@matrix,t_opts)
       @poly  = Statsample::Bivariate::Polychoric.new(@matrix)
     end
     it "should return similar values for two step ruby" do
@@ -42,35 +42,34 @@ describe Statsample::Bivariate::Tetrachoric do
   
   it "should raise error on contingence table without cases" do
     a,b,c,d=0,0,0,0
-    
-    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d)}.should raise_error(Statsample::Bivariate::Tetrachoric::RequerimentNotMeet)
+    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d, t_opts)}.should raise_error(Statsample::Bivariate::Tetrachoric::RequerimentNotMeet)
   end  
   it "should raise error on contingence table without cases on a row" do
   
     a,b,c,d=10,10,0,0
     
-    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d)}.should raise_error(Statsample::Bivariate::Tetrachoric::RequerimentNotMeet)
+    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d, t_opts)}.should raise_error(Statsample::Bivariate::Tetrachoric::RequerimentNotMeet)
   end
   it "should raise error on contingence table without cases on a column" do
     a,b,c,d=10,0,10,0
-    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d)}.should raise_error(Statsample::Bivariate::Tetrachoric::RequerimentNotMeet)
+    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d, t_opts)}.should raise_error(Statsample::Bivariate::Tetrachoric::RequerimentNotMeet)
   end
   it "should return correct values for perfect correlation" do
     a,b,c,d=10,0,0,10
-    tc  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d)
+    tc  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d,t_opts)
     tc.r.should==1
     tc.se.should==0
   end
   it "should return correct values for perfect inverse correlation" do 
     a,b,c,d=0,10,10,0
-    tc  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d)
+    tc  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d, t_opts)
     tc.r.should==-1
     tc.se.should==0
   end
   
   it "should return correct value for standard contingence table" do 
     a,b,c,d = 30,40,70,20
-    tc  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d)
+    tc  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d, t_opts)
     tc.r.should be_within(0.0001).of(-0.53980)
     tc.se.should be_within(0.0001).of(0.09940)
     tc.threshold_x.should be_within( 0.0001).of(-0.15731)
@@ -84,11 +83,25 @@ describe Statsample::Bivariate::Tetrachoric do
     # a  4    3
     # b  2    5
     a,b,c,d=4,3,2,5
-    tc1  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d)
-    tc2  = Statsample::Bivariate::Tetrachoric.new_with_vectors(x,y)
+    tc1  = Statsample::Bivariate::Tetrachoric.new(a,b,c,d, t_opts)
+    tc2  = Statsample::Bivariate::Tetrachoric.new_with_vectors(x,y, t_opts)
     tc1.r.should==tc2.r
     tc1.se.should==tc2.se
     tc2.summary.size.should>0
   end
+end
 
+describe "Statsample::Bivariate::Tetrachoric with ruby engine" do
+  it_should_behave_like 'tetrachoric implementation' do
+    let(:t_opts) { {:ruby_engine=>true}}
+  end
+end
+describe "Statsample::Bivariate::Tetrachoric with optimized engine" do
+  if Statsample::OPTIMIZED and Statsample::STATSAMPLE__.respond_to? :tetrachoric
+    it_should_behave_like 'tetrachoric implementation' do
+      let(:t_opts) { {:ruby_engine=>false}}
+    end    
+  else
+    pending("not optimized tetrachoric engine available") 
+  end
 end

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: statsample-bivariate-extension
 version: !ruby/object:Gem::Version 
-  hash: 95
+  hash: 93
   prerelease: false
   segments: 
   - 0
   - 16
-  - 0
-  version: 0.16.0
+  - 1
+  version: 0.16.1
 platform: ruby
 authors: 
 - Claudio Bustos
@@ -36,41 +36,25 @@ cert_chain:
   rpP0jjs0
   -----END CERTIFICATE-----
 
-date: 2010-11-14 00:00:00 -03:00
+date: 2010-12-22 00:00:00 -03:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
-  name: rubyforge
+  name: hoe
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
     none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
-        hash: 7
+        hash: 47
         segments: 
         - 2
+        - 8
         - 0
-        - 4
-        version: 2.0.4
+        version: 2.8.0
   type: :development
   version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: hoe
-  prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 19
-        segments: 
-        - 2
-        - 6
-        - 2
-        version: 2.6.2
-  type: :development
-  version_requirements: *id002
 description: |-
   Provides advanced bivariate statistics:
   * Tetrachoric correlation
@@ -99,11 +83,11 @@ files:
 - lib/statsample/bivariate/polychoric/processor.rb
 - lib/statsample/bivariate/tetrachoric.rb
 - references.txt
+- spec/polychoric_processor_spec.rb
+- spec/polychoric_spec.rb
 - spec/spec.opts
 - spec/spec_helper.rb
-- spec/statsample/bivariate/polychoric_processor_spec.rb
-- spec/statsample/bivariate/polychoric_spec.rb
-- spec/statsample/bivariate/tetrachoric_spec.rb
+- spec/tetrachoric_spec.rb
 has_rdoc: true
 homepage: http://ruby-statsample.rubyforge.org/
 licenses: []