statsample-bivariate-extension 0.16.1 → 1.1.0

data/Manifest.txt

@@ -4,7 +4,6 @@ README.txt
 Rakefile
 data/tetmat_matrix.txt
 data/tetmat_test.txt
-grab_references.rb
 lib/statsample/bivariate/extension_version.rb
 lib/statsample/bivariate/polychoric.rb
 lib/statsample/bivariate/polychoric/processor.rb

data/Rakefile

@@ -15,6 +15,7 @@ Hoe.spec 'statsample-bivariate-extension' do
   self.rubyforge_name = 'ruby-statsample'
   self.version=Statsample::Bivariate::EXTENSION_VERSION
   self.developer('Claudio Bustos', 'clbustos_at_gmail.com')
+  self.extra_deps << ["distribution", "~>0.6"]
 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="0.16.1" 
+    EXTENSION_VERSION="1.1.0" 
   end
 end
 

data/lib/statsample/bivariate/polychoric.rb

@@ -140,6 +140,8 @@ module Statsample
       # Returns the columns thresholds
       attr_reader :beta
       
+      attr_reader :failed
+      
       dirty_writer :max_iterations, :epsilon, :minimizer_type_two_step, :minimizer_type_joint_no_derivative, :minimizer_type_joint_derivative, :method
       dirty_memoize :r, :alpha, :beta
       # Default method
@@ -185,6 +187,7 @@ module Statsample
         }
         @r=nil
         @pd=nil
+        @failed=false
         compute_basic_parameters
       end
 
@@ -435,6 +438,8 @@ module Statsample
             message+=sprintf("%10.3e ", x[i])
           end
           message+=sprintf("f() = %7.3f\n"  , minimizer.f)+"\n";
+        rescue => e
+          @failed=true
         end while status == GSL::CONTINUE and iter < @max_iterations
         
         @iteration=iter
@@ -527,7 +532,7 @@ module Statsample
         pc=@nr.times.collect{ [0]*@nc}
         @nr.times { |i|
             @nc.times { |j|
-              pd[i][j]=Distribution::NormalBivariate.cdf(@alpha[i], @beta[j], rho)
+              pd[i][j]=Distribution::BivariateNormal.cdf(@alpha[i], @beta[j], rho)
               pc[i][j] = pd[i][j]
               pd[i][j] = pd[i][j] - pc[i-1][j] if i>0
               pd[i][j] = pd[i][j] - pc[i][j-1] if j>0
@@ -819,26 +824,34 @@ module Statsample
       
       def report_building(generator) # :nodoc: 
         compute if dirty?
+        
+        
         section=ReportBuilder::Section.new(:name=>@name)
-        t=ReportBuilder::Table.new(:name=>_("Contingence Table"), :header=>[""]+(@n.times.collect {|i| "Y=#{i}"})+["Total"])
-        @m.times do |i|
-          t.row(["X = #{i}"]+(@n.times.collect {|j| @matrix[i,j]}) + [@sumr[i]])
+        
+        if @failed
+          section.add("Failed to converge")
+        else        
+          t=ReportBuilder::Table.new(:name=>_("Contingence Table"), :header=>[""]+(@n.times.collect {|i| "Y=#{i}"})+["Total"])
+          @m.times do |i|
+            t.row(["X = #{i}"]+(@n.times.collect {|j| @matrix[i,j]}) + [@sumr[i]])
+          end
+          t.hr
+          t.row(["T"]+(@n.times.collect {|j| @sumc[j]})+[@total])
+          section.add(t)
+          section.add(sprintf("r: %0.4f",r))
+          t=ReportBuilder::Table.new(:name=>_("Thresholds"), :header=>["","Value"])
+          threshold_x.each_with_index {|val,i|
+            t.row([_("Threshold X %d") % i, sprintf("%0.4f", val)])
+          }
+          threshold_y.each_with_index {|val,i|
+            t.row([_("Threshold Y %d") % i, sprintf("%0.4f", val)])
+          }
+          section.add(t)
+          section.add(_("Iterations: %d") % @iteration) if @iteration
+          section.add(_("Test of bivariate normality: X^2 = %0.3f, df = %d, p= %0.5f" % [ chi_square, chi_square_df, 1-Distribution::ChiSquare.cdf(chi_square, chi_square_df)])) 
+          generator.parse_element(section)
         end
-        t.hr
-        t.row(["T"]+(@n.times.collect {|j| @sumc[j]})+[@total])
-        section.add(t)
-        section.add(sprintf("r: %0.4f",r))
-        t=ReportBuilder::Table.new(:name=>_("Thresholds"), :header=>["","Value"])
-        threshold_x.each_with_index {|val,i|
-          t.row([_("Threshold X %d") % i, sprintf("%0.4f", val)])
-        }
-        threshold_y.each_with_index {|val,i|
-          t.row([_("Threshold Y %d") % i, sprintf("%0.4f", val)])
-        }
-        section.add(t)
-        section.add(_("Iterations: %d") % @iteration)
-        section.add(_("Test of bivariate normality: X^2 = %0.3f, df = %d, p= %0.5f" % [ chi_square, chi_square_df, 1-Distribution::ChiSquare.cdf(chi_square, chi_square_df)])) 
-        generator.parse_element(section)
+        
       end
     end
   end

data/lib/statsample/bivariate/polychoric/processor.rb

@@ -16,7 +16,7 @@ module Statsample
         end
         
         def bipdf(i,j)
-           Distribution::NormalBivariate.pdf(a(i), b(j), rho)
+           Distribution::BivariateNormal.pdf(a(i), b(j), rho)
         end
         
         def loglike
@@ -111,7 +111,7 @@ module Statsample
                 a=(i==@nr-1) ? 100: alpha[i]
                 b=(j==@nc-1) ? 100: beta[j]
                 #puts "a:#{a} b:#{b}"
-                @pd[i][j]=Distribution::NormalBivariate.cdf(a, b, rho)
+                @pd[i][j]=Distribution::BivariateNormal.cdf(a, b, rho)
               end
               pc[i][j] = @pd[i][j]
               @pd[i][j] = @pd[i][j] - pc[i-1][j] if i>0

data/lib/statsample/bivariate/tetrachoric.rb

@@ -170,8 +170,8 @@ module Statsample
       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']
+        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
         #
@@ -265,8 +265,8 @@ module Statsample
         #        COMPUTE NORMAL DEVIATES FOR THE MARGINAL FREQUENCIES
         #        SINCE NO MARGINAL CAN BE 0.0, IE IS NOT CHECKED
         #
-        @zac = Distribution::Normal.p_value(@probac)
-        @zab = Distribution::Normal.p_value(@probab)
+        @zac = Distribution::Normal.p_value(@probac.to_f)
+        @zab = Distribution::Normal.p_value(@probab.to_f)
         @ss = Math::exp(-0.5 * (@zac ** 2 + @zab ** 2)).quo(TWOPI)
         #
         #        WHEN R IS 0.0, 1.0 OR -1.0, TRANSFER TO COMPUTE SDZERO

data/spec/tetrachoric_spec.rb

@@ -1,14 +1,17 @@
 $:.unshift(File.dirname(__FILE__)+"/../../")
-require 'spec_helper'
+require File.expand_path(File.dirname(__FILE__)+'/spec_helper')
 
 describe "Statsample::Bivariate tetrachoric extensions" do
+  before do
+	  @data_file=File.expand_path(File.dirname(__FILE__)+"/../data/tetmat_test.txt")
+  end
   it "should respond to tetrachoric method" 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(@data_file, %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(@data_file, %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])

metadata

@@ -1,127 +1,143 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: statsample-bivariate-extension
-version: !ruby/object:Gem::Version 
-  hash: 93
-  prerelease: false
-  segments: 
-  - 0
-  - 16
-  - 1
-  version: 0.16.1
+version: !ruby/object:Gem::Version
+  version: 1.1.0
+  prerelease: 
 platform: ruby
-authors: 
+authors:
 - Claudio Bustos
 autorequire: 
 bindir: bin
-cert_chain: 
-- |
-  -----BEGIN CERTIFICATE-----
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-  rpP0jjs0
-  -----END CERTIFICATE-----
-
-date: 2010-12-22 00:00:00 -03:00
-default_executable: 
-dependencies: 
-- !ruby/object:Gem::Dependency 
-  name: hoe
+cert_chain:
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+date: 2011-09-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: distribution
+  requirement: &15403740 !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '0.6'
+  type: :runtime
   prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  version_requirements: *15403740
+- !ruby/object:Gem::Dependency
+  name: hoe
+  requirement: &15402800 !ruby/object:Gem::Requirement
     none: false
-    requirements: 
-    - - ">="
-      - !ruby/object:Gem::Version 
-        hash: 47
-        segments: 
-        - 2
-        - 8
-        - 0
-        version: 2.8.0
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '2.12'
   type: :development
-  version_requirements: *id001
-description: |-
-  Provides advanced bivariate statistics:
-  * Tetrachoric correlation
-  * Polychoric correlation
-email: 
+  prerelease: false
+  version_requirements: *15402800
+description: !binary |-
+  UHJvdmlkZXMgYWR2YW5jZWQgYml2YXJpYXRlIHN0YXRpc3RpY3M6CiogVGV0
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+email:
 - clbustos_at_gmail.com
 executables: []
-
 extensions: []
-
-extra_rdoc_files: 
-- History.txt
-- Manifest.txt
-- README.txt
-- references.txt
-files: 
-- History.txt
-- Manifest.txt
-- README.txt
-- Rakefile
-- data/tetmat_matrix.txt
-- data/tetmat_test.txt
-- grab_references.rb
-- lib/statsample/bivariate/extension_version.rb
-- 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/tetrachoric_spec.rb
-has_rdoc: true
-homepage: http://ruby-statsample.rubyforge.org/
+extra_rdoc_files:
+- !binary |-
+  SGlzdG9yeS50eHQ=
+- !binary |-
+  TWFuaWZlc3QudHh0
+- !binary |-
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+files:
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+- !binary |-
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+- .gemtest
+homepage: !binary |-
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 licenses: []
-
 post_install_message: 
-rdoc_options: 
+rdoc_options:
 - --main
 - README.txt
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: ruby-statsample
-rubygems_version: 1.3.7
+rubygems_version: 1.8.10
 signing_key: 
 specification_version: 3
-summary: "Provides advanced bivariate statistics: * Tetrachoric correlation * Polychoric correlation"
+summary: !binary |-
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 test_files: []
-

data/grab_references.rb

@@ -1,28 +0,0 @@
-#!/usr/bin/env ruby1.9
-require 'reportbuilder'
-refs=[]
-Dir.glob "**/*.rb" do |f|
-	reference=false
-	File.open(f).each_line 	do |l|
-		
-		if l=~/== Reference/
-		    reference=true
-		elsif reference
-			if l=~/\*\s+(.+)/
-				refs.push $1
-			else
-				reference=false
-			end
-	        end
-	    
-	end
-end
-
-
-rb=ReportBuilder.new(:name=>"References") do |g|
-	refs.uniq.sort.each do |r|
-		g.text "* #{r}"
-	end
-end
-
-rb.save_text("references.txt")