statsample-bivariate-extension 0.13.4 → 0.16.0

data/History.txt

@@ -1,3 +1,9 @@
+=== 0.16.0 / 2010-11-14
+* Bug fix: Specs work without gsl. Counts iterations when using only ruby
+* Updated specs to rspec 2
+* Updated Manifest.txt
+* Added grab_references to retrieve references on package
+
 === 0.13.4 / 2010-08-18
 
 * Added cache for tetrachoric correlation matrix

data/Manifest.txt

@@ -4,10 +4,12 @@ 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/spec.opts
 spec/spec_helper.rb
 spec/statsample/bivariate/polychoric_processor_spec.rb

data/Rakefile

@@ -2,7 +2,8 @@
 # -*- ruby -*-
 
 require 'rubygems'
-require 'spec/rake/spectask'
+require 'rspec'
+require 'rspec/core/rake_task'
 require 'hoe'
 
 Hoe.plugin :git
@@ -19,10 +20,12 @@ end
 
 
 desc "Run all spec with RCov"
-Spec::Rake::SpecTask.new('test_with_rcov') do |t|
-  t.spec_files = FileList['spec/**/*.rb']
-  t.rcov = true
-  t.rcov_opts = ['--exclude', 'spec']
+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/grab_references.rb

@@ -0,0 +1,28 @@
+#!/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")

data/lib/statsample/bivariate/extension_version.rb

@@ -1,7 +1,7 @@
 module Statsample
   module Bivariate
     # Version  of bivariate extension
-    EXTENSION_VERSION="0.13.4" 
+    EXTENSION_VERSION="0.16.0" 
   end
 end
 

data/lib/statsample/bivariate/polychoric.rb

@@ -85,8 +85,7 @@ module Statsample
     # 
     # See extensive documentation on Uebersax(2002) and Drasgow(2006)
     #
-    # == References 
-    # 
+    # == Reference
     # * Drasgow F. (2006). Polychoric and polyserial correlations. In Kotz L, Johnson NL (Eds.), Encyclopedia of statistical sciences. Vol. 7 (pp. 69-74). New York: Wiley.
     # * Olsson, U. (1979) Maximum likelihood estimation of the polychoric correlation coefficient. Psychometrika 44, 443-460.
     # * 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
@@ -307,6 +306,7 @@ module Statsample
         @log+=min.log.to_table.to_s
         @r=min.x_minimum
         @loglike_model=-min.f_minimum
+        @iteration=min.iterations
         puts @log if @debug
         
       end

data/lib/statsample/bivariate/tetrachoric.rb

@@ -61,17 +61,17 @@ module Statsample
     #   tc.threshold_y # threshold for y variable
     #   tc.threshold_x # threshold for x variable
     #
-    # == References:
-    #
+    # == Reference:
     # * Brown, MB. (1977) Algorithm AS 116: the tetrachoric correlation and its standard error. <em>Applied Statistics, 26</em>, 343-351.
     # * Drasgow F. (2006). Polychoric and polyserial correlations. In Kotz L, Johnson NL (Eds.), Encyclopedia of statistical sciences. Vol. 7 (pp. 69-74). New York: Wiley.
     # * 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)
       include Summarizable
       attr_reader :r
       attr_accessor :name
-
+      
       TWOPI=Math::PI*2
       SQT2PI= 2.50662827
       RLIMIT = 0.9999
@@ -94,8 +94,8 @@ module Statsample
         v1a, v2a=Statsample.only_valid(v1,v2)
         v1a=v1a.dichotomize
         v2a=v2a.dichotomize
-        raise "v1 have only 0" if v1a.factors==[0]
-        raise "v2 have only 0" if v2a.factors==[0]
+        raise RequerimentNotMeet, "v1 have only 0" if v1a.factors==[0]
+        raise RequerimentNotMeet, "v2 have only 0" if v2a.factors==[0]
         a,b,c,d = 0,0,0,0
         v1a.each_index{|i|
           x,y=v1a[i],v2a[i]
@@ -172,7 +172,7 @@ module Statsample
         #        kdelta=4 MEANS TABLE HAS 0.0 ROW OR COLUMN, RUN IS TERMINATED
         #
 
-        raise "Rows and columns should have more than 0 items" if @kdelta==4
+        raise RequerimentNotMeet, "Rows and columns should have more than 0 items" if @kdelta==4
 
         #      GOTO (4, 1, 2 , 92), kdelta
         #

data/references.txt

@@ -0,0 +1,5 @@
+References
+* Brown, MB. (1977) Algorithm AS 116: the tetrachoric correlation and its standard error. <em>Applied Statistics, 26</em>, 343-351.
+* Drasgow F. (2006). Polychoric and polyserial correlations. In Kotz L, Johnson NL (Eds.), Encyclopedia of statistical sciences. Vol. 7 (pp. 69-74). New York: Wiley.
+* Olsson, U. (1979) Maximum likelihood estimation of the polychoric correlation coefficient. Psychometrika 44, 443-460.
+* 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

data/spec/spec_helper.rb

@@ -2,8 +2,7 @@
 
 $:.unshift File.join(File.dirname(__FILE__), '..', 'lib') 
 require "rubygems"
-require 'spec'
-require 'spec/autorun'
+require 'rspec'
 require 'statsample'
 require 'statsample/bivariate/tetrachoric'
 require 'statsample/bivariate/polychoric'

data/spec/statsample/bivariate/polychoric_processor_spec.rb

@@ -22,12 +22,12 @@ describe Statsample::Bivariate::Polychoric::Processor do
   end
   it "fd a loglike should be equal usign eq.6 and eq.13" do
     2.times {|k|
-      @processor.fd_loglike_a_eq6(k).should be_close @processor.fd_loglike_a_eq13(k), 1e-10
+      @processor.fd_loglike_a_eq6(k).should be_within(1e-10).of( @processor.fd_loglike_a_eq13(k))
     }
   end
   it "fd b loglike should be equal usign eq.6 and eq.14" do
     2.times {|m|
-      @processor.fd_loglike_b_eq6(m).should be_close @processor.fd_loglike_b_eq14(m), 1e-10
+      @processor.fd_loglike_b_eq6(m).should be_within(1e-10).of( @processor.fd_loglike_b_eq14(m))
     }
   end  
   it "fd rho should be equal usign fd_loglike_cell_rho and fd_loglike_rho" do

data/spec/statsample/bivariate/polychoric_spec.rb

@@ -24,30 +24,33 @@ describe Statsample::Bivariate::Polychoric do
     @poly.summary.size.should>0
   end
   def check_joint
-    @poly.r.should be_close(0.4192, 0.0001)
-    @poly.threshold_x[0].should be_close(-0.0297, 0.0001)
-    @poly.threshold_x[1].should be_close(1.1331, 0.0001)
+    @poly.r.should be_within( 0.0001).of(0.4192)
+    @poly.threshold_x[0].should be_within( 0.0001).of(-0.0297)
+    @poly.threshold_x[1].should be_within( 0.0001).of(1.1331)
 
-    @poly.threshold_y[0].should be_close(-0.2421, 0.0001)
-    @poly.threshold_y[1].should be_close(1.5938 ,0.0001)
-    @poly.chi_square.should be_close(11.54,0.01)
+    @poly.threshold_y[0].should be_within( 0.0001).of(-0.2421)
+    @poly.threshold_y[1].should be_within(0.0001).of(1.5938 )
+    @poly.chi_square.should be_within(0.01).of(11.54)
   end
   it "compute joint estimation (without derivative) using gsl" do
+    pending("requires rb-gsl") unless Statsample.has_gsl?
+    
     @poly.compute_one_step_mle_without_derivatives
     check_joint
-
   end
   it "compute joint estimation (with derivative) using gsl" do
+    pending("requires rb-gsl") unless Statsample.has_gsl?
+    
     @poly.compute_one_step_mle_with_derivatives
     check_joint
   end
   
   def check_two_step
-    @poly.r.should be_close(0.420, 0.001)
-    @poly.threshold_y[0].should be_close(-0.240 ,0.001)
-    @poly.threshold_x[0].should be_close(-0.027 ,0.001)
-    @poly.threshold_y[1].should be_close(1.578  ,0.001)
-    @poly.threshold_x[1].should be_close(1.137  ,0.001)
+    @poly.r.should be_within( 0.001).of(0.420)
+    @poly.threshold_y[0].should be_within(0.001).of(-0.240 )
+    @poly.threshold_x[0].should be_within(0.001).of(-0.027 )
+    @poly.threshold_y[1].should be_within(0.001).of(1.578  )
+    @poly.threshold_x[1].should be_within(0.001).of(1.137  )
   end
   it "should compute two step mle with ruby" do
       @poly.compute_two_step_mle_ruby
@@ -66,11 +69,11 @@ describe Statsample::Bivariate::Polychoric do
     @poly.method=:polychoric_series
     @poly.compute
     
-    @poly.r.should be_close(0.556, 0.001)
-    @poly.threshold_y[0].should be_close(-0.240 ,0.001)
-    @poly.threshold_x[0].should be_close(-0.027 ,0.001)
-    @poly.threshold_y[1].should be_close(1.578  ,0.001)
-    @poly.threshold_x[1].should be_close(1.137  ,0.001)
+    @poly.r.should be_within( 0.001).of(0.556)
+    @poly.threshold_y[0].should be_within(0.001).of(-0.240 )
+    @poly.threshold_x[0].should be_within(0.001).of(-0.027 )
+    @poly.threshold_y[1].should be_within(0.001).of(1.578  )
+    @poly.threshold_x[1].should be_within(0.001).of(1.137  )
   end
   
 end

data/spec/statsample/bivariate/tetrachoric_spec.rb

@@ -11,7 +11,7 @@ describe "Statsample::Bivariate tetrachoric extensions" do
     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_close(tcm_exp[i,k], 0.00001)
+        tcm_obs[i,j].should be_within( 0.00001).of(tcm_exp[i,k])
       end
     end
   end
@@ -27,12 +27,12 @@ describe Statsample::Bivariate::Tetrachoric do
     end
     it "should return similar values for two step ruby" do
       @poly.compute_two_step_mle_ruby
-      @tetra.r.should be_close(@poly.r,0.0001)
+      @tetra.r.should be_within(0.0001).of(@poly.r)
     end
     if Statsample.has_gsl?
       it "should return similar values for two step using gsl" do
         @poly.compute_two_step_mle_gsl
-        @tetra.r.should be_close(@poly.r,0.0001)
+        @tetra.r.should be_within(0.0001).of(@poly.r)
       end
     else
       it "shouldn't use two step gsl without rb-gsl"
@@ -43,17 +43,17 @@ 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(RuntimeError)
+    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d)}.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(RuntimeError)
+    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d)}.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(RuntimeError)
+    lambda {Statsample::Bivariate::Tetrachoric.new(a,b,c,d)}.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
@@ -71,10 +71,10 @@ describe Statsample::Bivariate::Tetrachoric do
   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.r.should be_close(-0.53980,0.0001)
-    tc.se.should be_close(0.09940,0.0001)
-    tc.threshold_x.should be_close(-0.15731, 0.0001)
-    tc.threshold_y.should be_close( 0.31864, 0.0001)
+    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)
+    tc.threshold_y.should be_within( 0.0001).of( 0.31864)
   end
   it "should return equal values for dataset and crosstab inputs" do 
     x=%w{a a a a b b b a b b a a b b}.to_vector

metadata

@@ -1,12 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: statsample-bivariate-extension
 version: !ruby/object:Gem::Version 
+  hash: 95
   prerelease: false
   segments: 
   - 0
-  - 13
-  - 4
-  version: 0.13.4
+  - 16
+  - 0
+  version: 0.16.0
 platform: ruby
 authors: 
 - Claudio Bustos
@@ -35,16 +36,18 @@ cert_chain:
   rpP0jjs0
   -----END CERTIFICATE-----
 
-date: 2010-08-18 00:00:00 -04:00
+date: 2010-11-14 00:00:00 -03:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: rubyforge
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 7
         segments: 
         - 2
         - 0
@@ -56,14 +59,16 @@ dependencies:
   name: hoe
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
+        hash: 19
         segments: 
         - 2
         - 6
-        - 1
-        version: 2.6.1
+        - 2
+        version: 2.6.2
   type: :development
   version_requirements: *id002
 description: |-
@@ -80,6 +85,7 @@ extra_rdoc_files:
 - History.txt
 - Manifest.txt
 - README.txt
+- references.txt
 files: 
 - History.txt
 - Manifest.txt
@@ -87,10 +93,12 @@ files:
 - 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/spec.opts
 - spec/spec_helper.rb
 - spec/statsample/bivariate/polychoric_processor_spec.rb
@@ -107,23 +115,27 @@ rdoc_options:
 require_paths: 
 - lib
 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 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
+      hash: 3
       segments: 
       - 0
       version: "0"
 requirements: []
 
 rubyforge_project: ruby-statsample
-rubygems_version: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: "Provides advanced bivariate statistics: * Tetrachoric correlation * Polychoric correlation"