statsample 0.10.0 → 0.11.0

data.tar.gz.sig

@@ -1,2 +1 @@
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data/History.txt

@@ -1,3 +1,12 @@
+=== 0.11.0 / 2010-04-16
+<b>New features:</b>
+* Added Statsample::Anova::TwoWay and Statsample::Anova::TwoWayWithVectors
+* Added Statsample.clone_only valid and Statsample::Dataset.clone_only_valid, for cheap copy on already clean vectors
+<b>Optimizations and bug fix</b> 
+* Removed library statistics2 from package. Used gem statistics2 instead, because have a extension version
+* Added example for Reliability class
+* Bug fix on Statsample::DominanceAnalysis
+
 === 0.10.0 / 2010-04-13
 
 <b>API modifications</b>

data/Manifest.txt

@@ -21,6 +21,7 @@ examples/parallel_analysis.rb
 examples/parallel_analysis_tetrachoric.rb
 examples/polychoric.rb
 examples/principal_axis.rb
+examples/reliability.rb
 examples/t_test.rb
 examples/tetrachoric.rb
 examples/vector.rb
@@ -31,9 +32,10 @@ lib/distribution/normal.rb
 lib/distribution/normalbivariate.rb
 lib/distribution/t.rb
 lib/spss.rb
-lib/statistics2.rb
 lib/statsample.rb
 lib/statsample/anova.rb
+lib/statsample/anova/oneway.rb
+lib/statsample/anova/twoway.rb
 lib/statsample/bivariate.rb
 lib/statsample/bivariate/polychoric.rb
 lib/statsample/bivariate/tetrachoric.rb
@@ -89,7 +91,10 @@ po/es/statsample.mo
 po/es/statsample.po
 po/statsample.pot
 setup.rb
+test/helpers_tests.rb
 test/test_anovaoneway.rb
+test/test_anovatwoway.rb
+test/test_anovatwowaywithdataset.rb
 test/test_anovawithvectors.rb
 test/test_bivariate.rb
 test/test_bivariate_polychoric.rb
@@ -104,7 +109,6 @@ test/test_dominance_analysis.rb
 test/test_factor.rb
 test/test_ggobi.rb
 test/test_gsl.rb
-test/test_helpers.rb
 test/test_histogram.rb
 test/test_logit.rb
 test/test_matrix.rb

data/README.txt

@@ -100,9 +100,12 @@ Optional:
 
 <b>Note</b>: Use gsl 1.12.109 or later.
 
-== DOWNLOAD
-* Gems and bugs report: http://rubyforge.org/projects/ruby-statsample/
-* SVN and Wiki: http://code.google.com/p/ruby-statsample/
+== RESOURCES
+
+* Source code on github: http://github.com/clbustos/statsample
+* API: http://ruby-statsample.rubyforge.org/statsample/
+* Bug report and feature request: http://code.google.com/p/ruby-statsample/issues/list
+
 
 == INSTALL:
 

data/Rakefile

@@ -1,18 +1,12 @@
 #!/usr/bin/ruby
 # -*- ruby -*-
 # -*- coding: utf-8 -*-
+$:.unshift(File.dirname(__FILE__)+'/lib/')
 
 require 'rubygems'
 require 'hoe'
 require './lib/statsample'
-
-
-
-
-
-if File.exists? './local_rakefile.rb'
-	require './local_rakefile'
-end
+Hoe.plugin :git
 
 desc "Ruby Lint"
 task :lint do
@@ -40,10 +34,10 @@ end
 
 h=Hoe.spec('statsample') do 
   self.version=Statsample::VERSION
-  self.testlib=:minitest
+  #self.testlib=:minitest
 	self.rubyforge_name = "ruby-statsample"
 	self.developer('Claudio Bustos', 'clbustos@gmail.com')
-	self.extra_deps << ["spreadsheet","~>0.6.0"] << ["svg-graph", "~>1.0"] << ["reportbuilder", "~>1.0"] << ["minimization", "~>0.2.0"] << ["fastercsv"] << ["dirty-memoize", "~>0.0"]
+	self.extra_deps << ["spreadsheet","~>0.6.0"] << ["svg-graph", "~>1.0"] << ["reportbuilder", "~>1.0"] << ["minimization", "~>0.2.0"] << ["fastercsv"] << ["dirty-memoize", "~>0.0"] << ["statistics2", "~>0.54"]
 	self.clean_globs << "test/images/*" << "demo/item_analysis/*" << "demo/Regression"
 	self.need_rdoc=false
 end
@@ -88,13 +82,4 @@ task :publicar_docs => [:clean, :docs] do
   }
   sh %{rsync #{h.rsync_args} #{local_dir}/ #{host}:#{remote_dir}}
 end
-    
-task :release => [:tag] do 
-end
-
-task :tag do	
-  sh %(svn commit -m "Version bump: #{Statsample::VERSION}")
-	sh %(svn cp https://ruby-statsample.googlecode.com/svn/reportbuilder/trunk https://ruby-statsample.googlecode.com/svn/statsample/tags/v#{Statsample::VERSION} -m "ReportBuilder #{Statsample::VERSION} tagged")
-end
-
 # vim: syntax=Ruby

data/examples/dominance_analysis.rb

@@ -25,4 +25,3 @@ rb.add(da)
 
 
 puts rb.to_text
-rb.save_rtf("dominance_analysis.rtf")

data/examples/parallel_analysis.rb

@@ -4,6 +4,7 @@ $:.unshift(File.dirname(__FILE__)+'/../lib/')
 require 'statsample'
 samples=100
 variables=30
+iterations=50
 rng = GSL::Rng.alloc()
 f1=samples.times.collect {rng.ugaussian()}.to_scale
 f2=samples.times.collect {rng.ugaussian()}.to_scale
@@ -16,7 +17,7 @@ variables.times do |i|
 end
 ds=vectors.to_dataset
 
-pa=Statsample::Factor::ParallelAnalysis.new(ds, :iterations=>10, :debug=>true)
+pa=Statsample::Factor::ParallelAnalysis.new(ds, :iterations=>iterations, :debug=>true)
 pca=Statsample::Factor::PCA.new(Statsample::Bivariate.correlation_matrix(ds))
 rb=ReportBuilder.new(:name=>"Parallel Analysis with simulation") do |g|
   g.text("There are 3 real factors on data")

data/examples/parallel_analysis_tetrachoric.rb

@@ -3,7 +3,7 @@ $:.unshift(File.dirname(__FILE__)+'/../lib/')
 
 require 'statsample'
 samples=1000
-variables=30
+variables=10
 rng = GSL::Rng.alloc()
 f1=samples.times.collect {rng.ugaussian()}.to_scale
 f2=samples.times.collect {rng.ugaussian()}.to_scale

data/examples/reliability.rb

@@ -0,0 +1,12 @@
+#!/usr/bin/ruby
+$:.unshift(File.dirname(__FILE__)+'/../lib')
+require 'statsample'
+samples=100
+a=samples.times.map {rand(100)}.to_scale
+ds=Statsample::Dataset.new
+20.times do |i|
+        ds["v#{i}"]=a.collect {|v| v+rand(20)}.to_scale
+end
+ds.update_valid_data
+rel=Statsample::Reliability::ItemAnalysis.new(ds)
+puts rel.summary

data/lib/statsample.rb

@@ -22,7 +22,6 @@
 require 'matrix'
 require 'distribution'
 require 'dirty-memoize'
-gem 'reportbuilder','~>1.0'
 require 'reportbuilder'
 class Numeric
   def square ; self * self ; end
@@ -112,7 +111,7 @@ module Statsample
       false
     end
   end
-  VERSION = '0.10.0'
+  VERSION = '0.11.0'
   SPLIT_TOKEN = ","
   autoload(:Database, 'statsample/converters')
   autoload(:Anova, 'statsample/anova')

data/lib/statsample/anova.rb

@@ -4,161 +4,19 @@ module Statsample
       def oneway(*args)
         OneWay.new(*args)
       end      
+      def twoway(*args)
+        TwoWay.new(*args)
+      end      
+      
       def oneway_with_vectors(*args)
         OneWayWithVectors.new(*args)
       end
-    end
-    # = Generic Anova one-way.
-    # You could enter the sum of squares or the mean squares. You
-    # should enter the degrees of freedom for numerator and denominator.
-    # == Usage
-    #  anova=Statsample::Anova::OneWay(:ss_num=>10,:ss_den=>20, :df_num=>2, :df_den=>10, @name=>"ANOVA for....")
-    class OneWay
-      include GetText
-       bindtextdomain("statsample")
-      attr_reader :df_num, :df_den, :ss_num, :ss_den, :ms_num, :ms_den, :ms_total, :df_total, :ss_total
-      # Name of ANOVA Analisys
-      attr_accessor :name
-      attr_accessor :name_denominator
-      attr_accessor :name_numerator
-      def initialize(opts=Hash.new)
-        # First see if sum of squares or mean squares are entered
-        raise ArgumentError, "You should set d.f." unless (opts.has_key? :df_num and opts.has_key? :df_den)
-        @df_num=opts.delete :df_num
-        @df_den=opts.delete :df_den
-        @df_total=@df_num+@df_den
-        if(opts.has_key? :ss_num and opts.has_key? :ss_den)
-          @ss_num = opts.delete :ss_num
-          @ss_den =opts.delete :ss_den
-          @ms_num =@ss_num.quo(@df_num)
-          @ms_den =@ss_den.quo(@df_den) 
-        elsif (opts.has_key? :ms_num and opts.has_key? :ms_den)
-          @ms_num =opts.delete :ms_num
-          @ms_den =opts.delete :ms_den
-          @ss_num =@ms_num * @df_num
-          @ss_den =@ss_den * @df_den
-        end
-        @ss_total=@ss_num+@ss_den
-        @ms_total=@ms_num+@ms_den
-        opts_default={:name=>"ANOVA",
-                      :name_denominator=>"Explained variance",
-                      :name_numerator=>"Unexplained variance"}
-        @opts=opts_default.merge(opts)
-        opts_default.keys.each {|k|
-          send("#{k}=", @opts[k])
-        }
-        @f_object=Statsample::Test::F.new(@ms_num,@ms_den,@df_num,@df_den)
-      end
-      # F value
-      def f
-        @f_object.f
-      end
-      # P-value of F test
-      def probability
-        @f_object.probability
-      end
-      # Summary of Anova analysis
-      def summary
-        ReportBuilder.new(:no_title=>true).add(self).to_text
-      end
-      def report_building(builder) #:nodoc:
-        builder.section(:name=>@name) do |b|
-          report_building_table(b)
-        end
-      end
-      def report_building_table(builder) #:nodoc:
-        builder.table(:name=>_("%s Table") % @name, :header=>%w{source ss df ms f p}.map {|v| _(v)}) do |t|
-          t.row([@name_numerator, sprintf("%0.3f",@ss_num),   @df_num, sprintf("%0.3f",@ms_num),  sprintf("%0.3f",f), sprintf("%0.3f", probability)])
-          t.row([@name_denominator, sprintf("%0.3f",@ss_den),  @df_den, sprintf("%0.3f",@ms_den), "", ""])
-          t.row([_("Total"), sprintf("%0.3f",@ss_total),  @df_total, sprintf("%0.3f",@ms_total),"",""])
-        end
-      end
-
-    end
-    # One Way Anova with vectors
-    # Example:
-    #   v1=[2,3,4,5,6].to_scale
-    #   v2=[3,3,4,5,6].to_scale
-    #   v3=[5,3,1,5,6].to_scale
-    #   anova=Statsample::Anova::OneWayWithVectors.new([v1,v2,v3])
-    #   anova.f
-    #   => 0.0243902439024391
-    #   anova.probability
-    #   => 0.975953044203438
-    #   anova.sst 
-    #   => 32.9333333333333
-    #
-    class OneWayWithVectors < OneWay
-      # Show on summary Levene test
-      attr_accessor :summary_levene
-      # Show on summary descriptives for vectors
-      attr_accessor :summary_descriptives
-      def initialize(*args)
-        if args[0].is_a? Array
-          @vectors=args.shift
-        else
-          @vectors=args.find_all {|v| v.is_a? Statsample::Vector}
-          opts=args.find {|v| v.is_a? Hash}
-        end
-        opts||=Hash.new
-        opts_default={:name=>_("Anova One-Way"), 
-                      :name_numerator=>"Between Groups",
-                      :name_denominator=>"Within Groups",
-                      :summary_descriptives=>false,
-                      :summary_levene=>false}
-        @opts=opts_default.merge(opts).merge(:ss_num=>ssbg, :ss_den=>sswg, :df_num=>df_bg, :df_den=>df_wg)
-        super(@opts)
-      end
-      alias  :sst :ss_total 
-      def levene
-        Statsample::Test.levene(@vectors, :name=>_("Test of Homogeneity of variances (Levene)"))
-      end
-      # Total mean
-      def total_mean
-        sum=@vectors.inject(0){|a,v| a+v.sum}
-        sum.quo(n)
-      end
-      # Sum of squares within groups
-      def sswg
-        @sswg||=@vectors.inject(0) {|total,vector| total+vector.ss }
-      end
-      # Sum of squares between groups
-      def ssbg
-        m=total_mean
-        @vectors.inject(0) do |total,vector|
-          total + (vector.mean-m).square * vector.size 
-        end
-      end
-      # Degrees of freedom within groups
-      def df_wg
-        @dk_wg||=n-k
-      end
-      def k
-        @k||=@vectors.size
-      end
-      # Degrees of freedom between groups 
-      def df_bg
-          k-1
-      end
-      # Total number of cases
-      def n
-          @vectors.inject(0){|a,v| a+v.size}
-      end
-      def report_building(builder) # :nodoc:
-        builder.section(:name=>@name) do |s|
-          if summary_descriptives
-            s.table(:name=>_("Descriptives"),:header=>%w{Name N Mean SD Min Max}.map {|v| _(v)}) do |t|
-              @vectors.each do |v|
-                t.row [v.name, v.n_valid, "%0.4f" % v.mean, "%0.4f" %  v.sd, "%0.4f" % v.min, "%0.4f" % v.max]
-              end
-            end
-          end
-          if summary_levene
-            s.parse_element(levene)
-          end
-          report_building_table(s)
-        end
+      def twoway_with_vectors(*args)
+        TwoWayWithVectors.new(*args)
       end
+      
     end
   end
 end
+require 'statsample/anova/oneway'
+require 'statsample/anova/twoway'

data/lib/statsample/anova/oneway.rb

@@ -0,0 +1,151 @@
+module Statsample
+  module Anova
+    # = Generic Anova one-way.
+    # You could enter the sum of squares or the mean squares. You
+    # should enter the degrees of freedom for numerator and denominator.
+    # == Usage
+    #  anova=Statsample::Anova::OneWay(:ss_num=>10,:ss_den=>20, :df_num=>2, :df_den=>10, @name=>"ANOVA for....")
+    class OneWay
+      include Summarizable
+      attr_reader :df_num, :df_den, :ss_num, :ss_den, :ms_num, :ms_den, :ms_total, :df_total, :ss_total
+      # Name of ANOVA Analisys
+      attr_accessor :name
+      attr_accessor :name_denominator
+      attr_accessor :name_numerator
+      def initialize(opts=Hash.new)
+        # First see if sum of squares or mean squares are entered
+        raise ArgumentError, "You should set d.f." unless (opts.has_key? :df_num and opts.has_key? :df_den)
+        @df_num=opts.delete :df_num
+        @df_den=opts.delete :df_den
+        @df_total=@df_num+@df_den
+        if(opts.has_key? :ss_num and opts.has_key? :ss_den)
+          @ss_num = opts.delete :ss_num
+          @ss_den =opts.delete :ss_den
+          @ms_num =@ss_num.quo(@df_num)
+          @ms_den =@ss_den.quo(@df_den) 
+        elsif (opts.has_key? :ms_num and opts.has_key? :ms_den)
+          @ms_num =opts.delete :ms_num
+          @ms_den =opts.delete :ms_den
+          @ss_num =@ms_num * @df_num
+          @ss_den =@ss_den * @df_den
+        end
+        @ss_total=@ss_num+@ss_den
+        @ms_total=@ms_num+@ms_den
+        opts_default={:name=>"ANOVA",
+                      :name_denominator=>"Explained variance",
+                      :name_numerator=>"Unexplained variance"}
+        @opts=opts_default.merge(opts)
+        opts_default.keys.each {|k|
+          send("#{k}=", @opts[k])
+        }
+        @f_object=Statsample::Test::F.new(@ms_num,@ms_den,@df_num,@df_den)
+      end
+      # F value
+      def f
+        @f_object.f
+      end
+      # P-value of F test
+      def probability
+        @f_object.probability
+      end
+      def report_building(builder) #:nodoc:
+        builder.section(:name=>@name) do |b|
+          report_building_table(b)
+        end
+      end
+      def report_building_table(builder) #:nodoc:
+        builder.table(:name=>_("%s Table") % @name, :header=>%w{source ss df ms f p}.map {|v| _(v)}) do |t|
+          t.row([@name_numerator, sprintf("%0.3f",@ss_num),   @df_num, sprintf("%0.3f",@ms_num),  sprintf("%0.3f",f), sprintf("%0.3f", probability)])
+          t.row([@name_denominator, sprintf("%0.3f",@ss_den),  @df_den, sprintf("%0.3f",@ms_den), "", ""])
+          t.row([_("Total"), sprintf("%0.3f",@ss_total),  @df_total, sprintf("%0.3f",@ms_total),"",""])
+        end
+      end
+
+    end
+    # One Way Anova with vectors
+    # Example:
+    #   v1=[2,3,4,5,6].to_scale
+    #   v2=[3,3,4,5,6].to_scale
+    #   v3=[5,3,1,5,6].to_scale
+    #   anova=Statsample::Anova::OneWayWithVectors.new([v1,v2,v3])
+    #   anova.f
+    #   => 0.0243902439024391
+    #   anova.probability
+    #   => 0.975953044203438
+    #   anova.sst 
+    #   => 32.9333333333333
+    #
+    class OneWayWithVectors < OneWay
+      # Show on summary Levene test
+      attr_accessor :summary_levene
+      # Show on summary descriptives for vectors
+      attr_accessor :summary_descriptives
+      def initialize(*args)
+        if args[0].is_a? Array
+          @vectors=args.shift
+        else
+          @vectors=args.find_all {|v| v.is_a? Statsample::Vector}
+          opts=args.find {|v| v.is_a? Hash}
+        end
+        opts||=Hash.new
+        opts_default={:name=>_("Anova One-Way"), 
+                      :name_numerator=>"Between Groups",
+                      :name_denominator=>"Within Groups",
+                      :summary_descriptives=>false,
+                      :summary_levene=>false}
+        @opts=opts_default.merge(opts).merge(:ss_num=>ssbg, :ss_den=>sswg, :df_num=>df_bg, :df_den=>df_wg)
+        super(@opts)
+      end
+      alias  :sst :ss_total 
+      def levene
+        Statsample::Test.levene(@vectors, :name=>_("Test of Homogeneity of variances (Levene)"))
+      end
+      # Total mean
+      def total_mean
+        sum=@vectors.inject(0){|a,v| a+v.sum}
+        sum.quo(n)
+      end
+      # Sum of squares within groups
+      def sswg
+        @sswg||=@vectors.inject(0) {|total,vector| total+vector.ss }
+      end
+      # Sum of squares between groups
+      def ssbg
+        m=total_mean
+        @vectors.inject(0) do |total,vector|
+          total + (vector.mean-m).square * vector.size 
+        end
+      end
+      # Degrees of freedom within groups
+      def df_wg
+        @dk_wg||=n-k
+      end
+      def k
+        @k||=@vectors.size
+      end
+      # Degrees of freedom between groups 
+      def df_bg
+          k-1
+      end
+      # Total number of cases
+      def n
+          @vectors.inject(0){|a,v| a+v.size}
+      end
+      def report_building(builder) # :nodoc:
+        builder.section(:name=>@name) do |s|
+          if summary_descriptives
+            s.table(:name=>_("Descriptives"),:header=>%w{Name N Mean SD Min Max}.map {|v| _(v)}) do |t|
+              @vectors.each do |v|
+                t.row [v.name, v.n_valid, "%0.4f" % v.mean, "%0.4f" %  v.sd, "%0.4f" % v.min, "%0.4f" % v.max]
+              end
+            end
+          end
+          if summary_levene
+            s.parse_element(levene)
+          end
+          report_building_table(s)
+        end
+      end
+    end
+  end
+end