statsample 0.11.1 → 0.11.2

data.tar.gz.sig

@@ -1,2 +1,2 @@
-
-�YH��P���&�D�ֆ=T����z���p��?^u)�~�)�
+��2�>Pfrg�*}�1���=�1�B�xQ*2���m��yН�:�qW3W�n�/��y�K��Ub)�4�KU�ާ>�B2�q����K�|Z�=V8؎���ݕҕ⹳:<��	R�K��
+�VW��}�5�j�}�i������$�RR�U�����^c�B�Ҽ�^h��>*���������@�����QhR��Τ�v��[��W3�\���]{!��\P��J��M�D�,�Hq-��b��%g�{U5

data/History.txt

@@ -1,3 +1,6 @@
+=== 0.11.2 / 2010-05-05
+* Updated dependency for 'extendedmatrix' to 0.2 (Matrix#build method)
+
 === 0.11.1 / 2010-05-04
 * Removed Matrix almost all Matrix extensions and replaced by dependency on 'extendmatrix' gem
 * Added dependency to gsl >=1.12.109. Polychoric with joint method fails without this explicit dependency

data/Rakefile

@@ -18,7 +18,9 @@ task :lint do
   }
 end
 
-
+task :release do
+system %{git push origin master}
+end
 desc "Update pot/po files."
 task :updatepo do
   require 'gettext/tools'
@@ -37,7 +39,7 @@ h=Hoe.spec('statsample') do
   #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"] << ["statistics2", "~>0.54"] << ["extendmatrix","~>0.1"] << ["gsl", "~>1.12.109"]
+	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"] << ["extendmatrix","~>0.2.0"] << ["gsl", "~>1.12.109"]
 	self.clean_globs << "test/images/*" << "demo/item_analysis/*" << "demo/Regression"
 	self.need_rdoc=false
 end

data/lib/statsample.rb

@@ -111,7 +111,7 @@ module Statsample
       false
     end
   end
-  VERSION = '0.11.1'
+  VERSION = '0.11.2'
   SPLIT_TOKEN = ","
   autoload(:Database, 'statsample/converters')
   autoload(:Anova, 'statsample/anova')

data/lib/statsample/factor/pca.rb

@@ -34,20 +34,23 @@ module Factor
     # Number of factors. Set by default to the number of factors
     # with eigen values > 1
     attr_accessor :m
+    # Use GSL if available
+    attr_accessor :use_gsl
     include GetText
     bindtextdomain("statsample")
     
     def initialize(matrix ,opts=Hash.new)
-      if matrix.respond_to? :to_gsl
-        matrix=matrix.to_gsl
-      end
+	@use_gsl=nil
       @name=_("Principal Component Analysis")
       @matrix=matrix
-      @n_variables=@matrix.size1
+      @n_variables=@matrix.column_size
       @m=nil
       opts.each{|k,v|
         self.send("#{k}=",v) if self.respond_to? k
       }
+      if @use_gsl.nil?
+        @use_gsl=Statsample.has_gsl?
+      end
       calculate_eigenpairs
       if @m.nil?
         # Set number of factors with eigenvalues > 1
@@ -67,9 +70,9 @@ module Factor
     # Feature vector for m factors
     def feature_vector(m=nil)
       m||=@m
-      omega_m=GSL::Matrix.zeros(@n_variables, m)
+      omega_m=::Matrix.build(@n_variables, m) {0}
       m.times do |i|
-        omega_m.set_col(i, @eigenpairs[i][1])
+        omega_m.column= i, @eigenpairs[i][1]
       end
       omega_m
     end
@@ -84,13 +87,13 @@ module Factor
     def component_matrix(m=nil)
       m||=@m
       raise "m should be > 0" if m<1
-      omega_m=GSL::Matrix.zeros(@n_variables, m)
+      omega_m=::Matrix.build(@n_variables, m) {0}
       gammas=[]
       m.times {|i|
-        omega_m.set_col(i, @eigenpairs[i][1])
+        omega_m.column=i, @eigenpairs[i][1]
         gammas.push(Math::sqrt(@eigenpairs[i][0]))
       }
-      gamma_m=GSL::Matrix.diagonal(gammas)
+      gamma_m=::Matrix.diagonal(*gammas)
       (omega_m*(gamma_m)).to_matrix
     end
     # Communalities for all variables given m factors
@@ -112,13 +115,30 @@ module Factor
     end
     
     def calculate_eigenpairs
-      eigval, eigvec= GSL::Eigen.symmv(@matrix)
+      if @use_gsl
+        calculate_eigenpairs_gsl
+      else
+        calculate_eigenpairs_ruby
+      end
+    end
+  
+    def calculate_eigenpairs_ruby
+      eigval, eigvec= @matrix.eigenvaluesJacobi, @matrix.cJacobiV
       @eigenpairs={}
-      eigval.each_index {|i|
-        @eigenpairs[eigval[i]]=eigvec.get_col(i)
+      eigval.to_a.each_index {|i|
+        @eigenpairs[eigval[i]]=eigvec.column(i)
       }
       @eigenpairs=@eigenpairs.sort.reverse
     end
+    def calculate_eigenpairs_gsl
+      eigval, eigvec= GSL::Eigen.symmv(@matrix.to_gsl)
+        @eigenpairs={}
+        eigval.each_index {|i|
+          @eigenpairs[eigval[i]]=eigvec.get_col(i)
+        }
+        @eigenpairs=@eigenpairs.sort.reverse
+    end
+    
     def summary
       ReportBuilder.new(:no_title=>true).add(self).to_text
     end

data/lib/statsample/matrix.rb

@@ -2,6 +2,10 @@ require 'extendmatrix'
 
 
 class ::Matrix
+  def to_matrix
+    self
+  end
+  
   def to_gsl
     out=[]
     self.row_size.times{|i|
@@ -13,6 +17,9 @@ end
 
 module GSL
   class Matrix
+    def to_gsl
+      self
+    end
     def to_matrix
       rows=self.size1
       cols=self.size2

data/test/test_factor.rb

@@ -3,15 +3,22 @@ require(File.dirname(__FILE__)+'/helpers_tests.rb')
 class StatsampleFactorTestCase < MiniTest::Unit::TestCase
   # Tested with SPSS and R
   def test_pca
-    if Statsample.has_gsl?
-      require 'gsl'
       a=[2.5, 0.5, 2.2, 1.9, 3.1, 2.3, 2.0, 1.0, 1.5, 1.1].to_scale
       b=[2.4, 0.7, 2.9, 2.2, 3.0, 2.7, 1.6, 1.1, 1.6, 0.9].to_scale
       a.recode! {|c| c-a.mean}
       b.recode! {|c| c-b.mean}
       ds={'a'=>a,'b'=>b}.to_dataset
       cov_matrix=Statsample::Bivariate.covariance_matrix(ds)
-      pca=Statsample::Factor::PCA.new(cov_matrix)
+      if Statsample.has_gsl?
+        pca=Statsample::Factor::PCA.new(cov_matrix,:use_gsl=>true)
+        pca_set(pca)
+      else
+        skip("Eigenvalues could be calculated with GSL (requires gsl)")
+      end
+      pca=Statsample::Factor::PCA.new(cov_matrix,:use_gsl=>false)
+      pca_set(pca)
+  end
+  def pca_set(pca)
       expected_eigenvalues=[1.284, 0.0490]
       expected_eigenvalues.each_with_index{|ev,i|
         assert_in_delta(ev,pca.eigenvalues[i],0.001)
@@ -21,31 +28,25 @@ class StatsampleFactorTestCase < MiniTest::Unit::TestCase
         assert_in_delta(ev,pca.communalities[i],0.001)
       }
       expected_cm=[0.768, 0.833]
-
       obs=pca.component_matrix(1).column(0).to_a
       expected_cm.each_with_index{|ev,i|
         assert_in_delta(ev,obs[i],0.001)
       }
 
-      expected_fm_1=GSL::Matrix[[0.677], [0.735]]
-      expected_fm_2=GSL::Matrix[[0.677,0.735], [0.735, -0.677]]
+      expected_fm_1=::Matrix[[0.677], [0.735]]
+      expected_fm_2=::Matrix[[0.677,0.735], [0.735, -0.677]]
       _test_matrix(expected_fm_1,pca.feature_vector(1))
       _test_matrix(expected_fm_2,pca.feature_vector(2))
       assert(pca.summary)
-    else
-      skip "PCA not tested. Requires GSL"
-    end
   end
 
   # Tested with R
   def test_principalaxis
-    if Statsample.has_gsl?
-      require 'gsl'
-      matrix=Matrix[
+      matrix=::Matrix[
       [1.0, 0.709501601093587, 0.877596585880047, 0.272219316266807],  [0.709501601093587, 1.0, 0.291633797330304, 0.871141831433844], [0.877596585880047, 0.291633797330304, 1.0, -0.213373722977167], [0.272219316266807, 0.871141831433844, -0.213373722977167, 1.0]]
       fa=Statsample::Factor::PrincipalAxis.new(matrix,:m=>1)
       
-      cm=Matrix[[0.923],[0.912],[0.507],[0.483]].to_gsl
+      cm=::Matrix[[0.923],[0.912],[0.507],[0.483]]
       
       _test_matrix(cm,fa.component_matrix)
       
@@ -59,42 +60,32 @@ class StatsampleFactorTestCase < MiniTest::Unit::TestCase
       fa=Statsample::Factor::PrincipalAxis.new(matrix,:smc=>false)
       assert_raise RuntimeError do
         fa.iterate
-
       end
+      assert(fa.summary.size>0)
 
-
-
-      assert(fa.summary)
-
-    else
-      skip "Principal Axis not tested. Requires GSL"
-    end
   end
 
 
   def test_rotation_varimax
-    if Statsample.has_gsl?
-      a = Matrix[ [ 0.4320,  0.8129,  0.3872]  ,
-        [0.7950, -0.5416,  0.2565]  ,
-        [0.5944,  0.7234, -0.3441],
-      [0.8945, -0.3921, -0.1863] ]
+    a = Matrix[ [ 0.4320,  0.8129,  0.3872]  ,
+      [0.7950, -0.5416,  0.2565]  ,
+      [0.5944,  0.7234, -0.3441],
+    [0.8945, -0.3921, -0.1863] ]
 
-      expected= Matrix[[-0.0204423,     0.938674,    -0.340334],
-        [0.983662, 0.0730206, 0.134997],
-        [0.0826106, 0.435975, -0.893379],
-      [0.939901, -0.0965213, -0.309596]].to_gsl
-      varimax=Statsample::Factor::Varimax.new(a)
-      assert(!varimax.rotated.nil?, "Rotated shouldn't be empty")
-      assert(!varimax.component_transformation_matrix.nil?, "Component matrix shouldn't be empty")
-      assert(!varimax.h2.nil?,"H2 shouldn't be empty")
-      _test_matrix(expected,varimax.rotated)
-    else
-      skip "Rotation not tested. Requires GSL"
-    end
+    expected= Matrix[[-0.0204423,     0.938674,    -0.340334],
+      [0.983662, 0.0730206, 0.134997],
+      [0.0826106, 0.435975, -0.893379],
+    [0.939901, -0.0965213, -0.309596]]
+    varimax=Statsample::Factor::Varimax.new(a)
+    assert(!varimax.rotated.nil?, "Rotated shouldn't be empty")
+    assert(!varimax.component_transformation_matrix.nil?, "Component matrix shouldn't be empty")
+    assert(!varimax.h2.nil?, "H2 shouldn't be empty")
+    
+    _test_matrix(expected,varimax.rotated)
   end
   def _test_matrix(a,b)
-    a.size1.times {|i|
-      a.size2.times {|j|
+    a.row_size.times {|i|
+      a.column_size.times {|j|
         assert_in_delta(a[i,j], b[i,j],0.001)
       }
     }

metadata

@@ -5,8 +5,8 @@ version: !ruby/object:Gem::Version
   segments: 
   - 0
   - 11
-  - 1
-  version: 0.11.1
+  - 2
+  version: 0.11.2
 platform: ruby
 authors: 
 - Claudio Bustos
@@ -35,7 +35,7 @@ cert_chain:
   rpP0jjs0
   -----END CERTIFICATE-----
 
-date: 2010-05-04 00:00:00 -04:00
+date: 2010-05-05 00:00:00 -04:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -139,8 +139,9 @@ dependencies:
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 1
-        version: "0.1"
+        - 2
+        - 0
+        version: 0.2.0
   type: :runtime
   version_requirements: *id008
 - !ruby/object:Gem::Dependency