statsample 0.10.0 → 0.11.0

data/lib/statsample/vector.rb

@@ -100,7 +100,7 @@ module Statsample
     end
     # Raises an exception if type of vector is inferior to t type
     def check_type(t)
-    raise NoMethodError if (t==:scale and @type!=:scale) or (t==:ordinal and @type==:nominal) or (t==:date)
+      raise NoMethodError if (t==:scale and @type!=:scale) or (t==:ordinal and @type==:nominal) or (t==:date)
     end
     private :check_type
 
@@ -153,10 +153,11 @@ module Statsample
     end
     # Returns a new vector, with data modified by block.
     # Equivalent to create a Vector after #collect on data 
-    def recode
-    @data.collect{|x|
-      yield x
-    }.to_vector(@type)
+    def recode(type=nil)
+      type||=@type
+      @data.collect{|x|
+        yield x
+      }.to_vector(type)
     end
     # Modifies current vector, with data modified by block.
     # Equivalent to #collect! on @data 

data/test/{test_helpers.rb → helpers_tests.rb}

@@ -35,4 +35,6 @@ module MiniTest
     end
   end
 end
+
 MiniTest::Unit.autorun
+

data/test/test_anovaoneway.rb

@@ -1,5 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
-
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 class StatsampleAnovaOneWayTestCase < MiniTest::Unit::TestCase
   context(Statsample::Anova::OneWay) do
     setup do

data/test/test_anovatwoway.rb

@@ -0,0 +1,38 @@
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
+class StatsampleAnovaTwoWayTestCase < MiniTest::Unit::TestCase
+  context(Statsample::Anova::TwoWay) do
+    setup do
+      @ss_a=192.2
+      @ss_b=57.8
+      @ss_axb=168.2
+      @ss_within=75.6
+      @df_a=@df_b=1
+      @df_within=16
+      @anova=Statsample::Anova::TwoWay.new(:ss_a=>@ss_a, :ss_b=>@ss_b, :ss_axb=>@ss_axb, :ss_within=>@ss_within , :df_a=>@df_a, :df_b=>@df_b, :df_within=>@df_within)
+    end
+    should "Statsample::Anova.twoway respond to #twoway" do
+    assert(Statsample::Anova.respond_to? :twoway)
+    end
+    should "return correct value for ms_a, ms_b and ms_axb" do
+      assert_in_delta(192.2, @anova.ms_a, 0.01)
+      assert_in_delta(57.8, @anova.ms_b, 0.01)
+      assert_in_delta(168.2, @anova.ms_axb, 0.01)
+      
+    end
+    should "return correct value for f " do
+      assert_in_delta(40.68, @anova.f_a, 0.01)
+      assert_in_delta(12.23, @anova.f_b, 0.01)
+      assert_in_delta(35.60, @anova.f_axb, 0.01)
+    end
+    should "return correct value for probability for f " do
+      assert(@anova.f_a_probability < 0.05)
+      assert(@anova.f_b_probability < 0.05)
+      assert(@anova.f_axb_probability < 0.05)
+    end
+
+    should "respond to summary" do
+      assert(@anova.respond_to? :summary)
+      assert(@anova.summary.size>0)
+    end
+  end
+end

data/test/test_anovatwowaywithdataset.rb

@@ -0,0 +1,49 @@
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
+# Reference:
+# * http://www.uwsp.edu/psych/Stat/13/anova-2w.htm#III
+class StatsampleAnovaTwoWayWithVectorsTestCase < MiniTest::Unit::TestCase
+  context(Statsample::Anova::TwoWayWithVectors) do
+    setup do
+      @pa=[5,4,3,4,2,18,19,14,12,15,6,7,5,8,4,6,9,5,9,3].to_scale
+      @pa.name="Passive Avoidance"
+      @a=[0,0,0,0,0,1,1,1,1,1,0,0,0,0,0,1,1,1,1,1].to_vector
+      @a.labels={0=>'0%',1=>'35%'}
+      @a.name='Diet'
+      @b=[0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1].to_vector
+      @b.labels={0=>'Young',1=>'Older'}
+      @b.name="Age"
+      @anova=Statsample::Anova::TwoWayWithVectors.new(:a=>@a,:b=>@b, :dependent=>@pa)
+    end
+    should "Statsample::Anova respond to #twoway_with_vectors" do
+    assert(Statsample::Anova.respond_to? :twoway_with_vectors)
+    end
+    should "#new returns the same as Statsample::Anova.twoway_with_vectors" do
+      @anova2=Statsample::Anova.twoway_with_vectors(:a=>@a,:b=>@b, :dependent=>@pa)
+      assert_equal(@anova.summary, @anova2.summary)
+    end
+    should "return correct value for ms_a, ms_b and ms_axb" do
+      assert_in_delta(192.2, @anova.ms_a, 0.01)
+      assert_in_delta(57.8, @anova.ms_b, 0.01)
+      assert_in_delta(168.2, @anova.ms_axb, 0.01)
+      
+    end
+    should "return correct value for f " do
+      assert_in_delta(40.68, @anova.f_a, 0.01)
+      assert_in_delta(12.23, @anova.f_b, 0.01)
+      assert_in_delta(35.60, @anova.f_axb, 0.01)
+    end
+    should "return correct value for probability for f " do
+      assert(@anova.f_a_probability < 0.05)
+      assert(@anova.f_b_probability < 0.05)
+      assert(@anova.f_axb_probability < 0.05)
+    end
+
+    should "respond to summary" do
+      
+      @anova.summary_descriptives=true
+      @anova.summary_levene=true
+      assert(@anova.respond_to? :summary)
+      assert(@anova.summary.size>0)
+    end
+  end
+end

data/test/test_anovawithvectors.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleAnovaOneWayWithVectorsTestCase < MiniTest::Unit::TestCase
   context(Statsample::Anova::OneWayWithVectors) do

data/test/test_bivariate.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleBivariateTestCase < MiniTest::Unit::TestCase
   def test_sum_of_squares

data/test/test_bivariate_polychoric.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleBivariatePolychoricTestCase < MiniTest::Unit::TestCase
   context Statsample::Bivariate do

data/test/test_codification.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleCodificationTestCase < MiniTest::Unit::TestCase
 

data/test/test_combination.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleCombinationTestCase < MiniTest::Unit::TestCase
   def test_basic

data/test/test_crosstab.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleCrosstabTestCase < MiniTest::Unit::TestCase
 

data/test/test_csv.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleCSVTestCase < MiniTest::Unit::TestCase
   def setup

data/test/test_dataset.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleDatasetTestCase < MiniTest::Unit::TestCase
   def setup
@@ -260,6 +260,7 @@ class StatsampleDatasetTestCase < MiniTest::Unit::TestCase
     assert_same(ds1['v1'], ds2['v1'])
     assert_equal(ds1.fields,ds2.fields)
     assert_not_same(ds1.fields,ds2.fields)
+    assert_equal(ds1.cases,ds2.cases)
 
     # partial clone
     ds3=ds1.clone('v1')
@@ -269,6 +270,8 @@ class StatsampleDatasetTestCase < MiniTest::Unit::TestCase
     assert_equal(ds3['v1'],ds_exp['v1'])
     assert_same(ds3['v1'],ds_exp['v1'])
     assert_equal(ds3.fields,ds_exp.fields)
+    assert_equal(ds3.cases,ds_exp.cases)
+
     assert_not_same(ds3.fields,ds_exp.fields)
      
   end
@@ -281,6 +284,8 @@ class StatsampleDatasetTestCase < MiniTest::Unit::TestCase
     assert_not_same(ds1,ds2)
     assert_equal(ds1['v1'],ds2['v1'])
     assert_not_same(ds1['v1'],ds2['v1'])
+    assert_equal(ds1.cases,ds2.cases)
+
     assert_equal(ds1.fields,ds2.fields)
     assert_not_same(ds1.fields,ds2.fields)
     ds1['v1'].type=:scale
@@ -292,6 +297,8 @@ class StatsampleDatasetTestCase < MiniTest::Unit::TestCase
     assert_equal(ds3['v1'],ds_exp['v1'])
     assert_not_same(ds3['v1'],ds_exp['v1'])
     assert_equal(ds3.fields,ds_exp.fields)
+    assert_equal(ds3.cases,ds_exp.cases)
+
     assert_not_same(ds3.fields,ds_exp.fields)
 
 

data/test/test_distribution.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 require 'distribution'
 

data/test/test_dominance_analysis.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleDominanceAnalysisTestCase < MiniTest::Unit::TestCase
   def test_dominance_univariate
@@ -21,6 +21,7 @@ class StatsampleDominanceAnalysisTestCase < MiniTest::Unit::TestCase
       assert_equal(expected_dominances[i], da.conditional_dominance_pairwise(a[0],a[1]))
       assert_equal(expected_g_dominances[i], da.general_dominance_pairwise(a[0],a[1]))
     end
+    assert(da.summary.size>0)
   end
   def test_dominance_multivariate
     m=Matrix[[1.0, -0.19, -0.358, -0.343, 0.359, 0.257], [-0.19, 1.0, 0.26, 0.29, -0.11, -0.11], [-0.358, 0.26, 1.0, 0.54, -0.49, -0.23], [-0.343, 0.29, 0.54, 1.0, -0.22, -0.41], [0.359, -0.11, -0.49, -0.22, 1.0, 0.62], [0.257, -0.11, -0.23, -0.41, 0.62, 1]]

data/test/test_factor.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleFactorTestCase < MiniTest::Unit::TestCase
   # Tested with SPSS and R

data/test/test_ggobi.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 require 'ostruct'
 class StatsampleGGobiTestCase < MiniTest::Unit::TestCase
 

data/test/test_gsl.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleGSLTestCase < MiniTest::Unit::TestCase

data/test/test_histogram.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 

data/test/test_logit.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleLogitTestCase < MiniTest::Unit::TestCase
   def test_logit_1

data/test/test_matrix.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleMatrixTestCase < MiniTest::Unit::TestCase

data/test/test_mle.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleMLETestCase < MiniTest::Unit::TestCase
   def setup

data/test/test_multiset.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleMultisetTestCase < MiniTest::Unit::TestCase

data/test/test_permutation.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsamplePermutationTestCase < MiniTest::Unit::TestCase

data/test/test_regression.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleRegressionTestCase < MiniTest::Unit::TestCase
   context "Example with missing data" do
@@ -19,7 +19,7 @@ class StatsampleRegressionTestCase < MiniTest::Unit::TestCase
       assert_in_delta(0.132, @lr.constant,0.001,"constant")
       assert_in_delta(0.195, @lr.coeffs_se['x'],0.001,"coeff x se")
       assert_in_delta(0.064, @lr.constant_se,0.001,"constant se")
-    end
+  end
   end
   def test_parameters
     @x=[13,20,10,33,15].to_vector(:scale)
@@ -45,7 +45,6 @@ class StatsampleRegressionTestCase < MiniTest::Unit::TestCase
     ds={'a'=>a,'b'=>b,'y'=>y}.to_dataset
     lr=Statsample::Regression::Multiple::RubyEngine.new(ds,'y')
     assert(lr.summary.size>0)
-    
   end
   def test_multiple_dependent
     complete=Matrix[
@@ -152,7 +151,7 @@ class StatsampleRegressionTestCase < MiniTest::Unit::TestCase
     assert_in_delta(639.6,lr.sst,0.001)
     assert_in_delta(583.76,lr.ssr,0.001)
     assert_in_delta(55.840,lr.sse,0.001)
-
+	assert(lr.summary.size>0, "#{name} without summary")
   end
   def model_test(lr,name='undefined')
     model_test_matrix(lr,name)

data/test/test_reliability.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleReliabilityTestCase < MiniTest::Unit::TestCase
@@ -12,6 +12,7 @@ class StatsampleReliabilityTestCase < MiniTest::Unit::TestCase
         @n_variables.times do |i|
           @ds[i]=base.collect {|v| v+rand()}.to_scale
         end
+        
         @ds.update_valid_data
         @k=@ds.fields.size
         @cm=Statsample::Bivariate.covariance_matrix(@ds)
@@ -94,11 +95,23 @@ class StatsampleReliabilityTestCase < MiniTest::Unit::TestCase
         @x4=[1,2,3,4,4,4,4,3,4,4,5,30].to_vector(:scale)
         @ds={'x1'=>@x1,'x2'=>@x2,'x3'=>@x3,'x4'=>@x4}.to_dataset
         @ia=Statsample::Reliability::ItemAnalysis.new(@ds)
-
+        @cov_matrix=Statsample::Bivariate.covariance_matrix(@ds)
       end     
       should "return correct values for item analysis" do 
         assert_in_delta(0.980,@ia.alpha,0.001)
         assert_in_delta(0.999,@ia.alpha_standarized,0.001)
+        var_mean=4.times.map{|m| @cov_matrix[m,m]}.to_scale.mean 
+        assert_in_delta(var_mean, @ia.variances_mean)
+        
+        covariances=[]
+        4.times.each {|i|
+          4.times.each {|j|
+            if i!=j 
+              covariances.push(@cov_matrix[i,j])
+            end
+          }
+        }
+        assert_in_delta(covariances.to_scale.mean, @ia.covariances_mean)
         assert_in_delta(0.999,@ia.item_total_correlation()['x1'],0.001)
         assert_in_delta(1050.455,@ia.stats_if_deleted()['x1'][:variance_sample],0.001)
       end

data/test/test_resample.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleResampleTestCase < MiniTest::Unit::TestCase

data/test/test_srs.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleSrsTestCase < MiniTest::Unit::TestCase

data/test/test_statistics.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleStatisicsTestCase < MiniTest::Unit::TestCase
 

data/test/test_stest.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleTestTestCase < MiniTest::Unit::TestCase

data/test/test_stratified.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleStratifiedTestCase < MiniTest::Unit::TestCase

data/test/test_svg_graph.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 require('statsample/graph')
 class StatsampleSvgGraphTestCase < MiniTest::Unit::TestCase
 

data/test/test_test_f.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleTestFTestCase < MiniTest::Unit::TestCase
   context(Statsample::Test::F) do 

data/test/test_test_t.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 class StatsampleTestTTestCase < MiniTest::Unit::TestCase
   include Statsample::Test

data/test/test_umannwhitney.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/test_helpers.rb')
+require(File.dirname(__FILE__)+'/helpers_tests.rb')
 
 
 class StatsampleUMannWhitneyTestCase < MiniTest::Unit::TestCase