statsample 0.15.1 → 0.16.0

data/lib/statsample/matrix.rb

@@ -1,22 +1,22 @@
-require 'extendmatrix'
-
-
 class ::Matrix
   def to_matrix
     self
   end
-  alias :eigenpairs_ruby :eigenpairs 
+  if defined? :eigenpairs
+    alias_method :eigenpairs_ruby, :eigenpairs
+  end
   
   if Statsample.has_gsl?
     # Optimize eigenpairs of extendmatrix module using gsl
     def eigenpairs
       eigval, eigvec= GSL::Eigen.symmv(self.to_gsl)
       ep=eigval.size.times.map {|i|
-        [eigval[i], eigvec.get_col(i)]
+        [eigval[i], eigvec.get_col(i).to_a]
       }
       ep.sort{|a,b| a[0]<=>b[0]}.reverse
     end
   end
+  
   def eigenvalues
     eigen[:eigenvalues]
   end

data/lib/statsample/mle/logit.rb

@@ -57,9 +57,9 @@ module Statsample
     # x: Matrix (NxM)
     # y: Matrix (Nx1)
     # p: Matrix (Mx1)
-    def second_derivative(x,y,p)
+    def second_derivative(x,y,p2)
       raise "x.rows!=y.rows" if x.row_size!=y.row_size
-      raise "x.columns!=p.rows" if x.column_size!=p.row_size             
+      raise "x.columns!=p.rows" if x.column_size!=p2.row_size             
       n = x.row_size
       k = x.column_size
       sd = Array.new(k)
@@ -70,15 +70,16 @@ module Statsample
       end
       n.times do |i|
         row = x.row(i).to_a
-        p_m = p_minus(row,p)
+        p_m = p_minus(row,p2)
         k.times do |j|
           k.times do |l|
-          sd[j][l] -= p_m *(1-p_m)*row[j]*row[l]
+          sd[j][l] -= (p_m*(1-p_m)*row[j]*row[l])
           end
         end
       end
       Matrix.rows(sd, true)
     end
+    
     private
     def p_minus(x_row,p)
       value = 0.0;

data/lib/statsample/multiset.rb

@@ -3,7 +3,10 @@ module Statsample
   # but with different number of cases. 
   # This is the base class for stratified and cluster sampling estimation
   class Multiset
-    attr_reader :fields, :datasets
+    # Name of fields
+    attr_reader :fields
+    # Array with Statsample::Dataset
+    attr_reader :datasets
     # To create a multiset
     # * Multiset.new(%w{f1 f2 f3}) # define only fields
     def initialize(fields)

data/lib/statsample/vector.rb

@@ -783,8 +783,15 @@ module Statsample
       check_type :scale
       Math::sqrt( variance_population(m) )
     end
+
+    # Population average deviation (denominator N)
+    def average_deviation_population( m = nil )
+      check_type :scale
+      m ||= mean
+      ( @scale_data.inject( 0 ) { |a, x| ( x - m ).abs + a } ).quo( n_valid )
+    end
+
     # Sample Variance (denominator n-1)
-    
     def variance_sample(m=nil)
       check_type :scale
       m||=mean
@@ -792,7 +799,6 @@ module Statsample
     end
     
     # Sample Standard deviation (denominator n-1)
-    
     def standard_deviation_sample(m=nil)
         check_type :scale
         
@@ -898,6 +904,7 @@ module Statsample
     
     alias_method :sdp, :standard_deviation_population
     alias_method :sds, :standard_deviation_sample
+    alias_method :adp, :average_deviation_population
     alias_method :cov, :coefficient_of_variation
     alias_method :variance, :variance_sample    
     alias_method :sd, :standard_deviation_sample

data/references.txt

@@ -20,3 +20,4 @@ References
 * http://stattrek.com/Lesson6/SRS.aspx
 * http://www.cut-the-knot.org/do_you_know/AllPerm.shtml
 * http://www.gnu.org/software/gsl/manual/html_node/The-histogram-struct.html
+* http://www.taygeta.com/random/gaussian.html

data/test/test_anovaoneway.rb

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

data/test/test_factor.rb

@@ -1,4 +1,4 @@
-require(File.dirname(__FILE__)+'/helpers_tests.rb')
+require(File.expand_path(File.dirname(__FILE__)+'/helpers_tests.rb'))
 
 class StatsampleFactorTestCase < MiniTest::Unit::TestCase
   include Statsample::Fixtures
@@ -28,33 +28,38 @@ class StatsampleFactorTestCase < MiniTest::Unit::TestCase
     }
   end
   def test_parallelanalysis_with_data
-    samples=100
-    variables=10
-    iterations=50
-    rng = GSL::Rng.alloc()
-    f1=samples.times.collect {rng.ugaussian()}.to_scale
-    f2=samples.times.collect {rng.ugaussian()}.to_scale    
-    vectors={}
-    variables.times do |i|
-      if i<5
-        vectors["v#{i}"]=samples.times.collect {|nv|
-          f1[nv]*5+f2[nv]*2+rng.ugaussian()
-        }.to_scale
-      else
-        vectors["v#{i}"]=samples.times.collect {|nv|
-          f2[nv]*5+f1[nv]*2+rng.ugaussian()
-        }.to_scale
+    if Statsample.has_gsl?
+      samples=100
+      variables=10
+      iterations=50
+      rng = Distribution::Normal.rng_ugaussian
+      f1=samples.times.collect {rng.call}.to_scale
+      f2=samples.times.collect {rng.call}.to_scale    
+      vectors={}
+      variables.times do |i|
+        if i<5
+          vectors["v#{i}"]=samples.times.collect {|nv|
+            f1[nv]*5+f2[nv]*2+rng.call
+          }.to_scale
+        else
+          vectors["v#{i}"]=samples.times.collect {|nv|
+            f2[nv]*5+f1[nv]*2+rng.call
+          }.to_scale
+        end
+        
       end
+      ds=vectors.to_dataset
       
+      pa1=Statsample::Factor::ParallelAnalysis.new(ds, :bootstrap_method=>:data, :iterations=>iterations)
+      pa2=Statsample::Factor::ParallelAnalysis.with_random_data(samples,variables,:iterations=>iterations,:percentil=>95)
+      3.times do |n|
+        var="ev_0000#{n+1}"
+        assert_in_delta(pa1.ds_eigenvalues[var].mean,pa2.ds_eigenvalues[var].mean,0.04)
+      end
+    else
+      skip("Too slow without GSL")
     end
-    ds=vectors.to_dataset
     
-    pa1=Statsample::Factor::ParallelAnalysis.new(ds, :bootstrap_method=>:data, :iterations=>iterations)
-    pa2=Statsample::Factor::ParallelAnalysis.with_random_data(samples,variables,:iterations=>iterations,:percentil=>95)
-    3.times do |n|
-      var="ev_0000#{n+1}"
-      assert_in_delta(pa1.ds_eigenvalues[var].mean,pa2.ds_eigenvalues[var].mean,0.04)
-    end
   end
   def test_parallelanalysis
     pa=Statsample::Factor::ParallelAnalysis.with_random_data(305,8,:iterations=>100,:percentil=>95)

data/test/test_reliability_icc.rb

@@ -128,8 +128,6 @@ class StatsampleReliabilityIccTestCase < MiniTest::Unit::TestCase
             d=a.recode{|i|i+rand(4)-2}
             @ds={'a'=>a,'b'=>b,'c'=>c,'d'=>d}.to_dataset
             
-            
-            
             @icc=Statsample::Reliability::ICC.new(@ds)
             @r=Rserve::Connection.new
             @r.assign('ds',@ds)

data/test/test_vector.rb

@@ -326,6 +326,10 @@ class StatsampleTestVector < MiniTest::Unit::TestCase
     a=[1,2,3,4,5,6].to_vector(:scale)
     assert_equal(17.5, a.sum_of_squared_deviation)
   end
+  def test_average_deviation
+    a=[1,2,3,4,5,6,7,8,9].to_scale
+    assert_equal(20.quo(9), a.average_deviation_population)
+  end
   def test_samples
     srand(1)
     assert_equal(100,@c.sample_with_replacement(100).size)

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 15
-  - 1
-  version: 0.15.1
+  - 16
+  - 0
+  version: 0.16.0
 platform: ruby
 authors: 
 - Claudio Bustos
@@ -35,13 +35,14 @@ cert_chain:
   rpP0jjs0
   -----END CERTIFICATE-----
 
-date: 2010-10-20 00:00:00 -03:00
+date: 2010-11-13 00:00:00 -03:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: spreadsheet
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
@@ -53,9 +54,10 @@ dependencies:
   type: :runtime
   version_requirements: *id001
 - !ruby/object:Gem::Dependency 
-  name: svg-graph
+  name: reportbuilder
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
@@ -66,89 +68,110 @@ dependencies:
   type: :runtime
   version_requirements: *id002
 - !ruby/object:Gem::Dependency 
-  name: reportbuilder
+  name: minimization
   prerelease: false
   requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
         segments: 
-        - 1
         - 0
-        version: "1.0"
+        - 2
+        - 0
+        version: 0.2.0
   type: :runtime
   version_requirements: *id003
 - !ruby/object:Gem::Dependency 
-  name: minimization
+  name: fastercsv
   prerelease: false
   requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 2
-        - 0
-        version: 0.2.0
+        version: "0"
   type: :runtime
   version_requirements: *id004
 - !ruby/object:Gem::Dependency 
-  name: fastercsv
+  name: dirty-memoize
   prerelease: false
   requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
-    - - ">="
+    - - ~>
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        version: "0"
+        - 0
+        version: "0.0"
   type: :runtime
   version_requirements: *id005
 - !ruby/object:Gem::Dependency 
-  name: dirty-memoize
+  name: extendmatrix
   prerelease: false
   requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 0
-        version: "0.0"
+        - 3
+        - 1
+        version: 0.3.1
   type: :runtime
   version_requirements: *id006
 - !ruby/object:Gem::Dependency 
-  name: extendmatrix
+  name: statsample-bivariate-extension
   prerelease: false
   requirement: &id007 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
-    - - ~>
+    - - ">"
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 3
-        - 1
-        version: 0.3.1
+        version: "0"
   type: :runtime
   version_requirements: *id007
 - !ruby/object:Gem::Dependency 
-  name: statsample-bivariate-extension
+  name: rserve-client
   prerelease: false
   requirement: &id008 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ~>
       - !ruby/object:Gem::Version 
         segments: 
         - 0
-        - 13
-        - 0
-        version: 0.13.0
+        - 2
+        - 5
+        version: 0.2.5
   type: :runtime
   version_requirements: *id008
 - !ruby/object:Gem::Dependency 
-  name: rubyforge
+  name: rubyvis
   prerelease: false
   requirement: &id009 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        - 2
+        - 2
+        version: 0.2.2
+  type: :runtime
+  version_requirements: *id009
+- !ruby/object:Gem::Dependency 
+  name: rubyforge
+  prerelease: false
+  requirement: &id010 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -158,11 +181,12 @@ dependencies:
         - 4
         version: 2.0.4
   type: :development
-  version_requirements: *id009
+  version_requirements: *id010
 - !ruby/object:Gem::Dependency 
   name: shoulda
   prerelease: false
-  requirement: &id010 !ruby/object:Gem::Requirement 
+  requirement: &id011 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -170,11 +194,26 @@ dependencies:
         - 0
         version: "0"
   type: :development
-  version_requirements: *id010
+  version_requirements: *id011
+- !ruby/object:Gem::Dependency 
+  name: minitest
+  prerelease: false
+  requirement: &id012 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 2
+        - 0
+        version: "2.0"
+  type: :development
+  version_requirements: *id012
 - !ruby/object:Gem::Dependency 
   name: hoe
   prerelease: false
-  requirement: &id011 !ruby/object:Gem::Requirement 
+  requirement: &id013 !ruby/object:Gem::Requirement 
+    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -184,7 +223,7 @@ dependencies:
         - 2
         version: 2.6.2
   type: :development
-  version_requirements: *id011
+  version_requirements: *id013
 description: |-
   A suite for basic and advanced statistics on Ruby. Tested on Ruby 1.8.7, 1.9.1, 1.9.2 (April, 2010) and JRuby 1.4 (Ruby 1.8.7 compatible).
   
@@ -242,6 +281,7 @@ files:
 - examples/polychoric.rb
 - examples/principal_axis.rb
 - examples/reliability.rb
+- examples/scatterplot.rb
 - examples/t_test.rb
 - examples/tetrachoric.rb
 - examples/u_test.rb
@@ -278,11 +318,7 @@ files:
 - lib/statsample/factor/principalaxis.rb
 - lib/statsample/factor/rotation.rb
 - lib/statsample/graph.rb
-- lib/statsample/graph/gdchart.rb
-- lib/statsample/graph/svgboxplot.rb
-- lib/statsample/graph/svggraph.rb
-- lib/statsample/graph/svghistogram.rb
-- lib/statsample/graph/svgscatterplot.rb
+- lib/statsample/graph/scatterplot.rb
 - lib/statsample/histogram.rb
 - lib/statsample/matrix.rb
 - lib/statsample/mle.rb
@@ -356,7 +392,6 @@ files:
 - test/test_statistics.rb
 - test/test_stest.rb
 - test/test_stratified.rb
-- test/test_svg_graph.rb
 - test/test_test_f.rb
 - test/test_test_t.rb
 - test/test_umannwhitney.rb
@@ -392,6 +427,7 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -399,6 +435,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       - 0
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
   requirements: 
   - - ">="
     - !ruby/object:Gem::Version 
@@ -408,7 +445,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: ruby-statsample
-rubygems_version: 1.3.6
+rubygems_version: 1.3.7
 signing_key: 
 specification_version: 3
 summary: A suite for basic and advanced statistics on Ruby
@@ -423,7 +460,6 @@ test_files:
 - test/test_anovawithvectors.rb
 - test/test_crosstab.rb
 - test/test_distribution.rb
-- test/test_svg_graph.rb
 - test/test_rserve_extension.rb
 - test/test_csv.rb
 - test/test_matrix.rb