statsample 1.5.0 → 2.0.0

data/test/test_wilcoxonsignedrank.rb

@@ -5,8 +5,8 @@ class StatsampleUMannWhitneyTestCase < Minitest::Test
   context Statsample::Test::WilcoxonSignedRank do
     context 'Example 1' do
       setup do
-        @v1 = [110, 122, 125, 120, 140, 124, 123, 137, 135, 145].to_numeric
-        @v2 = [125, 115, 130, 140, 140, 115, 140, 125, 140, 135].to_numeric
+        @v1 = Daru::Vector.new([110, 122, 125, 120, 140, 124, 123, 137, 135, 145])
+        @v2 = Daru::Vector.new([125, 115, 130, 140, 140, 115, 140, 125, 140, 135])
         @u = Statsample::Test::WilcoxonSignedRank.new(@v1, @v2)
       end
       should 'have same result using class or Test#u_mannwhitney' do
@@ -34,8 +34,8 @@ class StatsampleUMannWhitneyTestCase < Minitest::Test
 
     context 'Example 2' do
       setup do
-        @v2 = [78, 24, 64, 45, 64, 52, 30, 50, 64, 50, 78, 22, 84, 40, 90, 72].to_numeric
-        @v1 = [78, 24, 62, 48, 68, 56, 25, 44, 56, 40, 68, 36, 68, 20, 58, 32].to_numeric
+        @v2 = Daru::Vector.new([78, 24, 64, 45, 64, 52, 30, 50, 64, 50, 78, 22, 84, 40, 90, 72])
+        @v1 = Daru::Vector.new([78, 24, 62, 48, 68, 56, 25, 44, 56, 40, 68, 36, 68, 20, 58, 32])
         @u = Statsample::Test::WilcoxonSignedRank.new(@v1, @v2)
       end
       should 'have same result using class or Test#u_mannwhitney' do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: statsample
 version: !ruby/object:Gem::Version
-  version: 1.5.0
+  version: 2.0.0
 platform: ruby
 authors:
 - Claudio Bustos
@@ -9,22 +9,36 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-11 00:00:00.000000000 Z
+date: 2015-06-22 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: daru
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
 - !ruby/object:Gem::Dependency
   name: spreadsheet
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.6.5
+        version: 1.0.3
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.6.5
+        version: 1.0.3
 - !ruby/object:Gem::Dependency
   name: reportbuilder
   requirement: !ruby/object:Gem::Requirement
@@ -73,14 +87,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.3'
+        version: '0.4'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.3'
+        version: '0.4'
 - !ruby/object:Gem::Dependency
   name: rserve-client
   requirement: !ruby/object:Gem::Requirement
@@ -101,14 +115,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.5.0
+        version: 0.6.1
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.5.0
+        version: 0.6.1
 - !ruby/object:Gem::Dependency
   name: distribution
   requirement: !ruby/object:Gem::Requirement
@@ -143,14 +157,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '1.10'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '1.10'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
@@ -213,14 +227,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.5'
+        version: '5.7'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '5.5'
+        version: '5.7'
 - !ruby/object:Gem::Dependency
   name: gettext
   requirement: !ruby/object:Gem::Requirement
@@ -249,6 +263,34 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: nmatrix
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.1.0
+- !ruby/object:Gem::Dependency
+  name: gsl-nmatrix
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.17.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.17.0
 description: |
   A suite for basic and advanced statistics on Ruby. Tested on CRuby 1.9.3, 2.0.0
   and 2.1.1. See `.travis.yml` for more information.
@@ -257,7 +299,6 @@ description: |
 
   - Descriptive statistics: frequencies, median, mean,
   standard error, skew, kurtosis (and many others).
-  - Imports and exports datasets from and to Excel, CSV and plain text files.
   - Correlations: Pearson's r, Spearman's rank correlation (rho), point biserial,
   tau a, tau b and  gamma. Tetrachoric and Polychoric correlation provides by
   statsample-bivariate-extension gem.
@@ -287,8 +328,10 @@ extra_rdoc_files:
 - README.md
 - references.txt
 files:
+- ".build.sh"
 - ".gitignore"
 - ".travis.yml"
+- CONTRIBUTING.md
 - Gemfile
 - History.txt
 - LICENSE.txt
@@ -344,6 +387,7 @@ files:
 - lib/statsample/converter/spss.rb
 - lib/statsample/converters.rb
 - lib/statsample/crosstab.rb
+- lib/statsample/daru.rb
 - lib/statsample/dataset.rb
 - lib/statsample/dominanceanalysis.rb
 - lib/statsample/dominanceanalysis/bootstrap.rb
@@ -374,7 +418,6 @@ files:
 - lib/statsample/reliability/scaleanalysis.rb
 - lib/statsample/reliability/skillscaleanalysis.rb
 - lib/statsample/resample.rb
-- lib/statsample/rserve_extension.rb
 - lib/statsample/shorthand.rb
 - lib/statsample/srs.rb
 - lib/statsample/test.rb
@@ -387,7 +430,6 @@ files:
 - lib/statsample/test/umannwhitney.rb
 - lib/statsample/test/wilcoxonsignedrank.rb
 - lib/statsample/vector.rb
-- lib/statsample/vector/gsl.rb
 - lib/statsample/version.rb
 - po/es/statsample.mo
 - po/es/statsample.po
@@ -397,11 +439,7 @@ files:
 - test/fixtures/bank2.dat
 - test/fixtures/correlation_matrix.rb
 - test/fixtures/hartman_23.matrix
-- test/fixtures/repeated_fields.csv
-- test/fixtures/scientific_notation.csv
 - test/fixtures/stock_data.csv
-- test/fixtures/test_csv.csv
-- test/fixtures/test_xls.xls
 - test/fixtures/tetmat_matrix.txt
 - test/fixtures/tetmat_test.txt
 - test/helpers_tests.rb
@@ -416,7 +454,6 @@ files:
 - test/test_bivariate.rb
 - test/test_codification.rb
 - test/test_crosstab.rb
-- test/test_csv.rb
 - test/test_dataset.rb
 - test/test_dominance_analysis.rb
 - test/test_factor.rb
@@ -432,7 +469,6 @@ files:
 - test/test_reliability_icc.rb
 - test/test_reliability_skillscale.rb
 - test/test_resample.rb
-- test/test_rserve_extension.rb
 - test/test_srs.rb
 - test/test_statistics.rb
 - test/test_stest.rb
@@ -443,7 +479,6 @@ files:
 - test/test_umannwhitney.rb
 - test/test_vector.rb
 - test/test_wilcoxonsignedrank.rb
-- test/test_xls.rb
 homepage: https://github.com/sciruby/statsample
 licenses: []
 metadata: {}
@@ -452,12 +487,6 @@ post_install_message: |
 
   Thanks for installing statsample.
 
-  On *nix, you could install statsample-optimization
-  to retrieve gems gsl, statistics2 and a C extension
-  to speed some methods.
-
-  $ [sudo] gem install statsample-optimization
-
   *****************************************************
 rdoc_options:
 - "--main"

data/lib/statsample/rserve_extension.rb

@@ -1,20 +0,0 @@
-# Several additions to Statsample objects, to support
-# rserve-client
-
-module Statsample
-  class Vector
-    def to_REXP
-      Rserve::REXP::Wrapper.wrap(data_with_nils)
-    end
-  end
-  class Dataset
-    def to_REXP
-      names=@fields
-      data=@fields.map {|f|
-        Rserve::REXP::Wrapper.wrap(@vectors[f].data_with_nils)
-      }
-      l=Rserve::Rlist.new(data,names)
-      Rserve::REXP.create_data_frame(l)
-    end
-  end
-end

data/lib/statsample/vector/gsl.rb

@@ -1,106 +0,0 @@
-module Statsample
-  class Vector
-    module GSL_      
-      def clear_gsl
-        @gsl=nil
-      end
-      
-      def set_valid_data
-        clear_gsl
-        set_valid_data_ruby
-      end
-      def push(v)
-        # If data is GSL::Vector, should be converted first to an Array
-        if @data.is_a? GSL::Vector
-          @data=@data.to_a
-        end
-        push_ruby(v)
-      end
-      
-      def gsl
-        @gsl||=GSL::Vector.alloc(@numeric_data) if @numeric_data.size>0
-      end
-      
-      alias :to_gsl :gsl
-      def vector_standarized_compute(m,sd)
-        if flawed?
-          vector_standarized_compute_ruby(m,sd)
-        else
-          gsl.collect {|x| (x.to_f - m).quo(sd)}.to_numeric
-        end
-      end
-      
-      def vector_centered_compute(m)
-        if flawed?
-          vector_centered_compute_ruby(m)
-        else
-          gsl.collect {|x| (x.to_f - m)}.to_numeric
-        end
-      end
-      def sample_with_replacement(sample=1)
-        if(@type!=:numeric)
-          sample_with_replacement_ruby(sample)
-        else
-          r = GSL::Rng.alloc(GSL::Rng::MT19937,rand(10000))
-          Statsample::Vector.new(r.sample(gsl, sample).to_a,:numeric)
-        end
-      end
-      
-      def sample_without_replacement(sample=1)
-        if(@type!=:numeric)
-          sample_without_replacement_ruby(sample)
-        else
-          r = GSL::Rng.alloc(GSL::Rng::MT19937,rand(10000))
-          r.choose(gsl, sample).to_a
-        end
-      end
-      def median
-        if @type!=:numeric
-          median_ruby
-        else
-          sorted=GSL::Vector.alloc(@numeric_data.sort)
-          GSL::Stats::median_from_sorted_data(sorted)
-        end
-      end
-      
-      def sum 
-        check_type :numeric
-        gsl.nil? ? nil : gsl.sum
-      end
-      def mean
-        check_type :numeric
-        gsl.nil? ? nil : gsl.mean
-      end				
-      def variance_sample(m=nil)
-        check_type :numeric
-        m||=mean
-        gsl.nil? ? nil : gsl.variance_m
-      end
-      
-      def standard_deviation_sample(m=nil)
-        check_type :numeric
-        m||=mean
-        gsl.nil? ? nil : gsl.sd(m)
-      end
-
-      def variance_population(m=nil) # :nodoc:
-        check_type :numeric    
-        m||=mean
-        gsl.nil? ? nil : gsl.variance_with_fixed_mean(m)
-      end
-      def standard_deviation_population(m=nil) # :nodoc:
-        check_type :numeric
-        m||=mean
-        gsl.nil? ? nil : gsl.sd_with_fixed_mean(m)
-      end
-      def skew # :nodoc:
-        check_type :numeric
-        gsl.nil? ? nil : gsl.skew
-      end
-      def kurtosis # :nodoc:
-        check_type :numeric
-        gsl.nil? ? nil : gsl.kurtosis
-      end
-    end
-  end
-end

data/test/fixtures/repeated_fields.csv

@@ -1,7 +0,0 @@
-"id","name","age","city","a1","name","age"
-1,"Alex",20,"New York","a,b","a",3
-2,"Claude",23,"London","b,c","b",4
-3,"Peter",25,"London","a","c",5
-4,"Franz",27,"Paris",,"d",6
-5,"George","5,5","Tome","a,b,c","f",
-6,"Fernand",20,"London","c,b","f",8

data/test/fixtures/scientific_notation.csv

@@ -1,4 +0,0 @@
-x,y
-1,9.629587310436753e+127
-2,1.9341543147883677e+129
-3,3.88485279048245e+130

data/test/fixtures/test_csv.csv

@@ -1,7 +0,0 @@
-"id","name","age","city","a1"
-1,"Alex",20,"New York","a,b"
-2,"Claude",23,"London","b,c"
-3,"Peter",25,"London","a"
-4,"Franz",27,"Paris",
-5,"George","5,5","Tome","a,b,c"
-6,"Fernand",,,

data/test/test_csv.rb

@@ -1,63 +0,0 @@
-require 'helpers_tests.rb'
-
-class StatsampleCSVTestCase < Minitest::Test
-  def setup
-    @ds = Statsample::CSV.read('test/fixtures/test_csv.csv')
-  end
-
-  def test_read
-    header = %w(id name age city a1)
-    data = {
-      'id' => [1, 2, 3, 4, 5, 6].to_vector(:numeric),
-      'name' => %w(Alex Claude Peter Franz George Fernand).to_vector(:object),
-      'age' => [20, 23, 25, 27, 5.5, nil].to_vector(:numeric),
-      'city' => ['New York', 'London', 'London', 'Paris', 'Tome', nil].to_vector(:object),
-      'a1' => ['a,b', 'b,c', 'a', nil, 'a,b,c', nil].to_vector(:object)
-    }
-
-    ds_exp = Statsample::Dataset.new(data, header)
-
-    assert_equal(6, @ds.cases)
-    assert_equal(header, @ds.fields)
-
-    ds_exp.fields.each do |f|
-      assert_equal(ds_exp[f], @ds[f])
-    end
-
-    assert_equal(ds_exp, @ds)
-  end
-
-  def test_nil
-    assert_equal(nil, @ds['age'][5])
-  end
-
-  def test_repeated
-    ds = Statsample::CSV.read('test/fixtures/repeated_fields.csv')
-    assert_equal(%w(id name_1 age_1 city a1 name_2 age_2), ds.fields)
-    age = [3, 4, 5, 6, nil, 8].to_vector(:numeric)
-    assert_equal(age, ds['age_2'])
-  end
-
-  # Testing fix for SciRuby/statsample#19.
-  def test_accept_scientific_notation_as_float
-    ds = Statsample::CSV.read('test/fixtures/scientific_notation.csv')
-    assert_equal(%w(x y), ds.fields)
-    y = [9.629587310436753e+127, 1.9341543147883677e+129, 3.88485279048245e+130]
-    y.zip(ds['y']).each do |y_expected, y_ds|
-      assert_in_delta(y_expected, y_ds)
-    end
-
-  end
-
-  def test_write
-    filename = Tempfile.new('afile')
-    Statsample::CSV.write(@ds, filename.path)
-    ds2 = Statsample::CSV.read(filename.path)
-    i = 0
-
-    ds2.each_array do |row|
-      assert_equal(@ds.case_as_array(i), row)
-      i += 1
-    end
-  end
-end