statsample 2.0.1 → 2.0.2

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: cd72f54dcbf15cdf6413daf54551c8b9820d50fd
+  metadata.gz: ee62b72f947f9760824885a479c92ce6dbc55127
+  data.tar.gz: 7cb2c7057856eee78f69be2f7c1e43671cc8007e
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+  data.tar.gz: 8eeac7c1f6aca3ed959ff15cfd97407876d46dfb8d9adf13aa892831772b02209142d73a46ac1581e848cf020b86cfccb93e21bd9f450da106d08ed755d5bd1b

data/.travis.yml

@@ -1,14 +1,11 @@
 language:
   ruby
 
-env:
-  - CPLUS_INCLUDE_PATH=/usr/include/atlas C_INCLUDE_PATH=/usr/include/atlas
-
 rvm:
-  - '1.9.3'
   - '2.0'
   - '2.1'
   - '2.2'
+  - '2.3.0'
 
 matrix:
   fast_finish:
@@ -18,11 +15,9 @@ script: "bundle exec rake test"
 
 install:
   - gem install bundler
-  - ./.build.sh
   - bundle install
 
 before_install:
   - sudo apt-get update -qq
-  - sudo apt-get install -qq libatlas-base-dev
   - sudo apt-get install -y libgsl0-dev r-base r-base-dev
   - sudo Rscript -e "install.packages(c('Rserve','irr'),,'http://cran.us.r-project.org')"

data/CONTRIBUTING.md

@@ -2,27 +2,11 @@
 
 ## Installing statsample development dependencies
 
-If you want to run the full test suite, you will need the latest unreleased nmatrix and gsl-nmatrix ruby gems. They will be released upstream soon but please follow this procdure for now.
+Keep in mind that either nmatrix OR rb-gsl are NOT NECESSARY for using statsample. They are just required for an optional speed up. 
 
-Keep in mind that either nmatrix OR gsl-nmatrix are NOT NECESSARY for using statsample. They are just required for an optional speed up. 
+Statsample also works with [rb-gsl](https://github.com/sciruby/rb-gsl).
 
-Statsample also works with [rb-gsl](https://github.com/blackwinter/rb-gsl), though installing that will cause a problem if you have any nmatrix dependent code because narray and nmatrix have a namespace problem.
-
-To install dependencies, execute the following commands:
-
-  `export CPLUS_INCLUDE_PATH=/usr/include/atlas` 
-  `export C_INCLUDE_PATH=/usr/include/atlas`
-  `sudo apt-get update -qq`
-  `sudo apt-get install -qq libatlas-base-dev`
-  `sudo apt-get --purge remove liblapack-dev liblapack3 liblapack3gf`
-  `sudo apt-get install -y libgsl0-dev r-base r-base-dev`
-  `sudo Rscript -e "install.packages(c('Rserve','irr'),,'http://cran.us.r-project.org')"`
-
-Then execute the .build.sh script to clone and install the latest nmatrix and gsl-nmatrix on your system:
-
-  `./.build.sh`
-
-Then finally install remaining dependencies:
+Install dependencies:
 
   `bundle install`
 

data/History.txt

@@ -1,3 +1,6 @@
+=== 2.0.2 / 2016-03-11
+  * Update dependencies (spreadsheet, GSL)
+
 === 2.0.1 / 2015-08-19
   * Cleaned legacy containers in favor of `Daru::DataFrame` and `Daru::Vector`.
 

data/examples/chisquare_test.rb

@@ -0,0 +1,23 @@
+#!/usr/bin/ruby
+$:.unshift(File.dirname(__FILE__)+'/../lib')
+require 'statsample'
+
+Statsample::Analysis.store(Statsample::Test::ChiSquare) do
+  # Collect the two vectors with the categorical data (raw number of occurences) into one matrix. Here
+  #--------------------------------------------
+  #| category | observation 1 | observation 2 |
+  #|------------------------------------------|
+  #|    A     |      100      |      20       |
+  #|    B     |      50       |      70       |
+  #|    C     |      30       |      100      |
+  #|------------------------------------------|
+  #
+  m=Matrix[[100, 50, 30],[20, 70, 100]]
+  x_2=Statsample::Test.chi_square(m)
+  # after the test is done, look at the p-value.
+  puts x_2.probability
+end
+
+if __FILE__==$0
+  Statsample::Analysis.run_batch
+end

data/lib/statsample.rb

@@ -59,13 +59,13 @@ class Array
   end
 
   def mean
-    self.sum / size
+    sum.fdiv(size)
   end
 
   # Calcualte sum of squares
   def sum_of_squares(m=nil)
     m ||= mean
-    self.inject(0) {|a,x| a + (x-m).square }
+    inject(0) {|a,x| a + (x-m).square }
   end
 
   # Calculate sample variance
@@ -124,6 +124,7 @@ module Statsample
       cv = "@@#{library}"
       unless class_variable_defined? cv
         begin
+          gem library.to_s # activate gem
           require library.to_s
           class_variable_set(cv, true)
         rescue LoadError

data/lib/statsample/test/chisquare.rb

@@ -1,9 +1,26 @@
 module Statsample
   module Test
     module ChiSquare
-      class WithMatrix
+      module Shared
         attr_reader :df
         attr_reader :value
+
+        def to_f
+          @value
+        end
+
+        def chi_square
+          @value
+        end
+
+        def probability
+          1-Distribution::ChiSquare.cdf(@value.to_f,@df)
+        end
+      end
+
+      class WithMatrix
+        include Statsample::Test::ChiSquare::Shared
+
         def initialize(observed, expected=nil)
           @observed=observed
           @expected=expected or calculate_expected
@@ -11,33 +28,46 @@ module Statsample
           @df=(@observed.row_size-1)*(@observed.column_size-1)
           @value=compute_chi
         end
+
         def calculate_expected
           sum=@observed.total_sum
           @expected=Matrix.rows( @observed.row_size.times.map {|i|
             @observed.column_size.times.map {|j|
               (@observed.row_sum[i].quo(sum) * @observed.column_sum[j].quo(sum))*sum
             }
-          })          
-        end
-        def to_f
-          @value
-        end
-        def chi_square
-          @value
-        end
-        def probability
-          1-Distribution::ChiSquare.cdf(@value.to_f,@df)
+          })
         end
+
         def compute_chi
-            sum=0
-            (0...@observed.row_size).each {|i|
-              (0...@observed.column_size).each {|j|
+          sum=0
+          (0...@observed.row_size).each {|i|
+            (0...@observed.column_size).each {|j|
               sum+=((@observed[i, j] - @expected[i,j])**2).quo(@expected[i,j])
-              }
             }
-            sum
+          }
+          sum
+        end
+      end
+
+      class WithVector
+        include Statsample::Test::ChiSquare::Shared
+
+        def initialize(observed, expected)
+          @observed = observed
+          @expected = expected
+          raise "Observed size!=expected size" if @observed.size!=@expected.size
+          @df = @observed.size - 1
+          @value = compute_chi
+        end
+
+        def compute_chi
+          sum=0
+          (0...@observed.size).each {|i|
+            sum+=((@observed[i] - @expected[i])**2).quo(@expected[i])
+          }
+          sum
         end
       end
     end
   end
-end
+end

data/lib/statsample/version.rb

@@ -1,3 +1,3 @@
 module Statsample
-  VERSION = '2.0.1'
+  VERSION = '2.0.2'
 end

data/statsample.gemspec

@@ -61,7 +61,7 @@ Gem::Specification.new do |s|
   s.executables = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
 
   s.add_runtime_dependency 'daru', '~> 0.1'
-  s.add_runtime_dependency 'spreadsheet', '~> 1.0.3'
+  s.add_runtime_dependency 'spreadsheet', '~> 1.1'
   s.add_runtime_dependency 'reportbuilder', '~> 1.4'
   s.add_runtime_dependency 'minimization', '~> 0.2'
   s.add_runtime_dependency 'dirty-memoize', '~> 0.0.4'
@@ -79,6 +79,6 @@ Gem::Specification.new do |s|
   s.add_development_dependency 'minitest', '~> 5.7'
   s.add_development_dependency 'gettext', '~> 3.1'
   s.add_development_dependency 'mocha', '~> 1.1'
-  s.add_development_dependency 'nmatrix', '~> 0.1.0'
-  s.add_development_dependency 'rb-gsl', '~> 1.16'
+  s.add_development_dependency 'nmatrix', '~> 0.2.1'
+  s.add_development_dependency 'gsl', '~> 2.1'
 end

data/test/test_factor_pa.rb

@@ -53,7 +53,7 @@ class StatsampleFactorTestCase < Minitest::Test
 
   def test_parallelanalysis
     pa = Statsample::Factor::ParallelAnalysis.with_random_data(305, 8, iterations: 100, percentil: 95)
-    assert_in_delta(1.2454, pa.ds_eigenvalues[:ev_00001].mean, 0.01)
+    assert_in_delta(1.2454, pa.ds_eigenvalues[:ev_00001].mean, 0.05)
     assert_in_delta(1.1542, pa.ds_eigenvalues[:ev_00002].mean, 0.01)
     assert_in_delta(1.0836, pa.ds_eigenvalues[:ev_00003].mean, 0.01)
     assert(pa.summary.size > 0)

data/test/test_stest.rb

@@ -23,6 +23,20 @@ class StatsampleTestTestCase < Minitest::Test
     assert_equal(6, chi.df)
   end
 
+  def test_chi_square_vector
+    observed = Vector[20,30,15]
+    expected = Vector[20,20,20]
+    assert_nothing_raised do
+      Statsample::Test.chi_square(observed, expected)
+    end
+    chi = Statsample::Test.chi_square(observed, expected)
+
+    assert_in_delta(6.25, chi.chi_square, 0.0001)
+    assert_in_delta(0.04393, chi.probability, 0.00001)
+
+    assert_equal(2, chi.df)
+  end
+
   def test_u_mannwhitney
     a = Daru::Vector.new([1, 2, 3, 4, 5, 6])
     b = Daru::Vector.new([0, 5, 7, 9, 10, 11])

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: statsample
 version: !ruby/object:Gem::Version
-  version: 2.0.1
+  version: 2.0.2
 platform: ruby
 authors:
 - Claudio Bustos
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-19 00:00:00.000000000 Z
+date: 2016-03-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daru
@@ -31,14 +31,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.3
+        version: '1.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.3
+        version: '1.1'
 - !ruby/object:Gem::Dependency
   name: reportbuilder
   requirement: !ruby/object:Gem::Requirement
@@ -269,28 +269,28 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.2.1
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.0
+        version: 0.2.1
 - !ruby/object:Gem::Dependency
-  name: rb-gsl
+  name: gsl
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
+        version: '2.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.16'
+        version: '2.1'
 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.
@@ -328,7 +328,6 @@ extra_rdoc_files:
 - README.md
 - references.txt
 files:
-- ".build.sh"
 - ".gitignore"
 - ".travis.yml"
 - CONTRIBUTING.md
@@ -351,6 +350,7 @@ files:
 - data/locale/es/LC_MESSAGES/statsample.mo
 - doc_latex/manual/equations.tex
 - examples/boxplot.rb
+- examples/chisquare_test.rb
 - examples/correlation_matrix.rb
 - examples/dataset.rb
 - examples/dominance_analysis.rb
@@ -508,4 +508,46 @@ rubygems_version: 2.4.5
 signing_key: 
 specification_version: 4
 summary: A suite for basic and advanced statistics on Ruby
-test_files: []
+test_files:
+- test/fixtures/bank2.dat
+- test/fixtures/correlation_matrix.rb
+- test/fixtures/hartman_23.matrix
+- test/fixtures/stock_data.csv
+- test/fixtures/tetmat_matrix.txt
+- test/fixtures/tetmat_test.txt
+- test/helpers_tests.rb
+- test/test_analysis.rb
+- test/test_anova_contrast.rb
+- test/test_anovaoneway.rb
+- test/test_anovatwoway.rb
+- test/test_anovatwowaywithdataset.rb
+- test/test_anovawithvectors.rb
+- test/test_awesome_print_bug.rb
+- test/test_bartlettsphericity.rb
+- test/test_bivariate.rb
+- test/test_codification.rb
+- test/test_crosstab.rb
+- test/test_dominance_analysis.rb
+- test/test_factor.rb
+- test/test_factor_map.rb
+- test/test_factor_pa.rb
+- test/test_ggobi.rb
+- test/test_gsl.rb
+- test/test_histogram.rb
+- test/test_matrix.rb
+- test/test_multiset.rb
+- test/test_regression.rb
+- test/test_reliability.rb
+- test/test_reliability_icc.rb
+- test/test_reliability_skillscale.rb
+- test/test_resample.rb
+- test/test_srs.rb
+- test/test_statistics.rb
+- test/test_stest.rb
+- test/test_stratified.rb
+- test/test_test_f.rb
+- test/test_test_kolmogorovsmirnov.rb
+- test/test_test_t.rb
+- test/test_umannwhitney.rb
+- test/test_vector.rb
+- test/test_wilcoxonsignedrank.rb

data/.build.sh

@@ -1,15 +0,0 @@
-#!/bin/bash
-
-git clone https://github.com/SciRuby/nmatrix.git
-cd nmatrix
-gem build nmatrix.gemspec
-gem install nmatrix-0.1.0.gem
-cd ..
-rm -rf nmatrix
-git clone https://github.com/v0dro/gsl-nmatrix
-cd gsl-nmatrix
-gem build gsl-nmatrix.gemspec
-gem install gsl-nmatrix-1.17.gem
-cd ..
-rm -rf gsl-nmatrix
-