statsample-bivariate-extension 1.1.0 → 1.2.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 0f4674626beaba0a1ef4b15f739b2154692218b2
+  data.tar.gz: 6a1f7af3ecda48e76f9f57c6e9e869f30986dd95
+SHA512:
+  metadata.gz: 7cb0639430518c4cb0028129176682f85786e98aa0e64172ca498eb0adabfc6fe9aee5a11f681c93a34b255b2b87ca717127fdece5d85a3fbd3a566191ca0cbd
+  data.tar.gz: 2e81c0c2a86b0a6d1f4a744b9250398c18aa8b1f158c83dde2315f8a331ca049111384df0e603db25ac99236724fec16b465bd3403e03b662f19b27382e28c6a

data/.build.sh

@@ -0,0 +1,14 @@
+#!/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

data/.gitignore

@@ -0,0 +1,9 @@
+*.rbc
+coverage
+pkg
+tmp
+grab_references
+.autotest
+*~
+Gemfile.lock
+*.gem

data/.travis.yml

@@ -0,0 +1,27 @@
+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'
+
+matrix:
+  fast_finish:
+    true
+
+script: "bundle exec rspec"
+
+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

data/Gemfile

@@ -0,0 +1,2 @@
+source 'https://rubygems.org'
+gemspec

data/History.txt

@@ -1,3 +1,9 @@
+=== 1.2.0
+
+* Updated statsample dependency to 1.5.0
+* Added new dependency on daru (0.1.0)
+* Modernized gem. Added gemspec, Gemfile and specified dependencies.
+
 === 0.16.1 / 2010-12-22
 
 * Added support for optimized tetrachoric correlation calculation. Update statsample-optimization before report any error, please.

data/LICENSE.txt

@@ -0,0 +1,23 @@
+Copyright (c) 2010-2014, Claudio Bustos
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+this list of conditions and the following disclaimer in the documentation
+and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

data/{README.txt → README.md}

@@ -1,22 +1,24 @@
-= statsample-bivariate-extension
+# statsample-bivariate-extension
+
+[![Build Status](https://travis-ci.org/SciRuby/statsample-bivariate-extension.svg)](https://travis-ci.org/SciRuby/statsample-bivariate-extension)
 
 * http://ruby-statsample.rubyforge.org/
 
-== DESCRIPTION:
+## DESCRIPTION:
 
 Provides advanced bivariate statistics:
 * Tetrachoric correlation
 * Polychoric correlation
 
-== FEATURES/PROBLEMS:
+## FEATURES/PROBLEMS:
 
 * Statsample::Bivariate::Polychoric class provides polychoric correlation
 * Statsample::Bivariate::Tetrachoric class provides tetrachoric correlation
 
 
-== SYNOPSIS:
+## SYNOPSIS:
 
-=== Tetrachoric correlation
+### Tetrachoric correlation
 
     require 'statsample'
     a=40
@@ -26,7 +28,7 @@ Provides advanced bivariate statistics:
     tetra=Statsample::Bivariate::Tetrachoric.new(a,b,c,d)
     puts tetra.summary
     
-=== Polychoric correlation
+### Polychoric correlation
 
     require 'statsample'
     ct=Matrix[[58,52,1],[26,58,3],[8,12,9]]
@@ -35,16 +37,16 @@ Provides advanced bivariate statistics:
     puts poly.summary
 
 
-== REQUIREMENTS:
+## REQUIREMENTS:
 
 * Statsample
 
-== INSTALL:
+## INSTALL:
 
 This gem is a statsample dependency. If you want to install it separatly
 
-* sudo gem install statsample-bivariate-extension
+* gem install statsample-bivariate-extension
 
-== LICENSE:
+## LICENSE:
 
-GPL-2
+BSD 2-Clause (see LICENSE.txt)

data/lib/statsample/bivariate/extension_version.rb

@@ -1,7 +1,7 @@
 module Statsample
   module Bivariate
     # Version  of bivariate extension
-    EXTENSION_VERSION="1.1.0" 
+    EXTENSION_VERSION="1.2.0" 
   end
 end
 

data/lib/statsample/bivariate/polychoric.rb

@@ -9,7 +9,7 @@ module Statsample
     end
     
     # Polychoric correlation matrix.
-    # Order of rows and columns depends on Dataset#fields order
+    # Order of rows and columns depends on DataFrame#vectors order
     def self.polychoric_correlation_matrix(ds)
       cache={}
       matrix=ds.collect_matrix do |row,col|
@@ -30,7 +30,7 @@ module Statsample
         end
       end
       matrix.extend CovariateMatrix
-      matrix.fields=ds.fields
+      matrix.fields=ds.vectors.to_a
       matrix
     end
     

data/lib/statsample/bivariate/tetrachoric.rb

@@ -7,7 +7,7 @@ module Statsample
     end
 
     # Tetrachoric correlation matrix.
-    # Order of rows and columns depends on Dataset#fields order
+    # Order of rows and columns depends on DataFrame#vectors order
     def self.tetrachoric_correlation_matrix(ds)
       cache={}
       matrix=ds.collect_matrix do |row,col|
@@ -29,7 +29,7 @@ module Statsample
       end
       
       matrix.extend CovariateMatrix
-      matrix.fields=ds.fields
+      matrix.fields=ds.vectors.to_a
       matrix
     end
     # Compute tetrachoric correlation.

data/spec/polychoric_spec.rb

@@ -5,10 +5,10 @@ describe "Statsample::Bivariate polychoric extension" do
       Statsample::Bivariate.should respond_to(:polychoric)
     end
     it "should respond to method polychoric_correlation_matrix" do
-      a=([1,1,2,2,2,3,3,3,2,2,3,3,3]*4).to_scale
-      b=([1,2,2,2,1,3,2,3,2,2,3,3,2]*4).to_scale
-      c=([1,1,1,2,2,2,2,3,2,3,2,2,3]*4).to_scale
-      ds={'a'=>a,'b'=>b,'c'=>c}.to_dataset
+      a = Daru::Vector.new([1,1,2,2,2,3,3,3,2,2,3,3,3]*4)
+      b = Daru::Vector.new([1,2,2,2,1,3,2,3,2,2,3,3,2]*4)
+      c = Daru::Vector.new([1,1,1,2,2,2,2,3,2,3,2,2,3]*4)
+      ds= Daru::DataFrame.new({:a => a,:b => b,:c => c})
       Statsample::Bivariate.polychoric_correlation_matrix(ds).should be_instance_of(::Matrix)
     end
   end

data/spec/tetrachoric_spec.rb

@@ -9,9 +9,9 @@ describe "Statsample::Bivariate tetrachoric extensions" do
     Statsample::Bivariate.should respond_to(:tetrachoric)
   end
   it "should return correct tetrachoric_matrix"do
-    ds=Statsample::PlainText.read(@data_file, %w{a b c d e})
+    ds=Daru::DataFrame.from_plaintext(@data_file, [:a, :b, :c, :d, :e])
     tcm_obs=Statsample::Bivariate.tetrachoric_correlation_matrix(ds)
-    tcm_exp=Statsample::PlainText.read(@data_file, %w{a b c d e}).to_matrix
+    tcm_exp=Daru::DataFrame.from_plaintext(@data_file, [:a, :b, :c, :d, :e]).to_matrix
     tcm_obs.row_size.times do |i|
       tcm_obs.column_size do |j|
         tcm_obs[i,j].should be_within( 0.00001).of(tcm_exp[i,k])
@@ -79,8 +79,8 @@ shared_examples_for "tetrachoric implementation" do
     tc.threshold_y.should be_within( 0.0001).of( 0.31864)
   end
   it "should return equal values for dataset and crosstab inputs" do 
-    x=%w{a a a a b b b a b b a a b b}.to_vector
-    y=%w{0 0 1 1 0 0 1 1 1 1 0 0 1 1}.to_vector
+    x = Daru::Vector.new(%w{a a a a b b b a b b a a b b})
+    y = Daru::Vector.new(%w{0 0 1 1 0 0 1 1 1 1 0 0 1 1})
     # crosstab
     #    0    1
     # a  4    3

data/statsample-bivariate-extension.gemspec

@@ -0,0 +1,33 @@
+# coding: utf-8
+$:.unshift File.expand_path("../lib", __FILE__)
+
+require 'statsample/bivariate/extension_version.rb'
+
+Statsample::Bivariate::DESCRIPTION = <<MSG
+Polychoric and Tetrachoric extensions for Statsample::Bivariate.
+MSG
+
+Gem::Specification.new do |spec|
+  spec.name          = 'statsample-bivariate-extension'
+  spec.version       = Statsample::Bivariate::EXTENSION_VERSION
+  spec.authors       = ['Claudio Bustos']
+  spec.email         = ["clbustos@gmail.com"]
+  spec.summary       = %q{Polychoric and Tetrachoric extensions for Statsample::Bivariate.}
+  spec.description   = Statsample::Bivariate::DESCRIPTION
+  spec.homepage      = "https://github.com/SciRuby/statsample-bivariate-extension"
+  spec.license       = 'BSD-2'
+
+  spec.files         = `git ls-files -z`.split("\x0")
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency 'daru', '~> 0.1'
+  spec.add_runtime_dependency 'statsample', '~> 2.0'
+
+  spec.add_development_dependency 'bundler', '~> 1.10'
+  spec.add_development_dependency 'rake', '~> 10.4'
+  spec.add_development_dependency 'rspec'
+  spec.add_development_dependency 'nmatrix', '~> 0.1'
+  spec.add_development_dependency 'rb-gsl', '~> 1.16'
+end

metadata

@@ -1,143 +1,170 @@
 --- !ruby/object:Gem::Specification
 name: statsample-bivariate-extension
 version: !ruby/object:Gem::Version
-  version: 1.1.0
-  prerelease: 
+  version: 1.2.0
 platform: ruby
 authors:
 - Claudio Bustos
 autorequire: 
 bindir: bin
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-date: 2011-09-12 00:00:00.000000000 Z
+cert_chain: []
+date: 2015-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: distribution
-  requirement: &15403740 !ruby/object:Gem::Requirement
-    none: false
+  name: daru
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0.6'
+        version: '0.1'
   type: :runtime
   prerelease: false
-  version_requirements: *15403740
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: statsample
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
 - !ruby/object:Gem::Dependency
-  name: hoe
-  requirement: &15402800 !ruby/object:Gem::Requirement
-    none: false
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '2.12'
+        version: '10.4'
   type: :development
   prerelease: false
-  version_requirements: *15402800
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+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.4'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
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+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: nmatrix
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.1'
+- !ruby/object:Gem::Dependency
+  name: rb-gsl
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.16'
+description: |
+  Polychoric and Tetrachoric extensions for Statsample::Bivariate.
 email:
-- clbustos_at_gmail.com
+- clbustos@gmail.com
 executables: []
 extensions: []
-extra_rdoc_files:
-- !binary |-
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-- !binary |-
-  TWFuaWZlc3QudHh0
-- !binary |-
-  UkVBRE1FLnR4dA==
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+extra_rdoc_files: []
 files:
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-licenses: []
+- ".build.sh"
+- ".gitignore"
+- ".travis.yml"
+- Gemfile
+- History.txt
+- LICENSE.txt
+- README.md
+- Rakefile
+- data/tetmat_matrix.txt
+- data/tetmat_test.txt
+- lib/statsample/bivariate/extension_version.rb
+- lib/statsample/bivariate/polychoric.rb
+- lib/statsample/bivariate/polychoric/processor.rb
+- lib/statsample/bivariate/tetrachoric.rb
+- references.txt
+- spec/polychoric_processor_spec.rb
+- spec/polychoric_spec.rb
+- spec/spec.opts
+- spec/spec_helper.rb
+- spec/tetrachoric_spec.rb
+- statsample-bivariate-extension.gemspec
+homepage: https://github.com/SciRuby/statsample-bivariate-extension
+licenses:
+- BSD-2
+metadata: {}
 post_install_message: 
-rdoc_options:
-- --main
-- README.txt
+rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: ruby-statsample
-rubygems_version: 1.8.10
+rubyforge_project: 
+rubygems_version: 2.4.6
 signing_key: 
-specification_version: 3
-summary: !binary |-
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-test_files: []
+specification_version: 4
+summary: Polychoric and Tetrachoric extensions for Statsample::Bivariate.
+test_files:
+- spec/polychoric_processor_spec.rb
+- spec/polychoric_spec.rb
+- spec/spec.opts
+- spec/spec_helper.rb
+- spec/tetrachoric_spec.rb
+has_rdoc: 

data/Manifest.txt

@@ -1,16 +0,0 @@
-History.txt
-Manifest.txt
-README.txt
-Rakefile
-data/tetmat_matrix.txt
-data/tetmat_test.txt
-lib/statsample/bivariate/extension_version.rb
-lib/statsample/bivariate/polychoric.rb
-lib/statsample/bivariate/polychoric/processor.rb
-lib/statsample/bivariate/tetrachoric.rb
-references.txt
-spec/polychoric_processor_spec.rb
-spec/polychoric_spec.rb
-spec/spec.opts
-spec/spec_helper.rb
-spec/tetrachoric_spec.rb