Rsquared 0.0.1
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- data/.travis.yml +8 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +36 -0
- data/Rakefile +11 -0
- data/Rsquared.gemspec +24 -0
- data/install.sh +8 -0
- data/lib/Rsquared/version.rb +3 -0
- data/lib/constants.rb +24 -0
- data/lib/enumerableext.rb +46 -0
- data/lib/rsquared.rb +213 -0
- data/lib/version.rb +0 -0
- data/test/enumerable_tests.rb +44 -0
- data/test/helper_tests.rb +16 -0
- data/test/rsquared_tests.rb +42 -0
- metadata +124 -0
data/.travis.yml
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2013 Daniel Cohen
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# Rsquared
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A full featured Ruby statistics library with assumption verification to make using statistics easy,
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even with no background.
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[![Build Status](https://travis-ci.org/dacohen/Rsquared.png)](https://travis-ci.org/dacohen/Rsquared)
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## Installation
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Add this line to your application's Gemfile:
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gem 'Rsquared'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install Rsquared
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## Usage
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You can run a statistical test, with assumption checking by supplying an array of numerical data points:
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>> ttest = Rsquared::TTest.new(data)
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>> ttest.statistic #=> Float
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>> ttest.significant? #=> Boolean
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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data/Rsquared.gemspec
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'Rsquared/version'
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Gem::Specification.new do |spec|
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spec.name = "Rsquared"
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spec.version = Rsquared::VERSION
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spec.authors = ["Daniel Cohen"]
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spec.email = ["dcohen@gatech.edu"]
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spec.description = %q{A full-featured Ruby statistics library with assumption verification}
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spec.summary = %q{Provides statistical distributions, tests and verifies relevant assumptions}
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spec.homepage = "https://github.com/dacohen/Rsquared"
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spec.license = "MIT"
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spec.files = `git ls-files`.split($/)
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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spec.add_development_dependency "bundler", "~> 1.3"
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spec.add_development_dependency "rake"
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spec.add_development_dependency "distribution"
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end
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data/install.sh
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data/lib/constants.rb
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KSCV = [0.975, 0.842, 0.708, 0.624, 0.565, 0.521, 0.486, 0.457, 0.432, 0.410, 0.391, 0.375, 0.361, 0.349, 0.338, 0.328, 0.318, 0.309, 0.301, 0.294]
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module Rsquared
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class Upper
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def self.tail
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return 1
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end
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end
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class Lower
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def self.tail
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return -1
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end
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end
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class Two
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def self.sided
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return true
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end
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end
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class AssumptionError < StandardError
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end
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end
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module Enumerable
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def sum
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return self.inject(0){|acc, i| acc+i}
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end
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def mean
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return self.sum/self.length.to_f
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end
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def variance
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varsum = self.inject(0){|acc, i| acc + (i - self.mean)**2}
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return(varsum/(self.length.to_f-1.0))
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end
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def popvariance
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return self.variance*((self.length.to_f-1.0)/self.length.to_f)
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end
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def popstddev
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return Math.sqrt(self.popvariance)
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end
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def stddev
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return Math.sqrt(self.variance)
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end
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def skew
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thirdsum = self.inject(0){|acc, i| acc + (i - self.mean)**3}
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thirdmoment = thirdsum/self.length.to_f
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return thirdmoment / (self.popvariance)**(3.0/2.0)
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end
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def kurtosis
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fourthsum = self.inject(0){|acc, i| acc + (i - self.mean)**4}
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fourthmoment = fourthsum/self.length.to_f
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return (fourthmoment / (self.popvariance)**2)
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end
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def std
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result = []
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(0..self.length-1).each do |i|
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result[i] = (self[i] - self.mean)/self.stddev
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end
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return result
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end
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end
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data/lib/rsquared.rb
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require "Rsquared/version"
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require "rubygems"
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require "distribution"
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require "constants"
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require "complex"
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require "enumerableext.rb"
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module Rsquared
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##
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# KSTest implements the Kolomogorov-Smirnov test for normality
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# kstest = Rsquared::KSTest.new(data)
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# kstest.normal? => Boolean, indicates normality of data at 5% confidence
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#
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class KSTest
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##
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# Intitializes the test object with an array of numerical data
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#
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def initialize(data)
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@data = data.std.sort!
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fn = 0
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d = []
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range = @data.max - @data.min
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@data.each_with_index do |x, i|
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# Calculate Fn
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fn = i + 1
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d[i] = fn/@data.length.to_f - Distribution::Normal::cdf(x)
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fn = 0.0
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end
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@ksstat = d.max
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return @ksstat
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end
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##
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# Returns a boolean indiciating the significance of the test a the 5% level
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#
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def significant?
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if @ksstat > Helper::kscv(@data.length) then
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return true
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else
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return false
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end
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end
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##
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# Returns logical opposite of significance
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#
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def normal?
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!self.significant?
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end
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def inspect
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significant?
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end
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##
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# Returns the test statistic
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#
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def statistic
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@ksstat
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end
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end
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##
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# Tests for outliers on either side of the data
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# grubbs = Rsquared::GrubbsTest.new(data)
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# grubbs.significant? => Boolean
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#
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class GrubbsTest
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##
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# Initializes the Test object with an array of numerical data
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#
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def initialize(data)
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@data = data.sort
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@gstat = [((@data.mean - @data.min)/@data.stddev).abs, ((@data.mean - @data.max)/@data.stddev).abs].max
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end
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##
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# Returns a boolean indicating the significance of the test at the 5% level
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#
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def significant?(alpha=0.05)
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if @gstat > Helper::grubbscv(@data.length, alpha) then
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return true
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else
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return false
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end
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end
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def inspect
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significant?
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end
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##
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# Returns the test statistic as a float
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#
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def statistic
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@gstat
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end
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alias_method :outlier?, :significant?
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end
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##
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# Tests for deviation of sample mean from expected mean
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# ttest = Rsquared::TTest.new(data, mu0, sided)
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# mu0 is the expected value of the sample mean
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# Supply Rsquared::Upper.tail, Rsquared::Lower.tail or Rsquared::Two.sided
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# Use Upper.tail when you suspect that the sample mean will be greater than the expected mean
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# Use Lower.tail when you suspect that the sample mean will be smaller than the expected mean
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# Use Two.sided when you suspect neither
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class TTest
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##
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# Initializes the TTest object with the supplied arguments
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#
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def initialize(data, mu0, sided)
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@data = data
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@mu0 = mu0
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@sided = sided
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if KSTest.new(@data).significant? and @data.length < 40 then
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raise AssumptionException, "The data is not close enough to a normal distribution for such a small sample size"
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end
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if GrubbsTest.new(@data).outlier? then
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raise AssumptionException, "Your data has one or more outliers, which the T-Distribution cannot handle"
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end
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@tstat = (@data.mean - @mu0)/(data.stddev/Math.sqrt(@data.length))
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@pvalue = Distribution::T::cdf(@tstat, @data.length-1)
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if @sided == Upper.tail then
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@pvalue = 1.0-@pvalue
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elsif @sided == Two.sided then
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@pvalue = [(1.0-@pvalue)*2.0, @pvalue*2.0].min
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end
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end
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def inspect
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@pvalue
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end
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##
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# Returns the t-statistic
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#
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def statistic
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@tstat
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end
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##
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# Checks for significance at the supplied alpha level
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#
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def significant?(alpha=0.05)
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if @pvalue < alpha then
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return true
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else
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return false
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end
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end
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end
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##
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# The Helper module implements uncommon statistical functions directly
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# For use by experts only
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# = Example
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#
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# Rsquared::Helper::kscv(30) => 0.190
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#
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module Helper
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##
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# kscv(n) => Float
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# Estimates the 5% critical value of the Kolomogorov-Smirnov distribution given sample size
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#
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def kscv(n)
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if n < 1 then
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return 1.0
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elsif n < 21 then
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return KSCV[n-1]
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elsif n >= 20 and n < 25 then
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return 0.270
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elsif n >= 25 and n < 30 then
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return 0.240
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elsif n >= 30 and n < 35 then
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return 0.230
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elsif n > 35 then
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return 1.36/Math.sqrt(n)
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end
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end
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##
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# grubbscv(n, alpha) => Float
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# Calculates the Grubbs critical value
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#
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def grubbscv(n, alpha)
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tcv = Distribution::T::p_value(alpha/(2*n), n-2)
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return ((n-1)/Math.sqrt(n))*Math.sqrt(tcv**2/((n-2)+tcv**2))
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end
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module_function :kscv, :grubbscv
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end
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end
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data/lib/version.rb
ADDED
File without changes
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@@ -0,0 +1,44 @@
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1
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require 'test/unit'
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require 'rsquared'
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class EnumerableTest < Test::Unit::TestCase
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def test_sum
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assert_in_delta 15.0, [1,2,3,4,5].sum, 0.001
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end
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def test_mean
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assert_in_delta 3.0, [1,2,3,4,5].mean, 0.001
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end
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def test_variance
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assert_in_delta 2.5, [1,2,3,4,5].variance, 0.001
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end
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def test_stddev
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assert_in_delta 1.5811, [1,2,3,4,5].stddev, 0.001
|
20
|
+
end
|
21
|
+
|
22
|
+
def test_popvariance
|
23
|
+
assert_in_delta 2.0, [1,2,3,4,5].popvariance, 0.001
|
24
|
+
end
|
25
|
+
|
26
|
+
def test_popstddev
|
27
|
+
assert_in_delta 1.4142, [1,2,3,4,5].popstddev, 0.001
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_skew
|
31
|
+
assert_in_delta 0.0, [1,2,3,4,5].skew, 0.001
|
32
|
+
end
|
33
|
+
|
34
|
+
def test_kurtosis
|
35
|
+
assert_in_delta 1.7, [1,2,3,4,5].kurtosis, 0.1
|
36
|
+
end
|
37
|
+
|
38
|
+
def test_std
|
39
|
+
@checkvalues = [-1.2649, -0.63247, 0, 0.63257, 1.2649]
|
40
|
+
[1,2,3,4,5].std.each_with_index do |x, i|
|
41
|
+
assert_in_delta @checkvalues[i], x, 0.001
|
42
|
+
end
|
43
|
+
end
|
44
|
+
end
|
@@ -0,0 +1,16 @@
|
|
1
|
+
require 'test/unit'
|
2
|
+
require 'rsquared'
|
3
|
+
|
4
|
+
class HelperTest < Test::Unit::TestCase
|
5
|
+
|
6
|
+
def test_kscv
|
7
|
+
assert_equal 0.410, Rsquared::Helper::kscv(10)
|
8
|
+
assert_equal 0.240, Rsquared::Helper::kscv(27)
|
9
|
+
assert_in_delta 0.20273, Rsquared::Helper::kscv(45), 0.001
|
10
|
+
end
|
11
|
+
|
12
|
+
def test_grubbscv
|
13
|
+
assert_in_delta 2.91, Rsquared::Helper::grubbscv(30, 0.05), 0.01
|
14
|
+
end
|
15
|
+
|
16
|
+
end
|
@@ -0,0 +1,42 @@
|
|
1
|
+
require 'test/unit'
|
2
|
+
require 'rsquared'
|
3
|
+
|
4
|
+
module Test::Unit::Assertions
|
5
|
+
def refute(bool, *rest)
|
6
|
+
assert(!bool, *rest)
|
7
|
+
end
|
8
|
+
end
|
9
|
+
|
10
|
+
$data = [-105, 135, 40, 90, -55, -85, 70, 180, 140, -10, -105, 40, 185, -90, -90, 80, 70, -155, 345, 250, 10, -135, 80, 85, -40, 250, -20, 35, 305, -135]
|
11
|
+
|
12
|
+
class RsquaredTests < Test::Unit::TestCase
|
13
|
+
|
14
|
+
def test_KS
|
15
|
+
kstest = Rsquared::KSTest.new($data)
|
16
|
+
assert_in_delta 0.1046877, kstest.statistic, 0.001
|
17
|
+
assert kstest.normal?
|
18
|
+
end
|
19
|
+
|
20
|
+
def test_TTest
|
21
|
+
ttest = Rsquared::TTest.new($data, 0, Rsquared::Two.sided)
|
22
|
+
assert_in_delta 0.0763, ttest.inspect, 0.001
|
23
|
+
refute ttest.significant?
|
24
|
+
|
25
|
+
ttest = Rsquared::TTest.new($data, 0, Rsquared::Upper.tail)
|
26
|
+
assert_in_delta 0.03813, ttest.inspect, 0.001
|
27
|
+
assert ttest.significant?
|
28
|
+
end
|
29
|
+
|
30
|
+
def test_Grubbs
|
31
|
+
grubbs = Rsquared::GrubbsTest.new($data)
|
32
|
+
assert_in_delta 2.21, grubbs.statistic, 0.01
|
33
|
+
refute grubbs.significant?
|
34
|
+
refute grubbs.outlier?
|
35
|
+
|
36
|
+
data = $data + [800]
|
37
|
+
grubbs = Rsquared::GrubbsTest.new(data)
|
38
|
+
assert grubbs.significant?
|
39
|
+
assert grubbs.outlier?
|
40
|
+
|
41
|
+
end
|
42
|
+
end
|
metadata
ADDED
@@ -0,0 +1,124 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: Rsquared
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
hash: 29
|
5
|
+
prerelease:
|
6
|
+
segments:
|
7
|
+
- 0
|
8
|
+
- 0
|
9
|
+
- 1
|
10
|
+
version: 0.0.1
|
11
|
+
platform: ruby
|
12
|
+
authors:
|
13
|
+
- Daniel Cohen
|
14
|
+
autorequire:
|
15
|
+
bindir: bin
|
16
|
+
cert_chain: []
|
17
|
+
|
18
|
+
date: 2013-06-28 00:00:00 Z
|
19
|
+
dependencies:
|
20
|
+
- !ruby/object:Gem::Dependency
|
21
|
+
name: bundler
|
22
|
+
prerelease: false
|
23
|
+
requirement: &id001 !ruby/object:Gem::Requirement
|
24
|
+
none: false
|
25
|
+
requirements:
|
26
|
+
- - ~>
|
27
|
+
- !ruby/object:Gem::Version
|
28
|
+
hash: 9
|
29
|
+
segments:
|
30
|
+
- 1
|
31
|
+
- 3
|
32
|
+
version: "1.3"
|
33
|
+
type: :development
|
34
|
+
version_requirements: *id001
|
35
|
+
- !ruby/object:Gem::Dependency
|
36
|
+
name: rake
|
37
|
+
prerelease: false
|
38
|
+
requirement: &id002 !ruby/object:Gem::Requirement
|
39
|
+
none: false
|
40
|
+
requirements:
|
41
|
+
- - ">="
|
42
|
+
- !ruby/object:Gem::Version
|
43
|
+
hash: 3
|
44
|
+
segments:
|
45
|
+
- 0
|
46
|
+
version: "0"
|
47
|
+
type: :development
|
48
|
+
version_requirements: *id002
|
49
|
+
- !ruby/object:Gem::Dependency
|
50
|
+
name: distribution
|
51
|
+
prerelease: false
|
52
|
+
requirement: &id003 !ruby/object:Gem::Requirement
|
53
|
+
none: false
|
54
|
+
requirements:
|
55
|
+
- - ">="
|
56
|
+
- !ruby/object:Gem::Version
|
57
|
+
hash: 3
|
58
|
+
segments:
|
59
|
+
- 0
|
60
|
+
version: "0"
|
61
|
+
type: :development
|
62
|
+
version_requirements: *id003
|
63
|
+
description: A full-featured Ruby statistics library with assumption verification
|
64
|
+
email:
|
65
|
+
- dcohen@gatech.edu
|
66
|
+
executables: []
|
67
|
+
|
68
|
+
extensions: []
|
69
|
+
|
70
|
+
extra_rdoc_files: []
|
71
|
+
|
72
|
+
files:
|
73
|
+
- .travis.yml
|
74
|
+
- Gemfile
|
75
|
+
- LICENSE.txt
|
76
|
+
- README.md
|
77
|
+
- Rakefile
|
78
|
+
- Rsquared.gemspec
|
79
|
+
- install.sh
|
80
|
+
- lib/Rsquared/version.rb
|
81
|
+
- lib/constants.rb
|
82
|
+
- lib/enumerableext.rb
|
83
|
+
- lib/rsquared.rb
|
84
|
+
- lib/version.rb
|
85
|
+
- test/enumerable_tests.rb
|
86
|
+
- test/helper_tests.rb
|
87
|
+
- test/rsquared_tests.rb
|
88
|
+
homepage: https://github.com/dacohen/Rsquared
|
89
|
+
licenses:
|
90
|
+
- MIT
|
91
|
+
post_install_message:
|
92
|
+
rdoc_options: []
|
93
|
+
|
94
|
+
require_paths:
|
95
|
+
- lib
|
96
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
97
|
+
none: false
|
98
|
+
requirements:
|
99
|
+
- - ">="
|
100
|
+
- !ruby/object:Gem::Version
|
101
|
+
hash: 3
|
102
|
+
segments:
|
103
|
+
- 0
|
104
|
+
version: "0"
|
105
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
106
|
+
none: false
|
107
|
+
requirements:
|
108
|
+
- - ">="
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
hash: 3
|
111
|
+
segments:
|
112
|
+
- 0
|
113
|
+
version: "0"
|
114
|
+
requirements: []
|
115
|
+
|
116
|
+
rubyforge_project:
|
117
|
+
rubygems_version: 1.8.24
|
118
|
+
signing_key:
|
119
|
+
specification_version: 3
|
120
|
+
summary: Provides statistical distributions, tests and verifies relevant assumptions
|
121
|
+
test_files:
|
122
|
+
- test/enumerable_tests.rb
|
123
|
+
- test/helper_tests.rb
|
124
|
+
- test/rsquared_tests.rb
|