ruby-regress 0.0.1

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/LICENSE

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+Copyright (c) 2009 Trevor Fountain
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.mdown

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+# ruby-regress
+### A partial drop-in replacement for |STAT's regress
+
+`ruby-regress` is a tool for computing correlations and regression equations
+from two-variable input. It is designed to function as a drop-in replacement
+for Gary Perlman's `regress`, at least for those who use only the basic
+functionality that `regress` provides...
+
+## Installation
+
+Download the most recent source from Github:
+
+    git clone git://github.com/doches/ruby-regress.git
+
+then build and install the gem:
+
+    cd ruby-regress
+    rake build
+    sudo rake install
+
+## Usage
+
+ruby-regress installs a single command line tool called `regress`, which
+reads from `STDIN` and prints a report containing the correlation coefficient,
+plus some descriptive statistics, to `STDOUT`. For example, if we have a file in
+the current directory called `data.txt` containing two datasets:
+
+    1   12.0
+    2   11.0
+    3   13.0
+    4   14.0
+
+we can get the correlation coefficient between these two variables by:
+
+    cat data.txt | regress
+
+which will dump a load of statistical information about the datasets to
+the terminal.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "ruby-regress"
+    gem.summary = %Q{CLI tool for computing correlation (Pearson's r)}
+    gem.description = %Q{Ruby implementation of Gary Perlman's `regress` tool from (the difficult to obtain) |STAT package.}
+    gem.email = "doches@gmail.com"
+    gem.homepage = "http://github.com/doches/ruby-regress"
+    gem.authors = ["Trevor Fountain"]
+    gem.bindir = "bin"
+    gem.executables = %w{regress}
+    gem.add_development_dependency('wrong','>=0.2.0')
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+begin
+  require 'rcov/rcovtask'
+  Rcov::RcovTask.new do |test|
+    test.libs << 'test'
+    test.pattern = 'test/**/test_*.rb'
+    test.verbose = true
+  end
+rescue LoadError
+  task :rcov do
+    abort "RCov is not available. In order to run rcov, you must: sudo gem install spicycode-rcov"
+  end
+end
+
+task :test => :check_dependencies
+
+task :default => :test
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "ruby-regress #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/regress

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+#!/usr/bin/env ruby
+
+# Reads a file containing two whitespace-delimited columns of numerical data
+# and outputs Pearson's r and some assorted descriptive statistics.
+#
+# A partial drop-in replacement for |STAT's `regress` tool, with caveats:
+#
+#    + Does not compute SEest, F(), or prob()
+#    + Only handles two variables (no more!)
+#    + Does not calculate regression line, because I don't need it.
+#
+# ...and extra features:
+#
+#    + Ignores comment lines (lines starting with '#')
+#    + Ignores anything on a line /after/ a '#'
+
+$LOAD_PATH.unshift File.join(File.dirname(__FILE__),"..","lib")
+require 'ruby-regress'
+
+input = []
+STDIN.each_line do |line|
+  cols = line.strip.gsub(/#.+$/,'').split(/\s/).map { |x| x.to_f }
+	input.push cols if cols.size == 2
+end
+a,b = *[0,1].map { |i| input.collect { |x| x[i] } }
+
+regress = Regress.new(a,b)
+puts "Analysis for #{a.size} cases of 2 variables:"
+puts "Variable          REG          A "
+puts "Min#{sprintf("%18.4f",Regress.min(a))}#{sprintf("%11.4f ",Regress.min(b))}"
+puts "Max#{sprintf("%18.4f",Regress.max(a))}#{sprintf("%11.4f ",Regress.max(b))}"
+puts "Sum#{sprintf("%18.4f",Regress.sum(a))}#{sprintf("%11.4f ",Regress.sum(b))}"
+puts "Mean#{sprintf("%17.4f",Regress.mean(a))}#{sprintf("%11.4f ",Regress.mean(b))}"
+puts "SD#{sprintf("%19.4f",Regress.standard_deviation(a))}#{sprintf("%11.4f ",Regress.standard_deviation(b))}"
+puts ""
+puts "Correlation Matrix:"
+puts "REG            1.0000 "
+puts "A              #{sprintf("%1.4f",regress.r)}     1.0000 "
+puts "Variable          REG          A"
+puts ""
+#puts "Regression Equation for REG:"
+#puts "REG  =#{sprintf("%3.3f",Regress.slope)} A  +#{sprintf("%4.4f",Regress.intercept)}"
+#puts ""
+puts "Significance test for prediction of REG"
+puts "    Mult-R  R-Squared "
+puts " #{sprintf("%9.4f",regress.r)}  #{sprintf("%9.4f",regress.r**2)} "

data/lib/ruby-regress.rb

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+class Regress
+  attr_reader :r, :slope, :intercept
+  
+  # Create a Regress object from two vectors +a+ and +b+. Note that +a+ and +b+ must be of the same length.
+  def initialize(a,b)
+    raise "Regress#initialize expects two vectors of equal length (given vectors of lengths #{a.size}, #{b.size})." if a.size != b.size
+    
+    sa,sb = *[a,b].map { |d| Regress.sum(d) }
+    sa2,sb2 = *[a,b].map { |d| Regress.sum(Regress.square(d)) }
+    sab = Regress.multiply(a,b)
+    n = a.size
+    
+    @r = (n * sab - sa * sb) / (( (n * sa2 - sa**2) * (n * sb2 - sb**2) ) ** 0.5)
+  end
+  
+  def Regress.sum(vector)
+    vector.inject(0) { |s,x| s += x }
+  end
+  
+  def Regress.square(vector)
+    vector.map { |x| x**2 }
+  end
+  
+  def Regress.multiply(a,b)
+    (0..a.size-1).inject(0) { |s,i| s += a[i] * b[i] }
+  end
+  
+  def Regress.min(vector)
+    vector.sort.shift
+  end
+  
+  def Regress.max(vector)
+    vector.sort.pop
+  end
+  
+  def Regress.mean(vector)
+    Regress.sum(vector) / vector.size.to_f
+  end
+  
+  def Regress.standard_deviation(vector)
+    mean = Regress.mean(vector)
+    (vector.collect { |x| (x-mean)**2 }.inject(0) { |s,x| s += x } / (vector.size.to_f-1)) ** 0.5
+  end
+end

data/test/helper.rb

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+require 'rubygems'
+require 'test/unit'
+
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'ruby-regress'
+
+class Test::Unit::TestCase
+end

data/test/test_ruby-regress.rb

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+require 'helper'
+require 'ruby-regress'
+require 'wrong'
+
+module InDelta
+  def in_delta?(other,delta=0.01)
+    (self - other).abs < delta
+  end
+end
+
+class Float
+  include InDelta
+end
+
+class Fixnum
+  include InDelta
+end
+
+class TestRubyRegress < Test::Unit::TestCase
+  include Wrong::Assert
+  
+  def test_sums
+    @a = [72,65,80,36,50,21,79,64,44,55]
+    @b = [78,70,81,31,55,29,74,64,47,53]
+    
+    assert { Regress.sum(@a) == 566 }
+    assert { Regress.sum(@b) == 582 }
+    
+    assert { Regress.sum(Regress.square(@a)) == 35344 }
+    assert { Regress.sum(Regress.square(@b)) == 36962 }
+    
+    assert { Regress.multiply(@a,@b) == 36046 }
+  end
+  
+  def test_stats
+    @a = [68, 71, 62, 75, 58, 60, 67, 68, 71, 69, 68, 67, 63, 62, 60, 63, 65, 67, 63, 61]
+    
+    assert { Regress.min(@a).in_delta? 58 }
+    assert { Regress.max(@a).in_delta? 75 }
+    assert { Regress.sum(@a).in_delta? 1308 }
+    assert { Regress.mean(@a).in_delta? 65.4 }
+    assert { Regress.standard_deviation(@a).in_delta? 4.4057,0.0001 }
+  end
+  
+  def test_malformed_input
+    assert { rescuing { Regress.new([1,2], [1,2,3]) }.message == "Regress#initialize expects two vectors of equal length (given vectors of lengths 2, 3)." }
+  end
+  
+  # This example is for population standard deviation, not sample -- so let's make sure we get it wrong!
+  def test_sd_wikipedia_example
+    a = [2,4,4,4,5,5,7,9]
+    
+    assert { Regress.standard_deviation(a) != 2 }
+  end
+  
+  def test_correlation
+    @a = [68, 71, 62, 75, 58, 60, 67, 68, 71, 69, 68, 67, 63, 62, 60, 63, 65, 67, 63, 61]
+    @b = [4.1, 4.6, 3.8, 4.4, 3.2, 3.1, 3.8, 4.1, 4.3, 3.7, 3.5, 3.2, 3.7, 3.3, 3.4, 4.0, 4.1, 3.8, 3.4, 3.6]
+    
+    regress = Regress.new(@a, @b)
+    
+    assert { regress.r.in_delta? 0.73 }
+  end
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: ruby-regress
+version: !ruby/object:Gem::Version 
+  hash: 29
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- Trevor Fountain
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-08-25 00:00:00 +01:00
+default_executable: regress
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: wrong
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 23
+        segments: 
+        - 0
+        - 2
+        - 0
+        version: 0.2.0
+  type: :development
+  version_requirements: *id001
+description: Ruby implementation of Gary Perlman's `regress` tool from (the difficult to obtain) |STAT package.
+email: doches@gmail.com
+executables: 
+- regress
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.mdown
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.mdown
+- Rakefile
+- VERSION
+- bin/regress
+- lib/ruby-regress.rb
+- test/helper.rb
+- test/test_ruby-regress.rb
+has_rdoc: true
+homepage: http://github.com/doches/ruby-regress
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 3
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.7
+signing_key: 
+specification_version: 3
+summary: CLI tool for computing correlation (Pearson's r)
+test_files: 
+- test/helper.rb
+- test/test_ruby-regress.rb