bio-statsample-glm 0.1.0

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - 2.0.0
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+
+gem 'statsample', '>=1.2.0'
+# Add dependencies required to use your gem here.
+# Example:
+   gem "activesupport", "= 3.2.10"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "minitest", "~> 4.7.5"
+  gem "cucumber", ">= 0"
+  gem "bundler", "~> 1.3.5"
+  gem "jeweler", "~> 1.8.4"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+  gem "mocha", "~> 0.14.0"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Ankur Goel
+
+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.md

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+# bio-statsample-glm
+
+[![Build Status](https://secure.travis-ci.org/AnkurGel/bioruby-statsample-glm.png)](http://travis-ci.org/AnkurGel/bioruby-statsample-glm)
+
+Statsample-GLM is an extension to [Statsample](https://github.com/clbustos/statsample), a suite of advance statistics in Ruby. It includes modules for various regression techniques such as: 
+  
+  * Poisson Regression
+  * Logistic Regression
+  * Exponential Regression
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-statsample-glm
+```
+
+## Usage
+
+```ruby
+    require 'bio-statsample-glm'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/AnkurGel/bioruby-statsample-glm
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-statsample-glm](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2013 Ankur Goel. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-statsample-glm
+
+{<img
+src="https://secure.travis-ci.org/ankurgel/bioruby-statsample-glm.png"
+/>}[http://travis-ci.org/#!/ankurgel/bioruby-statsample-glm]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-statsample-glm
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-statsample-glm'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/ankurgel/bioruby-statsample-glm
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-statsample-glm
+
+== Copyright
+
+Copyright (c) 2013 Ankur Goel. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-statsample-glm"
+  gem.homepage = "http://github.com/AnkurGel/bioruby-statsample-glm"
+  gem.license = "MIT"
+  gem.summary = %Q{Generalized Linear Models for Statsample}
+  gem.description = %Q{Statsample-GLM is an extension to Statsample, an advance statistics suite in Ruby. This gem includes modules for Regression techniques such as Poisson Regression, Logistic Regression and Exponential Regression}
+  gem.email = "ankurgel@gmail.com"
+  gem.authors = ["Ankur Goel"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-statsample-glm #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/features/bio-statsample-glm.feature

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+Feature: something something
+  In order to something something
+  A user something something
+  something something something
+
+  Scenario: something something
+    Given inspiration
+    When I create a sweet new gem
+    Then everyone should see how awesome I am

data/features/support/env.rb

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+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'bio-statsample-glm'
+
+require 'test/unit/assertions'
+
+World(Test::Unit::Assertions)

data/lib/bio-statsample-glm.rb

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+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'statsample'
+require 'bio-statsample-glm/regression'

data/lib/bio-statsample-glm/regression.rb

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+require 'bio-statsample-glm/regression/poisson'
+require 'bio-statsample-glm/regression/logistic'
+module Statsample
+  module Regression
+    include Statsample::VectorShorthands
+
+    # = Generalized linear models
+    # == Parameters
+    #
+    # * x = model matrix
+    # * y = response vector
+    # * method = symbol; choice of glm strategy, default = :poisson
+    #
+    # == Usage
+    #    require 'bio-statsample-glm'
+    #    x1=Statsample::Vector.new([0.537322309644812,-0.717124209978434,-0.519166718891331,0.434970973986765,-0.761822002215759,1.51170030921189,0.883854199811195,-0.908689798854196,1.70331977539793,-0.246971150634099,-1.59077593922623,-0.721548040910253,0.467025703920194,-0.510132788447137,0.430106510266798,-0.144353683251536,-1.54943800728303,0.849307651309298,-0.640304240933579,1.31462478279425,-0.399783455165345,0.0453055645017902,-2.58212161987746,-1.16484414309359,-1.08829266466281,-0.243893919684792,-1.96655661929441,0.301335373291024,-0.665832694463588,-0.0120650855753837,1.5116066367604,0.557300353673344,1.12829931872045,0.234443748015922,-2.03486690662651,0.275544751380246,-0.231465849558696,-0.356880153225012,-0.57746647541923,1.35758352580655,1.23971669378224,-0.662466275100489,0.313263561921793,-1.08783223256362,1.41964722846899,1.29325100940785,0.72153880625103,0.440580131022748,0.0351917814720056, -0.142353224879252],:scale)
+    #    x2=Statsample::Vector.new([-0.866655707911859,-0.367820249977585,0.361486610435,0.857332626245179,0.133438466268095,0.716104533073575,1.77206093023382,-0.10136697295802,-0.777086491435508,-0.204573554913706,0.963353531412233,-1.10103024900542,-0.404372761837392,-0.230226345183469,0.0363730246866971,-0.838265540390497,1.12543549657924,-0.57929175648001,-0.747060244805248,0.58946979365152,-0.531952663697324,1.53338594419818,0.521992029051441,1.41631763288724,0.611402316795129,-0.518355638373296,-0.515192557101107,-0.672697937866108,1.84347042325327,-0.21195540664804,-0.269869371631611,0.296155694010096,-2.18097898069634,-1.21314663927206,1.49193669881581,1.38969280369493,-0.400680808117106,-1.87282814976479,1.82394870451051,0.637864732838274,-0.141155946382493,0.0699950644281617,1.32568550595165,-0.412599258349398,0.14436832227506,-1.16507785388489,-2.16782049922428,0.24318371493798,0.258954871320764,-0.151966534521183],:scale)
+    #    y=Statsample::Vector.new([0,0,1,0,1,1,1,1,0,1,1,1,1,0,1,0,1,1,0,1,0,1,1,1,1,0,0,1,1,0,0,1,0,0,1,1,0,0,1,1,0,1,1,1,1,0,0,0,1,1],:scale)
+    #    x=Statsample::Dataset.new({"i"=>intercept,"x1"=>x1,"x2"=>x2})
+    #    obj = Statsample::Regression.glm(x, y, :binomial)
+    #    #=> Logistic Regression object
+    #
+    # == Returns
+    #    GLM object for given method.
+    def self.glm(x, y, method=:poisson)
+      if method.downcase.to_sym == :poisson
+        obj = Statsample::Regression::GLM::Poisson.new(x,y)
+      elsif method.downcase.to_sym == :binomial
+        obj = Statsample::Regression::GLM::Logistic.new(x,y)
+      end
+      obj
+      #now, #irwls method is available to be called on returned obj
+    end
+
+
+    def self.irwls(x, y, mu, w, j, h, epsilon = 1e-7, max_iter = 100)
+      b = Matrix.column_vector(Array.new(x.column_size,0.0))
+      converged = false
+      1.upto(max_iter) do |i|
+        #conversion from : (solve(j(x,b)) %*% h(x,b,y))
+
+        intermediate = (j.call(x,b).inverse * h.call(x,b,y))
+        b_new = b - intermediate
+
+        if((b_new - b).map(&:abs)).to_a.flatten.inject(:+) < epsilon
+          converged = true
+          b = b_new
+          break
+        end
+        b = b_new
+      end
+      ss = j.call(x,b).inverse.diagonal.map{ |x| -x}.map{ |y| Math.sqrt(y) }
+      values = mu.call(x,b)
+
+      residuals = y - values.column_vectors.map(&:to_a).flatten
+      df_residuals = y.count - x.column_size
+      return [create_vector(b.column_vectors[0]), create_vector(ss), create_vector(values.to_a.flatten),
+              residuals, max_iter, df_residuals, converged]
+    end
+
+    private
+    def self.create_vector(arr)
+      Statsample::Vector.new(arr, :scale)
+    end
+  end
+end

data/lib/bio-statsample-glm/regression/logistic.rb

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+module Statsample
+  module Regression
+    module GLM
+
+      class Logistic
+
+        # a named vector of coefficients
+        attr_reader :coefficients
+        #
+        attr_reader :se
+        # The fitted mean values
+        attr_reader :fit
+        # the _working_ residuals; that is the residuals in the final iteration of the IRWLS fit.
+        attr_reader :residuals
+        # The residuals degree of freedom
+        attr_reader :df
+        # Number of iterations used for convergence
+        attr_reader :iter
+        # Boolean. Tells whether the IRWLS for the given model converged or not
+        attr_reader :converged
+
+        def initialize(x, y)
+          @x = x
+          @y = y
+        end
+
+        def self.mu(x, b)
+          matrix_mul = x * b
+          numerator = matrix_mul.map { |y| Math.exp(y) }
+          denominator = numerator.map { |y| 1 + y }
+
+          numerator.each_with_index { |e, r, c|
+            numerator[r,c] = numerator[r,c].to_f / denominator[r,c].to_f
+          }
+        end
+
+        def self.w(x, b)
+          mus = mu(x,b).column_vectors.map(&:to_a).flatten
+          mus_intermediate = mus.collect { |x| 1 - x }
+          w = mus.zip(mus_intermediate).collect { |x| x.inject(:*) }
+          w_mat = Matrix.I(w.size)
+          w_enum = w.to_enum
+          return w_mat.map do |x|
+            x.eql?(1) ? w_enum.next : x
+          end
+        end
+
+        def self.h(x,b,y)
+          x_t = x.transpose
+          mu_flat = mu(x,b).column_vectors.map(&:to_a).flatten
+          column_data = y.zip(mu_flat).collect { |x| x.inject(:-) }
+          x_t * Matrix.column_vector(column_data)
+        end
+
+        def self.j(x,b)
+          w_matrix = w(x, b)
+          jacobian_matrix = x.transpose * w_matrix * x
+          jacobian_matrix.map { |x| -x }
+        end
+
+        def to_s
+          sprintf("Logistic Regression (Statsample::Regression::GLM;:Logistic)")
+        end
+
+        # = Iteratively reweighted least squares
+        #   Computes irwls for given model and parameters.
+        #
+        # == Usage
+        #    require 'bio-statsample-glm'
+        #    x1=Statsample::Vector.new([0.537322309644812,-0.717124209978434,-0.519166718891331,0.434970973986765,-0.761822002215759,1.51170030921189,0.883854199811195,-0.908689798854196,1.70331977539793,-0.246971150634099,-1.59077593922623,-0.721548040910253,0.467025703920194,-0.510132788447137,0.430106510266798,-0.144353683251536,-1.54943800728303,0.849307651309298,-0.640304240933579,1.31462478279425,-0.399783455165345,0.0453055645017902,-2.58212161987746,-1.16484414309359,-1.08829266466281,-0.243893919684792,-1.96655661929441,0.301335373291024,-0.665832694463588,-0.0120650855753837,1.5116066367604,0.557300353673344,1.12829931872045,0.234443748015922,-2.03486690662651,0.275544751380246,-0.231465849558696,-0.356880153225012,-0.57746647541923,1.35758352580655,1.23971669378224,-0.662466275100489,0.313263561921793,-1.08783223256362,1.41964722846899,1.29325100940785,0.72153880625103,0.440580131022748,0.0351917814720056, -0.142353224879252],:scale)
+        #    x2=Statsample::Vector.new([-0.866655707911859,-0.367820249977585,0.361486610435,0.857332626245179,0.133438466268095,0.716104533073575,1.77206093023382,-0.10136697295802,-0.777086491435508,-0.204573554913706,0.963353531412233,-1.10103024900542,-0.404372761837392,-0.230226345183469,0.0363730246866971,-0.838265540390497,1.12543549657924,-0.57929175648001,-0.747060244805248,0.58946979365152,-0.531952663697324,1.53338594419818,0.521992029051441,1.41631763288724,0.611402316795129,-0.518355638373296,-0.515192557101107,-0.672697937866108,1.84347042325327,-0.21195540664804,-0.269869371631611,0.296155694010096,-2.18097898069634,-1.21314663927206,1.49193669881581,1.38969280369493,-0.400680808117106,-1.87282814976479,1.82394870451051,0.637864732838274,-0.141155946382493,0.0699950644281617,1.32568550595165,-0.412599258349398,0.14436832227506,-1.16507785388489,-2.16782049922428,0.24318371493798,0.258954871320764,-0.151966534521183],:scale)
+        #    y=Statsample::Vector.new([0,0,1,0,1,1,1,1,0,1,1,1,1,0,1,0,1,1,0,1,0,1,1,1,1,0,0,1,1,0,0,1,0,0,1,1,0,0,1,1,0,1,1,1,1,0,0,0,1,1],:scale)
+        #    x=Statsample::Dataset.new({"i"=>intercept,"x1"=>x1,"x2"=>x2})
+        #    obj = Statsample::Regression.glm(x, y, :binomial)
+        #    #=> Logistic Regression object
+        #    obj.irlws
+        #    #=> Array of returned values
+        #    obj.coefficients
+        #    #=> named vector of coefficients
+
+        def irwls
+          x, y = @x, @y
+          #calling irwls on Regression and passing equivalent methods in lambdas.
+          #Ruby_level+=awesome!
+          @coefficients, @se, @fit, @residuals, @df, @iter, @converged = Statsample::Regression.irwls(
+              x,y, ->l,m{self.class.mu(l,m)}, ->l,m{self.class.w(l,m)},
+              ->l,m{self.class.j(l,m)}, ->k,l,m{self.class.h(k,l,m)}
+          )
+        end
+      end
+
+    end
+  end
+end

data/lib/bio-statsample-glm/regression/poisson.rb

@@ -0,0 +1,76 @@
+module Statsample
+  module Regression
+    module GLM
+
+      class Poisson
+
+        # a named vector of coefficients
+        attr_reader :coefficients
+        #
+        attr_reader :se
+        # The fitted mean values
+        attr_reader :fit
+        # the _working_ residuals; that is the residuals in the final iteration of the IRWLS fit.
+        attr_reader :residuals
+        # The residuals degree of freedom
+        attr_reader :df
+        # Number of iterations used for convergence
+        attr_reader :iter
+        # Boolean. Tells whether the IRWLS for the given model converged or not
+        attr_reader :converged
+
+        def initialize(x, y)
+          @x = x
+          @y = y
+        end
+
+        def self.mu(x, b, link=:log)
+          if link.downcase.to_sym == :log
+            (x * b).map { |y| Math.exp(y) }
+          elsif link.downcase.to_sym == :sqrt
+            (x * b).collect { |y| y**2 }
+          end
+        end
+
+        def self.w(x, b)
+          poisson_mu = mu(x,b)
+          mu_flat = poisson_mu.column_vectors.map(&:to_a).flatten
+
+          w_mat = Matrix.I(mu_flat.size)
+          mu_enum = mu_flat.to_enum
+          return w_mat.map do |x|
+            x.eql?(1) ? mu_enum.next : x
+          end
+        end
+
+        def self.h(x, b, y)
+          x_t = x.transpose
+          mu_flat = mu(x,b).column_vectors.map(&:to_a).flatten
+          column_data = y.zip(mu_flat).collect { |x| x.inject(:-) }
+          x_t * Matrix.columns([column_data])
+        end
+
+        def self.j(x, b)
+          w_matrix = w(x, b)
+          jacobian_matrix = x.transpose * w_matrix * x
+          jacobian_matrix.map { |x| -x }
+        end
+
+        def to_s
+          sprintf("Logistic Regression (Statsample::Regression::GLM;:Logistic)")
+        end
+
+        def irwls
+          x,y = @x,@y
+          #calling irwls on Regression and passing equivalent methods in lambdas.
+          #Ruby_level+=awesome!
+          @coefficients, @se, @fit, @residuals, @df, @iter, @converged = Statsample::Regression.irwls(
+              x,y, ->l,m{self.class.mu(l,m)}, ->l,m{self.class.w(l,m)},
+              ->l,m{self.class.j(l,m)}, ->k,l,m{self.class.h(k,l,m)}
+          )
+        end
+
+      end
+    end
+  end
+end

data/test/helper.rb

@@ -0,0 +1,79 @@
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'minitest/unit'
+require 'shoulda'
+require 'shoulda-context'
+require 'mocha/setup'
+
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-statsample-glm'
+module MiniTest
+  class Unit
+    class TestCase
+      include Shoulda::Context::Assertions
+      include Shoulda::Context::InstanceMethods
+      extend Shoulda::Context::ClassMethods
+      def self.should_with_gsl(name,&block)
+        should(name) do
+          if Statsample.has_gsl?
+            instance_eval(&block)
+          else
+            skip("Requires GSL")
+          end
+        end
+      end
+    end
+  end
+
+  module Assertions
+    def assert_similar_vector(exp, obs, delta=1e-10,msg=nil)
+      msg||="Different vectors #{exp} - #{obs}"
+      assert_equal(exp.size, obs.size)
+      exp.data_with_nils.each_with_index {|v,i|
+        assert_in_delta(v,obs[i],delta)
+      }
+    end
+    def assert_equal_vector(exp,obs,delta=1e-10,msg=nil)
+      assert_equal(exp.size, obs.size, "Different size.#{msg}")
+      exp.size.times {|i|
+        assert_in_delta(exp[i],obs[i],delta, "Different element #{i}. \nExpected:\n#{exp}\nObserved:\n#{obs}.#{msg}")
+      }
+    end
+    def assert_equal_matrix(exp,obs,delta=1e-10,msg=nil)
+      assert_equal(exp.row_size, obs.row_size, "Different row size.#{msg}")
+      assert_equal(exp.column_size, obs.column_size, "Different column size.#{msg}")
+      exp.row_size.times {|i|
+        exp.column_size.times {|j|
+          assert_in_delta(exp[i,j],obs[i,j], delta, "Different element #{i},#{j}\nExpected:\n#{exp}\nObserved:\n#{obs}.#{msg}")
+        }
+      }
+    end
+    alias :assert_raise :assert_raises unless method_defined? :assert_raise
+    alias :assert_not_equal :refute_equal unless method_defined? :assert_not_equal
+    alias :assert_not_same :refute_same unless method_defined? :assert_not_same
+    unless method_defined? :assert_nothing_raised
+      def assert_nothing_raised(msg=nil)
+        msg||="Nothing should be raised, but raised %s"
+        begin
+          yield
+          not_raised=true
+        rescue Exception => e
+          not_raised=false
+          msg=sprintf(msg,e)
+        end
+        assert(not_raised,msg)
+      end
+    end
+  end
+end
+
+MiniTest::Unit.autorun

data/test/test_glm.rb

@@ -0,0 +1,37 @@
+require(File.expand_path(File.dirname(__FILE__)+'/helper.rb'))
+
+class StatsampleRegressionGlm < MiniTest::Unit::TestCase
+
+  context("Example") do
+    setup do
+      x1=Statsample::Vector.new([0.537322309644812,-0.717124209978434,-0.519166718891331,0.434970973986765,-0.761822002215759,1.51170030921189,0.883854199811195,-0.908689798854196,1.70331977539793,-0.246971150634099,-1.59077593922623,-0.721548040910253,0.467025703920194,-0.510132788447137,0.430106510266798,-0.144353683251536,-1.54943800728303,0.849307651309298,-0.640304240933579,1.31462478279425,-0.399783455165345,0.0453055645017902,-2.58212161987746,-1.16484414309359,-1.08829266466281,-0.243893919684792,-1.96655661929441,0.301335373291024,-0.665832694463588,-0.0120650855753837,1.5116066367604,0.557300353673344,1.12829931872045,0.234443748015922,-2.03486690662651,0.275544751380246,-0.231465849558696,-0.356880153225012,-0.57746647541923,1.35758352580655,1.23971669378224,-0.662466275100489,0.313263561921793,-1.08783223256362,1.41964722846899,1.29325100940785,0.72153880625103,0.440580131022748,0.0351917814720056, -0.142353224879252],:scale)
+      x2=Statsample::Vector.new([-0.866655707911859,-0.367820249977585,0.361486610435,0.857332626245179,0.133438466268095,0.716104533073575,1.77206093023382,-0.10136697295802,-0.777086491435508,-0.204573554913706,0.963353531412233,-1.10103024900542,-0.404372761837392,-0.230226345183469,0.0363730246866971,-0.838265540390497,1.12543549657924,-0.57929175648001,-0.747060244805248,0.58946979365152,-0.531952663697324,1.53338594419818,0.521992029051441,1.41631763288724,0.611402316795129,-0.518355638373296,-0.515192557101107,-0.672697937866108,1.84347042325327,-0.21195540664804,-0.269869371631611,0.296155694010096,-2.18097898069634,-1.21314663927206,1.49193669881581,1.38969280369493,-0.400680808117106,-1.87282814976479,1.82394870451051,0.637864732838274,-0.141155946382493,0.0699950644281617,1.32568550595165,-0.412599258349398,0.14436832227506,-1.16507785388489,-2.16782049922428,0.24318371493798,0.258954871320764,-0.151966534521183],:scale)
+      @y_log=Statsample::Vector.new([0,0,1,0,1,1,1,1,0,1,1,1,1,0,1,0,1,1,0,1,0,1,1,1,1,0,0,1,1,0,0,1,0,0,1,1,0,0,1,1,0,1,1,1,1,0,0,0,1,1],:scale)
+      @y_pois=Statsample::Vector.new([1,2,1,3,3,1,10,1,1,2,15,0,0,2,1,2,18,2,1,1,1,8,18,13,7,1,1,0,26,0,2,2,0,0,25,7,0,0,21,0,0,1,5,0,3,0,0,1,0,0],:scale)
+      intercept=Statsample::Vector.new([1]*50,:scale)
+      @df=Statsample::Dataset.new({"i"=>intercept,"x1"=>x1,"x2"=>x2})
+    end
+
+    context("Logistic") do
+      setup do
+        @glm=Statsample::Regression.glm(@df.to_matrix,@y_log,:binomial)
+        @glm.irwls
+      end
+
+      should "report correct coefficientes" do
+        assert_similar_vector(@glm.coefficients,[0.675603176233325,-0.312493754568903,2.28671333346264])
+      end
+    end
+
+    context("Poisson") do
+      setup do
+        @glm=Statsample::Regression.glm(@df.to_matrix,@y_pois,:poisson)
+        @glm.irwls
+      end
+
+      should "report correct coefficientes" do
+        assert_similar_vector(@glm.coefficients,[0.32993246633711,-0.586359358356708,1.28511323439258])
+      end
+    end
+  end
+end

metadata

@@ -0,0 +1,246 @@
+--- !ruby/object:Gem::Specification
+name: bio-statsample-glm
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+  prerelease: 
+platform: ruby
+authors:
+- Ankur Goel
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-09-23 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: statsample
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.2.0
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.2.10
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - '='
+      - !ruby/object:Gem::Version
+        version: 3.2.10
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.7.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 4.7.5
+- !ruby/object:Gem::Dependency
+  name: cucumber
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.3.5
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: mocha
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.14.0
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.14.0
+description: Statsample-GLM is an extension to Statsample, an advance statistics suite
+  in Ruby. This gem includes modules for Regression techniques such as Poisson Regression,
+  Logistic Regression and Exponential Regression
+email: ankurgel@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- features/bio-statsample-glm.feature
+- features/step_definitions/bio-statsample-glm_steps.rb
+- features/support/env.rb
+- lib/bio-statsample-glm.rb
+- lib/bio-statsample-glm/regression.rb
+- lib/bio-statsample-glm/regression/logistic.rb
+- lib/bio-statsample-glm/regression/poisson.rb
+- test/helper.rb
+- test/test_glm.rb
+homepage: http://github.com/AnkurGel/bioruby-statsample-glm
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+      segments:
+      - 0
+      hash: 797002845
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.25
+signing_key: 
+specification_version: 3
+summary: Generalized Linear Models for Statsample
+test_files: []