agglomerative_clustering 0.0.1

checksums.yaml

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+SHA1:
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data/.gitignore

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+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalisation:
+/.bundle/
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# Gemfile.lock
+# .ruby-version
+# .ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+outliers.csv
+points.csv

data/.rspec

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+--color
+--format documentation
+--require spec_helper

data/Gemfile

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+source "https://rubygems.org"
+gemspec
+gem 'factory_girl'

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    agglomerative_clustering (0.0.1)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (4.1.6)
+      i18n (~> 0.6, >= 0.6.9)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.1)
+      tzinfo (~> 1.1)
+    diff-lcs (1.2.5)
+    factory_girl (4.4.0)
+      activesupport (>= 3.0.0)
+    i18n (0.6.11)
+    json (1.8.1)
+    minitest (5.4.2)
+    rake (10.3.2)
+    rspec (3.1.0)
+      rspec-core (~> 3.1.0)
+      rspec-expectations (~> 3.1.0)
+      rspec-mocks (~> 3.1.0)
+    rspec-core (3.1.6)
+      rspec-support (~> 3.1.0)
+    rspec-expectations (3.1.2)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.1.0)
+    rspec-mocks (3.1.3)
+      rspec-support (~> 3.1.0)
+    rspec-support (3.1.2)
+    thread_safe (0.3.4)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  agglomerative_clustering!
+  bundler (~> 1.7)
+  factory_girl
+  rake (~> 10.0)
+  rspec

data/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2014 Bryan Mulvihill
+
+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/LICENSE.txt

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+Copyright (c) 2014 Bryan Mulvihill
+
+MIT License
+
+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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+# AgglomerativeClustering
+
+Hierarchical Agglomerative Clustering Algorithm
+
+Input Set of 3 dimensional points, group into nearest k clusters
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'agglomerative_clustering'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install agglomerative_clustering
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it ( https://github.com/[my-github-username]/agglomerative_clustering/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+

data/agglomerative_clustering.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'agglomerative_clustering/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "agglomerative_clustering"
+  spec.version       = AgglomerativeClustering::VERSION
+  spec.authors       = ["Bryan Mulvihill"]
+  spec.email         = ["bmulvihill@pinsonault.com"]
+  spec.summary       = %q{Ruby Agglomerative Clustering Algorithm}
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  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_development_dependency "bundler", "~> 1.7"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency 'rspec'
+end

data/cluster.rb

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+#!/usr/bin/env ruby
+require 'agglomerative_clustering'
+
+set = AgglomerativeClustering::Set.new(AgglomerativeClustering::Linkage::Single.new)
+for i in 0..99
+  x = Random.rand(0..100)
+  y = Random.rand(0..100)
+  z = Random.rand(0..100)
+  p = Point.new(x,y,z)
+  set.push(p)
+end
+for i in 100..199
+  x = Random.rand(200..299)
+  y = Random.rand(200..299)
+  z = Random.rand(200..299)
+  p = Point.new(x,y,z)
+  set.push(p)
+end
+for i in 200..299
+  x = Random.rand(400..499)
+  y = Random.rand(400..499)
+  z = Random.rand(400..499)
+  p = Point.new(x,y,z)
+  set.push(p)
+end
+
+percentage = 80
+distance = 150
+
+open('points.csv', 'w') do |f|
+  set.points.each do |point|
+    f << "#{point.x},#{point.y},#{point.z}\n"
+  end
+end
+
+open('outliers.csv', 'w') do |f|
+  set.find_outliers(percentage, distance).each do |point|
+    f << "#{point.x},#{point.y},#{point.z}\n"
+  end
+end
+
+if set.outliers.any?
+  puts 'Outliers Removed from Set:'
+  set.outliers.each do |outlier|
+    puts outlier
+  end
+else
+  puts "There are no outliers where #{percentage}% of the points lie at a distance greater than #{distance}"
+end
+
+clusters = set.cluster(3)
+clusters.each_with_index do |cluster, index|
+  open("cluster#{index}.csv", 'w') do |f|
+    cluster.points.each do |point|
+      f << "#{point.x},#{point.y},#{point.z}\n"
+    end
+  end
+end

data/lib/agglomerative_clustering.rb

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+require "agglomerative_clustering/version"
+require "agglomerative_clustering/euclidean_distance"
+require "agglomerative_clustering/linkage/base"
+require "agglomerative_clustering/linkage/single"
+require "agglomerative_clustering/linkage/complete"
+require "agglomerative_clustering/linkage/average"
+require "agglomerative_clustering/linkage/center"
+require "agglomerative_clustering/point"
+require "agglomerative_clustering/cluster"
+require "agglomerative_clustering/set"

data/lib/agglomerative_clustering/cluster.rb

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+module AgglomerativeClustering
+  class Cluster
+    attr_reader :points
+
+    def initialize(point)
+      points << point
+    end
+
+    def points
+      @points ||= []
+    end
+
+    def merge(cluster)
+      cluster.points.each { |point| points << point }
+      self
+    end
+
+  end
+end

data/lib/agglomerative_clustering/euclidean_distance.rb

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+module AgglomerativeClustering
+  module EuclideanDistance
+    def euclidean_distance point1, point2
+      # Thanks to https://blog.philipcunningham.org/posts/ruby-euclidean-distance
+      Math.sqrt(point1.zip(point2).map{|a,b| a-b}.map{|d| d*d}.reduce(:+))
+    end
+  end
+end

data/lib/agglomerative_clustering/linkage/average.rb

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+module AgglomerativeClustering
+  module Linkage
+    class Average < Base
+
+      def calculate_distance(cluster1, cluster2)
+        distances = []
+        cluster1.points.each do |point1|
+          cluster2.points.each do |point2|
+            distances << euclidean_distance(point1, point2)
+          end
+        end
+        distances.inject(:+)/distances.size
+      end
+
+      def clusters_to_merge
+        @clusters_to_merge ||= []
+      end
+    end
+  end
+end

data/lib/agglomerative_clustering/linkage/base.rb

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+module AgglomerativeClustering
+  module Linkage
+    class Base
+      include EuclideanDistance
+
+      def cluster(clusters)
+        min_cluster_dist = 1.0/0
+        clusters.each_with_index do |cluster1, index|
+          clusters[index + 1..clusters.size].each do |cluster2|
+            distance = calculate_distance(cluster1, cluster2)
+            if distance < min_cluster_dist
+              min_cluster_dist = distance
+              @clusters_to_merge = [cluster1, cluster2]
+            end
+          end
+        end
+        clusters_to_merge
+      end
+      
+    end
+  end
+end

data/lib/agglomerative_clustering/linkage/center.rb

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+module AgglomerativeClustering
+  module Linkage
+    class Center < Base
+
+      def calculate_distance(cluster1, cluster2)
+        point1, point2 = center_point(cluster1), center_point(cluster2)
+        euclidean_distance(point1, point2)
+      end
+
+      def center_point cluster
+        cluster.points.first.zip(*cluster.points[1..cluster.points.size-1]).map { |a,b| (a + b)/cluster.points.size.to_f }
+      end
+
+      def clusters_to_merge
+        @clusters_to_merge ||= []
+      end
+
+    end
+  end
+end

data/lib/agglomerative_clustering/linkage/complete.rb

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+module AgglomerativeClustering
+  module Linkage
+    class Complete < Base
+
+      def calculate_distance(cluster1, cluster2)
+        max_point_distance = 0
+        cluster1.points.each do |point1|
+          cluster2.points.each do |point2|
+            distance = euclidean_distance(point1, point2)
+            max_point_distance = distance if distance > max_point_distance
+          end
+        end
+        max_point_distance
+      end
+
+      def clusters_to_merge
+        @clusters_to_merge ||= []
+      end
+
+    end
+  end
+end

data/lib/agglomerative_clustering/linkage/single.rb

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+module AgglomerativeClustering
+  module Linkage
+    class Single < Base
+
+      def calculate_distance(cluster1, cluster2)
+        min_point_distance = 1.0/0
+        cluster1.points.each do |point1|
+          cluster2.points.each do |point2|
+            distance = euclidean_distance(point1, point2)
+            min_point_distance = distance if distance < min_point_distance
+          end
+        end
+        min_point_distance
+      end
+
+      def clusters_to_merge
+        @clusters_to_merge ||= []
+      end
+    end
+  end
+end

data/lib/agglomerative_clustering/point.rb

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+Point = Struct.new(:x, :y, :z) do
+  attr_accessor :index
+end

data/lib/agglomerative_clustering/set.rb

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+require 'matrix'
+module AgglomerativeClustering
+  class Set
+    include EuclideanDistance
+    attr_reader :points
+
+    def initialize(linkage)
+      @linkage = linkage
+      @points = []
+    end
+
+    def push point
+      point.index = points.size
+      points << point
+    end
+
+    def clusters
+      @clusters ||= points.map{ |point| AgglomerativeClustering::Cluster.new(point) }
+    end
+
+    def distance_matrix
+      @distance_matrix ||= build_distance_matrix
+    end
+
+    def print_distance_matrix
+      puts distance_matrix.to_a.map(&:inspect)
+    end
+
+    def cluster total_clusters
+      clusters_to_merge =[]
+      while clusters.size > total_clusters
+        clusters_to_merge = @linkage.cluster(clusters)
+        merge_clusters(clusters_to_merge)
+      end
+      clusters
+    end
+
+    def merge_clusters(min_clusters)
+      min_clusters[0].merge(min_clusters[1])
+      clusters.reject! { |cluster| cluster == min_clusters[1] }
+      min_clusters[0]
+    end
+
+    def outliers
+      set_outliers.uniq
+    end
+
+    def find_outliers percentage_of_clusters, distance
+      distance_matrix.each_with_index do |index, row, column|
+        count_hash[row] ||= 0
+        count_hash[row] += 1 if distance_matrix[row, column] > distance
+        set_outliers << points[row] if count_hash[row]/(distance_matrix.row_count - 1) > percentage_of_clusters/100
+      end
+      points.reject! { |point| outliers.include?(point) }
+      outliers
+    end
+
+    private
+
+    def set_outliers
+      @set_outliers ||= []
+    end
+
+    def count_hash
+      @count_hash ||= {}
+    end
+
+    def build_distance_matrix
+      Matrix.build(points.size, points.size) do |row, column|
+        euclidean_distance(points[row], points[column]).round(2)
+      end
+    end
+
+  end
+end

data/lib/agglomerative_clustering/version.rb

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+module AgglomerativeClustering
+  VERSION = "0.0.1"
+end

data/spec/factories/lib/agglomerative_clustering/cluster.rb

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+FactoryGirl.define do
+  factory :cluster, class: AgglomerativeClustering::Cluster do
+    initialize_with { new(FactoryGirl.build(:point)) }
+  end
+end

data/spec/factories/lib/agglomerative_clustering/point.rb

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+FactoryGirl.define do
+  factory :point, class: Point do
+    x { Random.rand(1000) }
+    y { Random.rand(1000) }
+    z { Random.rand(1000) }
+  end
+end

data/spec/factories/lib/agglomerative_clustering/set.rb

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+FactoryGirl.define do
+  factory :set, class: AgglomerativeClustering::Set do
+    initialize_with { new(AgglomerativeClustering::Linkage::Single.new) }
+  end
+end

data/spec/lib/agglomerative_clustering/cluster_spec.rb

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+describe AgglomerativeClustering::Cluster do
+
+  context '#merge' do
+    it 'will merge two clusters' do
+      cluster1 = FactoryGirl.build(:cluster)
+      cluster2 = FactoryGirl.build(:cluster)
+      points = cluster1.points + cluster2.points
+      expect(cluster1.merge(cluster2).points).to eql(points)
+    end
+  end
+end

data/spec/lib/agglomerative_clustering/euclidean_distance_spec.rb

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+describe AgglomerativeClustering::EuclideanDistance do
+  before do
+    class Dummy
+      include AgglomerativeClustering::EuclideanDistance
+    end
+  end
+
+  context '#distance' do
+    it 'will return the distance between two points' do
+      p1 = FactoryGirl.build(:point, x: -1, y: 2, z: 3)
+      p2 = FactoryGirl.build(:point, x: 4 ,y: 0, z: -3)
+      expect(Dummy.new.euclidean_distance(p1,p2).round(3)).to eql(8.062)
+    end
+  end
+end

data/spec/lib/agglomerative_clustering/linkage/average_spec.rb

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+describe AgglomerativeClustering::Linkage::Average do
+
+  context '#calculate_distance' do
+    it 'will calculate distance between clusters based on the average distnace between points' do
+      average_linkage = AgglomerativeClustering::Linkage::Average.new
+      point1 = FactoryGirl.build(:point, x: 1, y: 1, z: 1)
+      point2 = FactoryGirl.build(:point, x: 7, y: 7, z: 7)
+      point3 = FactoryGirl.build(:point, x: 2, y: 2, z: 2)
+      point4 = FactoryGirl.build(:point, x: 5, y: 5, z: 5)
+      cluster1 = AgglomerativeClustering::Cluster.new(point1)
+      cluster2 = AgglomerativeClustering::Cluster.new(point2)
+      cluster3 = AgglomerativeClustering::Cluster.new(point3)
+      cluster4 = AgglomerativeClustering::Cluster.new(point4)
+      cluster1 = cluster1.merge(cluster2)
+      cluster3 = cluster3.merge(cluster4)
+      distance1 = average_linkage.euclidean_distance(point1, point3)
+      distance2 = average_linkage.euclidean_distance(point1, point4)
+      distance3 = average_linkage.euclidean_distance(point2, point3)
+      distance4 = average_linkage.euclidean_distance(point2, point4)
+      average_distance = (distance1 + distance2 + distance3 + distance4)/4
+      expect(average_linkage.calculate_distance(cluster1, cluster3)).to eql(average_distance)
+    end
+  end
+  
+end

data/spec/lib/agglomerative_clustering/linkage/base_spec.rb

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+describe AgglomerativeClustering::Linkage::Base do
+
+  context '#cluster' do
+    it 'will return the clusters where min distance is closest' do
+      single_linkage = AgglomerativeClustering::Linkage::Single.new
+      set = FactoryGirl.build(:set)
+      set.push(FactoryGirl.build(:point))
+      set.push(FactoryGirl.build(:point))
+      expect(single_linkage.cluster(set.clusters)).to eql([set.clusters[0], set.clusters[1]])
+    end
+  end
+
+end

data/spec/lib/agglomerative_clustering/linkage/center_spec.rb

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+describe AgglomerativeClustering::Linkage::Center do
+
+  context '#calculate_distance' do
+    it 'will calculate distance between clusters based on the center distance between points' do
+      center_linkage = AgglomerativeClustering::Linkage::Center.new
+      point1 = FactoryGirl.build(:point, x: 1, y: 1, z: 1)
+      point2 = FactoryGirl.build(:point, x: 2, y: 2, z: 2)
+      point3 = FactoryGirl.build(:point, x: 7, y: 7, z: 7)
+      point4 = FactoryGirl.build(:point, x: 5, y: 5, z: 5)
+      cluster1 = AgglomerativeClustering::Cluster.new(point1)
+      cluster2 = AgglomerativeClustering::Cluster.new(point2)
+      cluster3 = AgglomerativeClustering::Cluster.new(point3)
+      cluster4 = AgglomerativeClustering::Cluster.new(point4)
+      cluster1 = cluster1.merge(cluster2)
+      cluster3 = cluster3.merge(cluster4)
+      center_point1 = Point.new(1.5, 1.5, 1.5)
+      center_point2 = Point.new(6, 6, 6)
+      center_distance = center_linkage.euclidean_distance(center_point1, center_point2)
+      expect(center_linkage.calculate_distance(cluster1, cluster3)).to eql(center_distance)
+    end
+  end
+
+end

data/spec/lib/agglomerative_clustering/linkage/complete_spec.rb

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+describe AgglomerativeClustering::Linkage::Complete do
+
+  context '#calculate_distance' do
+    it 'will calculate distance between clusters based on the max distnace between points' do
+      complete_linkage = AgglomerativeClustering::Linkage::Complete.new
+      min_point = FactoryGirl.build(:point, x: 1, y: 1, z: 1)
+      max_point = FactoryGirl.build(:point, x: 7, y: 7, z: 7)
+      cluster1 = AgglomerativeClustering::Cluster.new(min_point)
+      cluster2 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 2, y: 2, z: 2))
+      cluster3 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 5, y: 5, z: 5))
+      cluster4 = AgglomerativeClustering::Cluster.new(max_point)
+      cluster1 = cluster1.merge(cluster2)
+      cluster3 = cluster3.merge(cluster4)
+      max_distance = complete_linkage.euclidean_distance(min_point, max_point)
+      expect(complete_linkage.calculate_distance(cluster1, cluster3)).to eql(max_distance)
+    end
+  end
+  
+end

data/spec/lib/agglomerative_clustering/linkage/single_spec.rb

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+describe AgglomerativeClustering::Linkage::Single do
+
+  context '#calculate_distance' do
+    it 'will calculate distance between clusters based on the min distnace between points' do
+      single_linkage = AgglomerativeClustering::Linkage::Single.new
+      min_point = FactoryGirl.build(:point, x: 2, y: 2, z: 2)
+      max_point = FactoryGirl.build(:point, x: 5, y: 5, z: 5)
+      cluster1 = AgglomerativeClustering::Cluster.new(min_point)
+      cluster2 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 1, y: 1, z: 1))
+      cluster3 = AgglomerativeClustering::Cluster.new(FactoryGirl.build(:point, x: 7, y: 7, z: 7))
+      cluster4 = AgglomerativeClustering::Cluster.new(max_point)
+      cluster1 = cluster1.merge(cluster2)
+      cluster3 = cluster3.merge(cluster4)
+      min_distance = single_linkage.euclidean_distance(min_point, max_point)
+      expect(single_linkage.calculate_distance(cluster1, cluster3)).to eql(min_distance)
+    end
+  end
+  
+end

data/spec/lib/agglomerative_clustering/set_spec.rb

@@ -0,0 +1,75 @@
+describe AgglomerativeClustering::Set do
+
+  before do
+    @set = FactoryGirl.build(:set)
+    @point1 = FactoryGirl.build(:point, x:2, y:2, z:3)
+    @point2 = FactoryGirl.build(:point, x:1, y:4, z:1)
+    @point3 = FactoryGirl.build(:point, x:5, y:2, z:2)
+    @point4 = FactoryGirl.build(:point, x:5, y:2, z:3)
+    @set.push(@point1)
+    @set.push(@point2)
+    @set.push(@point3)
+    @set.push(@point4)
+  end
+
+  context '#cluster' do
+    it 'will return clusters of points based on requested number of clusters' do
+      expect(@set.cluster(3).size).to eql(3)
+    end
+
+    it 'will cluster points that are closest to each other' do
+      @point5 = FactoryGirl.build(:point, x:5, y:2, z:4)
+      @point6 = FactoryGirl.build(:point, x:5, y:3, z:4)
+      @point7 = FactoryGirl.build(:point, x:15, y:20, z:21)
+      @point8 = FactoryGirl.build(:point, x:18, y:21, z:21)
+      @point9 = FactoryGirl.build(:point, x:16, y:22, z:21)
+      @set.push(@point5)
+      @set.push(@point6)
+      @set.push(@point7)
+      @set.push(@point8)
+      @set.push(@point9)
+      clusters = @set.cluster(3)
+      clusters[0].points.each do |point|
+        expect([@point1, @point2].include?(point)).to be true
+      end
+      clusters[1].points.each do |point|
+        expect([@point3, @point4, @point5, @point6].include?(point)).to be true
+      end
+      clusters[2].points.each do |point|
+        expect([@point7, @point8, @point9].include?(point)).to be true
+      end
+    end
+  end
+
+  context '#merge_clusters' do
+    it 'will merge two clusters into one and update the distance matrix' do
+      expect(@set.merge_clusters([@set.clusters[0],@set.clusters[1]]).points).to eql([@point1, @point2])
+    end
+  end
+
+  context '#find_outliers' do
+    it 'will return a list of outliers' do
+      outlier1 = FactoryGirl.build(:point, x:100, y:200, z:300)
+      outlier2 = FactoryGirl.build(:point, x:-100, y:-200, z:-300)
+      @set.push(outlier1)
+      @set.push(outlier2)
+
+      percentage_of_points = 90
+      distance = 10
+      expect(@set.find_outliers(percentage_of_points, distance)).to eql([outlier1, outlier2])
+    end
+  end
+
+  context '#outliers' do
+    it 'will return the set of points without outliers' do
+      outlier1 = FactoryGirl.build(:point, x:100, y:200, z:300)
+      outlier2 = FactoryGirl.build(:point, x:-100, y:-200, z:-300)
+      @set.push(outlier1)
+      @set.push(outlier2)
+      percentage_of_points = 90
+      distance = 10
+      @set.find_outliers(percentage_of_points, distance)
+      expect(@set.outliers).to eql([outlier1,outlier2])
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -0,0 +1,7 @@
+require 'factory_girl'
+require 'agglomerative_clustering'
+
+RSpec.configure do |config|
+  config.include FactoryGirl::Syntax::Methods
+  FactoryGirl.find_definitions
+end

metadata

@@ -0,0 +1,133 @@
+--- !ruby/object:Gem::Specification
+name: agglomerative_clustering
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Bryan Mulvihill
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-10-30 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: 
+email:
+- bmulvihill@pinsonault.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- LICENSE.txt
+- README.md
+- Rakefile
+- agglomerative_clustering.gemspec
+- cluster.rb
+- lib/agglomerative_clustering.rb
+- lib/agglomerative_clustering/cluster.rb
+- lib/agglomerative_clustering/euclidean_distance.rb
+- lib/agglomerative_clustering/linkage/average.rb
+- lib/agglomerative_clustering/linkage/base.rb
+- lib/agglomerative_clustering/linkage/center.rb
+- lib/agglomerative_clustering/linkage/complete.rb
+- lib/agglomerative_clustering/linkage/single.rb
+- lib/agglomerative_clustering/point.rb
+- lib/agglomerative_clustering/set.rb
+- lib/agglomerative_clustering/version.rb
+- outliers.csv
+- points.csv
+- spec/factories/lib/agglomerative_clustering/cluster.rb
+- spec/factories/lib/agglomerative_clustering/point.rb
+- spec/factories/lib/agglomerative_clustering/set.rb
+- spec/lib/agglomerative_clustering/cluster_spec.rb
+- spec/lib/agglomerative_clustering/euclidean_distance_spec.rb
+- spec/lib/agglomerative_clustering/linkage/average_spec.rb
+- spec/lib/agglomerative_clustering/linkage/base_spec.rb
+- spec/lib/agglomerative_clustering/linkage/center_spec.rb
+- spec/lib/agglomerative_clustering/linkage/complete_spec.rb
+- spec/lib/agglomerative_clustering/linkage/single_spec.rb
+- spec/lib/agglomerative_clustering/set_spec.rb
+- spec/spec_helper.rb
+homepage: ''
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.2
+signing_key: 
+specification_version: 4
+summary: Ruby Agglomerative Clustering Algorithm
+test_files:
+- spec/factories/lib/agglomerative_clustering/cluster.rb
+- spec/factories/lib/agglomerative_clustering/point.rb
+- spec/factories/lib/agglomerative_clustering/set.rb
+- spec/lib/agglomerative_clustering/cluster_spec.rb
+- spec/lib/agglomerative_clustering/euclidean_distance_spec.rb
+- spec/lib/agglomerative_clustering/linkage/average_spec.rb
+- spec/lib/agglomerative_clustering/linkage/base_spec.rb
+- spec/lib/agglomerative_clustering/linkage/center_spec.rb
+- spec/lib/agglomerative_clustering/linkage/complete_spec.rb
+- spec/lib/agglomerative_clustering/linkage/single_spec.rb
+- spec/lib/agglomerative_clustering/set_spec.rb
+- spec/spec_helper.rb