onedclusterer 0.1.0

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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+.idea

data/.travis.yml

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+language: ruby
+rvm:
+  - 2.1.0
+before_install: gem install bundler -v 1.10.6

data/CODE_OF_CONDUCT.md

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+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, we pledge to respect all people who contribute through reporting issues, posting feature requests, updating documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for everyone, regardless of level of experience, gender, gender identity and expression, sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+
+Examples of unacceptable behavior by participants include the use of sexual language or imagery, derogatory comments or personal attacks, trolling, public or private harassment, insults, or other unprofessional conduct.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed from the project team.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by opening an issue or contacting one or more of the project maintainers.
+
+This Code of Conduct is adapted from the [Contributor Covenant](http://contributor-covenant.org), version 1.0.0, available at [http://contributor-covenant.org/version/1/0/0/](http://contributor-covenant.org/version/1/0/0/)

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in onedclusterer.gemspec
+gemspec

data/LICENSE.txt

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+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
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data/README.md

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+# Onedclusterer
+
+a tiny ruby library for one-dimensional clustering methods.
+
+## Usage
+
+### Ckmeans.1d.dp
+
+A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.  
+https://cran.r-project.org/web/packages/Ckmeans.1d.dp/index.html
+
+```ruby
+require 'onedclusterer'
+data = [1259.61,2024.82,1855.75,1559.04,1707.65,1107.1,2155.8]
+ckmeans = OnedClusterer::Ckmeans.new(data, 1, 7) # chooses an optimal number clusters between 1 and 7
+p ckmeans.bounds # => [0, 1259.61, 1855.75, 2155.8]
+p ckmeans.clusters # => [[1107.1, 1259.61], [1559.04, 1707.65, 1855.75], [2024.82, 2155.8]]
+
+# exact number of clusters can be requested instead of min and max
+ckmeans = OnedClusterer::Ckmeans.new(data, 4)
+p ckmeans.bounds # => [0, 1259.61, 1559.04, 1855.75, 2155.8]
+p ckmeans.clusters # => [[1107.1, 1259.61], [1559.04], [1707.65, 1855.75], [2024.82, 2155.8]]  
+```
+
+### Jenks natural breaks:
+
+The Jenks natural breaks classification method seeks to reduce the variance within classes and maximize the variance between classes.  
+http://en.wikipedia.org/wiki/Jenks_natural_breaks_optimization  
+http://www.macwright.org/2013/02/18/literate-jenks.html
+
+```ruby
+require 'onedclusterer'
+data = [1259.61,2024.82,1855.75,1559.04,1707.65,1107.1,2155.8]
+jenks = OnedClusterer::Jenks.new(data, 4)
+p jenks.bounds # => [0, 1259.61, 1559.04, 1855.75, 2155.8]
+p jenks.clusters # => [[1107.1, 1259.61], [1559.04], [1707.65, 1855.75], [2024.82, 2155.8]]
+```
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'onedclusterer'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install onedclusterer
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake test` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/Hamdiakoguz/onedclusterer. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/*_test.rb']
+end
+
+task :default => :test

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "onedclusterer"
+
+require "pry"
+Pry.start

data/bin/setup

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+#!/bin/bash
+set -euo pipefail
+IFS=$'\n\t'
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/onedclusterer.rb

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+require "onedclusterer/version"
+require "onedclusterer/jenks"
+require "onedclusterer/ckmeans"
+
+
+module OnedClusterer
+end

data/lib/onedclusterer/ckmeans.rb

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+require 'matrix'
+require_relative 'clusterer'
+
+module OnedClusterer
+
+ # Ckmeans clustering is an improvement on heuristic-based clustering
+ # approaches like Jenks. The algorithm was developed in
+ # [Haizhou Wang and Mingzhou Song](http://journal.r-project.org/archive/2011-2/RJournal_2011-2_Wang+Song.pdf)
+ # as a [dynamic programming](https://en.wikipedia.org/wiki/Dynamic_programming) approach
+ # to the problem of clustering numeric data into groups with the least
+ # within-group sum-of-squared-deviations.
+ #
+ # Minimizing the difference within groups - what Wang & Song refer to as
+ # `withinss`, or within sum-of-squares, means that groups are optimally
+ # homogenous within and the data is split into representative groups.
+ # This is very useful for visualization, where you may want to represent
+ # a continuous variable in discrete color or style groups. This function
+ # can provide groups that emphasize differences between data.
+ #
+ # being a dynamic approach, this algorithm is based on two matrices that
+ # store incrementally-computed values for squared deviations and backtracking
+ # indexes.
+ #
+ # This implementation is ported from original c++ implementation.
+ #
+ ## References
+ # _Ckmeans.1d.dp: Optimal k-means Clustering in One Dimension by Dynamic
+ # Programming_ Haizhou Wang and Mingzhou Song ISSN 2073-4859
+ #
+ # from []The R Journal Vol. 3/2, December 2011](http://journal.r-project.org/archive/2011-2/RJournal_2011-2.pdf)
+
+  class Ckmeans
+    include Clusterer
+
+    attr_reader :data, :kmin, :kmax, :cluster_details
+
+    # Input:
+    #  data -- a vector of numbers, not necessarily sorted
+    #  kmin -- the minimum number of clusters expected
+    #  kmax -- the maximum number of clusters expected
+    # If only kmin is given exactly kmin clusters will be returned
+    # else algorithm chooses an optimal number between Kmin and Kmax
+    def initialize(data, kmin, kmax = kmin)
+      @data_size = data.size
+      @data = data.sort # All arrays here is considered starting at position 1, position 0 is not used.
+      @kmin = kmin
+      @unique = data.uniq.size
+      @kmax = @unique < kmax ? @unique : kmax
+
+      raise ArgumentError, "kmin can not be greater than kmax." if kmin > kmax
+      raise ArgumentError, "kmin can not be greater than data size." if kmin > @data_size
+      raise ArgumentError, "kmax can not be greater than data size." if kmax > @data_size
+    end
+
+    # returns clustered data as array and sets :cluster_details
+    def clusters
+      @clusters_result ||=begin
+        if @unique <= 1 # A single cluster that contains all elements
+          return [data]
+        end
+
+        rows = @data_size
+        cols = kmax
+
+        distance = *Matrix.zero(cols + 1, rows + 1) # 'D'
+        backtrack = *Matrix.zero(cols + 1, rows + 1) # 'B'
+
+        fill_dp_matrix(data.insert(0, nil), distance, backtrack)
+
+        # Choose an optimal number of levels between Kmin and Kmax
+        kopt = select_levels(data, backtrack, kmin, kmax)
+        backtrack = backtrack[0..kopt]
+
+        results = []
+        backtrack(backtrack) do |k, left, right|
+          results[k] = data[left..right]
+        end
+        results.drop(1)
+      end
+    end
+
+    def bounds
+      @bounds ||= clusters.map { |cluster| cluster.last }.insert(0, 0)
+    end
+
+    private
+
+    def backtrack(matrix)
+      right = matrix[0].size - 1
+
+      for k in (matrix.size - 1).downto 1
+        left = matrix[k][right]
+
+        yield k, left, right
+
+        if k > 1
+          right = left - 1
+        end
+      end
+    end
+
+    def fill_dp_matrix(data, distance, backtrack)
+      for i in 1..kmax
+        distance[i][1] = 0.0
+        backtrack[i][1] = 1
+      end
+
+      for k in 1..kmax
+        mean_x1 = data[1]
+
+        for i in ([2,k].max)..@data_size
+          if k == 1
+            distance[k][i] = distance[k][i-1] + (i-1) / Float(i) * (data[i] - mean_x1) ** 2
+            mean_x1 = ((i - 1) * mean_x1 + data[i]) / Float(i)
+            backtrack[1][i] = 1
+          else
+            d = 0.0 # the sum of squared distances from x_j ,. . ., x_i to their mean
+            mean_xj = 0.0
+
+            for j in i.downto k
+              d = d + (i - j) / Float(i - j + 1) * (data[j] - mean_xj) ** 2
+              mean_xj = (data[j] + (i - j) * mean_xj) / Float(i - j + 1)
+
+              if j == i
+                distance[k][i] = d
+                backtrack[k][i] = j
+                distance[k][i] += distance[k - 1][j - 1] unless j == 1
+              else
+                if j == 1
+                  if d <= distance[k][i]
+                    distance[k][i] = d
+                    backtrack[k][i] = j
+                  end
+                elsif d + distance[k - 1][j - 1] < distance[k][i]
+                    distance[k][i] = d + distance[k - 1][j - 1]
+                    backtrack[k][i] = j
+                end
+              end
+            end
+          end
+        end
+      end
+
+    end
+
+    # Choose an optimal number of levels between Kmin and Kmax
+    def select_levels(data, backtrack, kmin, kmax)
+      return kmin if kmin == kmax
+
+      method = :normal # "uniform" or "normal"
+
+      kopt = kmin
+
+      base = 1 # The position of first element in x: 1 or 0.
+      n = data.size - base
+
+      max_bic = 0.0
+
+      for k in kmin..kmax
+        cluster_sizes = []
+        kbacktrack = backtrack[0..k]
+        backtrack(kbacktrack) do |cluster, left, right|
+          cluster_sizes[cluster] = right - left + 1
+        end
+
+        index_left = base
+        index_right = 0
+
+        likelihood = 0
+        bin_left, bin_right = 0
+        for i in 0..(k-1)
+          points_in_bin = cluster_sizes[i + base]
+          index_right = index_left + points_in_bin - 1
+
+          if data[index_left] < data[index_right]
+            bin_left = data[index_left]
+            bin_right = data[index_right]
+          elsif data[index_left] == data[index_right]
+            bin_left = index_left == base ? data[base] : (data[index_left-1] + data[index_left]) / 2
+            bin_right = index_right < n-1+base ? (data[index_right] + data[index_right+1]) / 2 : data[n-1+base]
+          else
+            raise "ERROR: binLeft > binRight"
+          end
+
+          bin_width = bin_right - bin_left
+          if method == :uniform
+            likelihood += points_in_bin * Math.log(points_in_bin / bin_width / n)
+          else
+            mean = 0.0
+            variance = 0.0
+
+            for j in index_left..index_right
+              mean += data[j]
+              variance += data[j] ** 2
+            end
+            mean /= points_in_bin
+            variance = (variance - points_in_bin * mean ** 2) / (points_in_bin - 1) if points_in_bin > 1
+
+            if variance > 0
+              for j in index_left..index_right
+                likelihood += - (data[j] - mean) ** 2 / (2.0 * variance)
+              end
+              likelihood += points_in_bin * (Math.log(points_in_bin / Float(n))
+                - 0.5 * Math.log( 2 * Math::PI * variance))
+            else
+              likelihood += points_in_bin * Math.log(1.0 / bin_width / n)
+            end
+          end
+
+          index_left = index_right + 1
+        end
+
+        # Compute the Bayesian information criterion
+        bic = 2 * likelihood - (3 * k - 1) * Math.log(Float(n))
+
+        if k == kmin
+          max_bic = bic
+          kopt = kmin
+        elsif bic > max_bic
+          max_bic = bic
+          kopt = k
+        end
+
+      end
+
+      kopt
+    end
+
+  end
+
+end

data/lib/onedclusterer/clusterer.rb

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+module OnedClusterer
+
+  # Common methods fo all
+  module Clusterer
+
+    # Returns zero based index of cluster which a value belongs to
+    # value must be in data array
+    def classify(value)
+      raise ArgumentError, "value: #{value} must be in data array" unless @data.include?(value)
+
+      bounds[1..-1].index { |bound| value <= bound }
+    end
+
+    # Returns inclusive interval limits
+    def intervals
+      first, *rest = bounds.each_cons(2).to_a
+      [first, *rest.map {|lower, upper| [data[data.rindex(lower) + 1] , upper] }]
+    end
+  end
+end

data/lib/onedclusterer/jenks.rb

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+require 'matrix'
+require_relative 'clusterer'
+
+module OnedClusterer
+  # [Jenks natural breaks optimization](http://en.wikipedia.org/wiki/Jenks_natural_breaks_optimization)
+  #
+  # Adapted from javascript implementation: https://gist.github.com/tmcw/4977508
+  class Jenks
+    include Clusterer
+
+    attr_reader :data, :n_classes
+
+    # @param data one dimensional numerical array
+    # @param n_classes number of classes
+    def initialize(data, n_classes)
+      @data = data.sort
+      @n_classes = n_classes
+
+      raise ArgumentError, "Number of classes can not be greater than size of data array." if n_classes > data.size
+      raise ArgumentError, "Number of classes can not be less than 1." if n_classes < 1
+
+      @lower_class_limits, @variance_combinations = matrices
+    end
+
+    # get clustered array with `n` number of clusters
+    def clusters(n = n_classes)
+      bounds_iter = bounds(n).drop(1).each_with_index
+      result = Array.new(n) { [] }
+
+      data.each do |value|
+        bound, index = bounds_iter.peek
+        if value > bound
+          bounds_iter.next
+          index += 1
+        end
+        result[index].push(value)
+      end
+
+      result
+    end
+
+    # get bounds array for `n` number of classes
+    def bounds(n = n_classes)
+      raise ArgumentError, "n must be lesser than or equal to n_classes: #{n_classes}" if n > n_classes
+
+      k = data.size
+      bounds = []
+
+      # the calculation of classes will never include the upper and
+      # lower bounds, so we need to explicitly set them
+      bounds[n] = data.last
+      bounds[0] = 0
+
+      for countNum in n.downto 2
+        id = @lower_class_limits[k][countNum]
+        bounds[countNum - 1] = data[id - 2]
+        k = id - 1
+      end
+
+      bounds
+    end
+
+    private
+
+    # Compute the matrices required for Jenks breaks. These matrices
+    # can be used for any classing of data with `classes <= n_classes`
+    def matrices
+      rows = data.size
+      cols = n_classes
+
+      # in the original implementation, these matrices are referred to
+      # as `LC` and `OP`
+      # * lower_class_limits (LC): optimal lower class limits
+      # * variance_combinations (OP): optimal variance combinations for all classes
+      lower_class_limits = *Matrix.zero(rows + 1, cols + 1)
+      variance_combinations = *Matrix.zero(rows + 1, cols + 1)
+
+      # the variance, as computed at each step in the calculation
+      variance = 0
+
+      for i in 1..cols
+        lower_class_limits[1][i]    = 1
+        variance_combinations[1][i] = 0
+        for j in 2..rows
+          variance_combinations[j][i] = Float::INFINITY
+        end
+      end
+
+      for l in 2..rows
+        sum         = 0 # `SZ` originally. this is the sum of the values seen thus far when calculating variance.
+        sum_squares = 0 # `ZSQ` originally. the sum of squares of values seen thus far
+        w           = 0 # `WT` originally. This is the number of data points considered so far.
+
+        for m in 1..l
+          lower_class_limit = l - m + 1 # `III` originally
+          val = data[lower_class_limit - 1]
+
+          # here we're estimating variance for each potential classing
+          # of the data, for each potential number of classes. `w`
+          # is the number of data points considered so far.
+          w += 1
+
+          # increase the current sum and sum-of-squares
+          sum += val
+          sum_squares += (val ** 2)
+
+          # the variance at this point in the sequence is the difference
+          # between the sum of squares and the total x 2, over the number
+          # of samples.
+          variance = sum_squares - (sum ** 2) / w
+
+          i4 = lower_class_limit - 1 # `IV` originally
+          if i4 != 0
+            for j in 2..cols
+             # if adding this element to an existing class
+             # will increase its variance beyond the limit, break
+             # the class at this point, setting the lower_class_limit
+             # at this point.
+             if variance_combinations[l][j] >= (variance + variance_combinations[i4][j - 1])
+               lower_class_limits[l][j] = lower_class_limit
+               variance_combinations[l][j] = variance +
+                 variance_combinations[i4][j - 1]
+             end
+            end
+          end
+        end
+
+        lower_class_limits[l][1] = 1
+        variance_combinations[l][1] = variance
+      end
+
+      [lower_class_limits, variance_combinations]
+    end
+  end
+end

data/lib/onedclusterer/version.rb

@@ -0,0 +1,3 @@
+module OnedClusterer
+  VERSION = "0.1.0"
+end

data/onedclusterer.gemspec

@@ -0,0 +1,24 @@
+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'onedclusterer/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "onedclusterer"
+  spec.version       = OnedClusterer::VERSION
+  spec.authors       = ["Hamdi Akoguz"]
+  spec.email         = ["hamdiakoguz@gmail.com"]
+
+  spec.summary       = %q{a tiny ruby library for one-dimensional clustering methods.}
+  spec.homepage      = "https://github.com/Hamdiakoguz/onedclusterer"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.10"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "minitest"
+  spec.add_development_dependency "pry"
+end

metadata

@@ -0,0 +1,114 @@
+--- !ruby/object:Gem::Specification
+name: onedclusterer
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Hamdi Akoguz
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2015-10-10 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.10'
+- !ruby/object:Gem::Dependency
+  name: 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: minitest
+  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'
+- !ruby/object:Gem::Dependency
+  name: pry
+  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:
+- hamdiakoguz@gmail.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/onedclusterer.rb
+- lib/onedclusterer/ckmeans.rb
+- lib/onedclusterer/clusterer.rb
+- lib/onedclusterer/jenks.rb
+- lib/onedclusterer/version.rb
+- onedclusterer.gemspec
+homepage: https://github.com/Hamdiakoguz/onedclusterer
+licenses: []
+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: 2.2.3
+signing_key: 
+specification_version: 4
+summary: a tiny ruby library for one-dimensional clustering methods.
+test_files: []