buncher 1.0.11 → 1.0.12

data/Gemfile

@@ -0,0 +1,20 @@
+# -*- ruby -*-
+
+# DO NOT EDIT THIS FILE. Instead, edit Rakefile, and run `rake bundler:gemfile`.
+
+source "https://rubygems.org/"
+
+
+gem "minitest", "~>5.6", :group => [:development, :test]
+gem "rdoc", "~>4.0", :group => [:development, :test]
+gem "rake-compiler", "~>0.7", :group => [:development, :test]
+gem "hoe-bundler", ">=1.1", :group => [:development, :test]
+gem "hoe-gemspec", ">=1.0", :group => [:development, :test]
+gem "hoe-git", ">=1.4", :group => [:development, :test]
+gem "minitest-focus", ">=0", :group => [:development, :test]
+gem "rake", ">=0.9", :group => [:development, :test]
+gem "gnuplot", ">=0", :group => [:development, :test]
+gem "rubystats", ">=0", :group => [:development, :test]
+gem "hoe", "~>3.13", :group => [:development, :test]
+
+# vim: syntax=ruby

data/Manifest.txt

@@ -1,6 +1,7 @@
 .autotest
 History.txt
 Manifest.txt
+Gemfile
 README.txt
 Rakefile
 ext/buncher/cluster.cpp

data/Rakefile

@@ -1,10 +1,12 @@
 # -*- ruby -*-
 
 require "rubygems"
+gem "hoe"
 require "hoe"
 
+Hoe.plugin :gemspec
+Hoe.plugin :bundler
 Hoe.plugin :git
-Hoe.plugin :debugging # for gdb
 Hoe.plugin :compiler
 # Hoe.plugin :gem_prelude_sucks
 # Hoe.plugin :inline
@@ -15,7 +17,17 @@ Hoe.plugin :minitest
 
 Hoe.spec "buncher" do
   developer("Robert Mathews", "rob@drync.com")
-  self.extra_dev_deps
+    self.extra_dev_deps += [
+    ["hoe-bundler",     ">= 1.1"],
+    ["hoe-gemspec",     ">= 1.0"],
+    ["hoe-git",         ">= 1.4"],
+    ["minitest",        "> 2.2.2"],
+    ["minitest-focus"],
+    ["rake",            ">= 0.9"],
+    ["rake-compiler",   "> 0.9.2"],
+    ['gnuplot'],
+    ['rubystats']
+  ]
 
   license "MIT" # this should match the license in the README
 end

data/lib/buncher.rb

@@ -1,6 +1,6 @@
 require 'buncher/buncher'
 module Buncher
-  VERSION = "1.0.11"
+  VERSION = "1.0.12"
   # your cluster needs to look like this. Make a bunch of them and pass them in. It's ok to pass in empty elements to start.
   class Cluster
     attr_accessor :elements
@@ -60,7 +60,12 @@ module Buncher
 
   # run the clustering algorithm until we have calculated the best number of clusters, taken from this paper:
   # http://papers.nips.cc/paper/2526-learning-the-k-in-k-means.pdf
+  # min_size: force at least min_size clusters to be created.
+  # plausable: return a hash of #plausable values for k. Sometimes the data has multiple possible answers, so return
+  # the top n of them in a hash of score=>plausable solutions. lowest scores are best, but sometimes there are 
+  # "ties".
   def self.cluster(elements, weights,options={})
+    plausable=options[:plausable] || 1
     solutions={}
     min_size=options[:min_size] || 1
     # try all the sizes of clusters up to #elements. Ok, sure we could probably do something like 50% .. ok, I did
@@ -79,11 +84,14 @@ module Buncher
       solutions[last_fK]=centers if number_clusters >= min_size
       # break if number_clusters == 3 ## debugging
     end
-    min_fK =solutions.keys.sort.first || 1.0
-    if min_fK > 0.85
-      elements.map {|ele| Cluster.new(ele,[ele])} # ie, not clustered at all
+    solutions.select! {|min_fK| min_fK <= 0.85}
+    min_fKs =solutions.keys.sort[0...plausable] || [1.0]
+    if options[:plausable]
+      solutions.select {|key| min_fKs.include?(key)}
+    elsif !min_fKs.empty?
+      solutions[min_fKs.first]
     else
-      solutions[min_fK]
+      elements.map {|ele| Cluster.new(ele,[ele])} # ie, not clustered at all
     end
   end
 end

data/test/test_buncher.rb

@@ -110,8 +110,9 @@ class TestBuncher < Minitest::Test
   # focus
   def test_min_size_works
       elements =  init_data(100,1)
-      new_centers = Buncher::cluster(elements,[1]*2,:min_size=>2)
-      assert(new_centers.size >=2,"at least 2 centers")
+      new_centers = Buncher::cluster(elements,[1]*2,:min_size=>2,:plausable=>3)
+      assert(new_centers.kind_of? Hash)
+      assert(new_centers.first.size >=2,"at least 2 centers")
   end
   def test_gaussian_distribution_of_100_points_in_3_clusters
     1.times do |run|
@@ -124,6 +125,7 @@ class TestBuncher < Minitest::Test
         graphfile = "/tmp/#{run}_centers_#{centers.size}.png"
         plot(graphfile,elements,centers, initial_centers)
       }
+      new_centers=new_centers.first
       puts "run #{run}: k is #{new_centers.size}, seed was #{srand}"
       puts "ERROR "*4 if new_centers.size != 3
       puts

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: buncher
 version: !ruby/object:Gem::Version
-  version: 1.0.11
+  version: 1.0.12
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-02 00:00:00.000000000 Z
+date: 2015-05-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: minitest
@@ -59,6 +59,118 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: '0.7'
+- !ruby/object:Gem::Dependency
+  name: hoe-bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.1'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.1'
+- !ruby/object:Gem::Dependency
+  name: hoe-gemspec
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !ruby/object:Gem::Dependency
+  name: hoe-git
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '1.4'
+- !ruby/object:Gem::Dependency
+  name: minitest-focus
+  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: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0.9'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0.9'
+- !ruby/object:Gem::Dependency
+  name: gnuplot
+  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: rubystats
+  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: hoe
   requirement: !ruby/object:Gem::Requirement
@@ -94,6 +206,7 @@ files:
 - .autotest
 - History.txt
 - Manifest.txt
+- Gemfile
 - README.txt
 - Rakefile
 - ext/buncher/cluster.cpp
@@ -118,6 +231,9 @@ required_ruby_version: !ruby/object:Gem::Requirement
   - - ! '>='
     - !ruby/object:Gem::Version
       version: '0'
+      segments:
+      - 0
+      hash: 630999455354425102
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: