plot_statistics 0.1.0

data/.document

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

data/.gitignore

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

data/LICENSE

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+Copyright (c) 2009 Asa Wilson
+
+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.rdoc

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+= plot_statistics
+
+Description goes here.
+
+== Note on Patches/Pull Requests
+ 
+* Fork the project.
+* Make your feature addition or bug fix.
+* Add tests for it. This is important so I don't break it in a
+  future version unintentionally.
+* Commit, do not mess with rakefile, version, or history.
+  (if you want to have your own version, that is fine but bump version in a commit by itself I can ignore when I pull)
+* Send me a pull request. Bonus points for topic branches.
+
+== Copyright
+
+Copyright (c) 2010 Asa Wilson. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+
+begin
+  require 'jeweler'
+  Jeweler::Tasks.new do |gem|
+    gem.name = "plot_statistics"
+    gem.summary = %Q{Statistics on clam plots}
+    gem.description = %Q{This is a gem I built for my wife to analyze various clam plots.}
+    gem.email = "acvwilson@gmail.com"
+    gem.homepage = "http://github.com/acvwilson/plot_statistics"
+    gem.authors = ["Asa Wilson"]
+
+    gem.files.include %w(lib/plot_statistics/*.rb)
+
+    gem.add_development_dependency "rspec", ">= 1.2.9"
+    # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+  end
+  Jeweler::GemcutterTasks.new
+rescue LoadError
+  puts "Jeweler (or a dependency) not available. Install it with: gem install jeweler"
+end
+
+require 'spec/rake/spectask'
+Spec::Rake::SpecTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.spec_files = FileList['spec/**/*_spec.rb']
+end
+
+Spec::Rake::SpecTask.new(:rcov) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :spec => :check_dependencies
+
+task :default => :spec
+
+require 'rake/rdoctask'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "plot_statistics #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/bin/plot_statistics

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+#!/usr/bin/env ruby
+
+begin
+  require 'plot_statistics'
+rescue LoadError
+  require 'rubygems'
+  gem     'plot_statistics'
+  require 'plot_statistics'
+end
+
+ARGV.each do |file_name|
+  file = File.new(file_name)
+
+  puts "\n"
+  puts '##########################'
+  puts "#   #{file_name}"
+  puts '##########################'
+  puts "\n"
+
+  lines = file.readlines
+
+  clams = lines.map do |line|
+    x, y = line.strip.split("\t")
+    PlotStatistics::Clam.new(:x => x.to_i, :y => y.to_i)
+  end
+
+  actual_plot = PlotStatistics::ClamPlot.new(clams)
+  monte_carlo = PlotStatistics::MonteCarlo.new(actual_plot.number_of_clams)
+
+  puts actual_plot.inspect
+  puts monte_carlo.inspect
+end

data/lib/plot_statistics.rb

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+class PlotStatistics
+  require 'ostruct'
+
+  require File.dirname(__FILE__) + '/plot_statistics/clam.rb'
+  require File.dirname(__FILE__) + '/plot_statistics/clam_plot'
+  require File.dirname(__FILE__) + '/plot_statistics/monte_carlo'
+end

data/lib/plot_statistics/clam.rb

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+class PlotStatistics
+  class Clam
+    attr_accessor :x, :y, :distances
+
+    def initialize(params={})
+      @x = params[:x]
+      @y = params[:y]
+      @distances = params[:distances] || []
+    end
+
+    def self.create_random
+      new( :x => rand(100), :y => rand(100) )
+    end
+  end
+end

data/lib/plot_statistics/clam_plot.rb

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+class PlotStatistics
+  class ClamPlot
+    attr_accessor :clams, :stats
+
+    AREA_OF_PLOT  = 10_000
+    MAX_RADIUS    = 50
+
+    def initialize(clams)
+      @clams = clams
+      setup_clam_distances(@clams)
+      @stats = OpenStruct.new(:k_ts => [], :l_ts => [])
+      calculate_stats
+    end
+
+    def self.create_random(number_of_clams)
+      clams = (1..number_of_clams).map { Clam.create_random }
+      new(clams)
+    end
+
+    def number_of_clams
+      clams.size
+    end
+
+    def setup_clam_distances(clams)
+      clams.each_with_index do |reference_clam, i|
+        # next if (clams.size - 1) < i
+        clams[(i + 1)..-1].each do |other_clam|
+          distance = distance_between_clams(reference_clam, other_clam)
+          reference_clam.distances << distance
+          other_clam.distances << distance
+        end
+      end
+    end
+
+    def distance_between_clams(clam1, clam2)
+      Math.sqrt((clam1.x - clam2.x) ** 2 + (clam1.y - clam2.y) ** 2)
+    end
+
+    def calculate_stats
+      (1..MAX_RADIUS).each do |radius|
+        circle_proportion = 1.0
+
+        sums = clams.inject(0) do |sum, clam|
+          clams_inside_circle = clam.distances.select { |distance| distance <= radius }
+
+          clams_inside_circle.inject(0) do |sum, inside_clam|
+            ( circle_proportion * 1.0 ) / ( number_of_clams ** 2 )
+          end
+        end
+
+        k_t = AREA_OF_PLOT * sums
+        l_t = radius - Math.sqrt( k_t / Math::PI)
+
+        stats.k_ts << k_t
+        stats.l_ts << l_t
+      end
+    end
+  end
+end

data/lib/plot_statistics/monte_carlo.rb

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+class PlotStatistics
+  class MonteCarlo
+    attr_accessor :plots, :stats
+
+    def initialize(number_of_clams, number_of_plots=100)
+      @plots = (1..number_of_plots).map { ClamPlot.create_random number_of_clams }
+      @stats = OpenStruct.new(:mean        => OpenStruct.new(:k_ts => [], :l_ts => []),
+                              :upper_limit => OpenStruct.new(:k_ts => [], :l_ts => []),
+                              :lower_limit => OpenStruct.new(:k_ts => [], :l_ts => []))
+      calculate_means
+      calculate_limits
+    end
+
+    def calculate_means
+      (0...ClamPlot::MAX_RADIUS).each do |radius|
+        stats.mean.k_ts << average_k(radius)
+        stats.mean.l_ts << average_l(radius)
+      end
+    end
+
+    def calculate_limits
+      (0...ClamPlot::MAX_RADIUS).each do |radius|
+        threshold_k = standard_deviation_k(radius) * 2
+        threshold_l = standard_deviation_l(radius) * 2
+
+        stats.upper_limit.k_ts << (stats.mean.k_ts[radius] + threshold_k)
+        stats.upper_limit.l_ts << (stats.mean.l_ts[radius] + threshold_l)
+        stats.lower_limit.k_ts << (stats.mean.k_ts[radius] - threshold_k)
+        stats.lower_limit.l_ts << (stats.mean.l_ts[radius] - threshold_l)
+      end
+    end
+
+    def standard_deviation_k(radius)
+      sum = plots.inject(0) do |sum, plot|
+        (plot.stats.k_ts[radius] - stats.mean.k_ts[radius]) ** 2
+      end
+
+      Math.sqrt(sum / number_of_plots)
+    end
+
+    def standard_deviation_l(radius)
+      sum = plots.inject(0) do |sum, plot|
+        (plot.stats.l_ts[radius] - stats.mean.l_ts[radius]) ** 2
+      end
+
+      Math.sqrt(sum / number_of_plots)
+    end
+
+    def number_of_plots
+      plots.size
+    end
+
+    def average_k(radius)
+      sum = plots.inject(0) do |sum, plot|
+        plot.stats.k_ts[radius]
+      end
+
+      sum / number_of_plots
+    end
+
+    def average_l(radius)
+      sum = plots.inject(0) do |sum, plot|
+        plot.stats.l_ts[radius]
+      end
+
+      sum / number_of_plots
+    end
+  end
+end

data/plot_statistics.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run the gemspec command
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = %q{plot_statistics}
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Asa Wilson"]
+  s.date = %q{2010-03-03}
+  s.default_executable = %q{plot_statistics}
+  s.description = %q{This is a gem I built for my wife to analyze various clam plots.}
+  s.email = %q{acvwilson@gmail.com}
+  s.executables = ["plot_statistics"]
+  s.extra_rdoc_files = [
+    "LICENSE",
+     "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+     ".gitignore",
+     "LICENSE",
+     "README.rdoc",
+     "Rakefile",
+     "VERSION",
+     "bin/plot_statistics",
+     "lib/plot_statistics.rb",
+     "lib/plot_statistics/clam.rb",
+     "lib/plot_statistics/clam_plot.rb",
+     "lib/plot_statistics/monte_carlo.rb",
+     "plot_statistics.gemspec",
+     "spec/plot_statistics_spec.rb",
+     "spec/spec.opts",
+     "spec/spec_helper.rb"
+  ]
+  s.homepage = %q{http://github.com/acvwilson/plot_statistics}
+  s.rdoc_options = ["--charset=UTF-8"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = %q{1.3.6}
+  s.summary = %q{Statistics on clam plots}
+  s.test_files = [
+    "spec/plot_statistics_spec.rb",
+     "spec/spec_helper.rb"
+  ]
+
+  if s.respond_to? :specification_version then
+    current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION
+    s.specification_version = 3
+
+    if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<rspec>, [">= 1.2.9"])
+    else
+      s.add_dependency(%q<rspec>, [">= 1.2.9"])
+    end
+  else
+    s.add_dependency(%q<rspec>, [">= 1.2.9"])
+  end
+end
+

data/spec/plot_statistics_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "PlotStatistics" do
+  it "fails" do
+    fail "hey buddy, you should probably rename this file and start specing for real"
+  end
+end

data/spec/spec.opts

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+--color

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.dirname(__FILE__))
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+require 'plot_statistics'
+require 'spec'
+require 'spec/autorun'
+
+Spec::Runner.configure do |config|
+  
+end

metadata

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+--- !ruby/object:Gem::Specification 
+name: plot_statistics
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 1
+  - 0
+  version: 0.1.0
+platform: ruby
+authors: 
+- Asa Wilson
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-03-03 00:00:00 -05:00
+default_executable: plot_statistics
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 1
+        - 2
+        - 9
+        version: 1.2.9
+  type: :development
+  version_requirements: *id001
+description: This is a gem I built for my wife to analyze various clam plots.
+email: acvwilson@gmail.com
+executables: 
+- plot_statistics
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- bin/plot_statistics
+- lib/plot_statistics.rb
+- lib/plot_statistics/clam.rb
+- lib/plot_statistics/clam_plot.rb
+- lib/plot_statistics/monte_carlo.rb
+- plot_statistics.gemspec
+- spec/plot_statistics_spec.rb
+- spec/spec.opts
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/acvwilson/plot_statistics
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.6
+signing_key: 
+specification_version: 3
+summary: Statistics on clam plots
+test_files: 
+- spec/plot_statistics_spec.rb
+- spec/spec_helper.rb