plot_statistics 0.1.0 → 0.2.0

data/{README.rdoc → README.markdown}

@@ -1,9 +1,16 @@
-= plot_statistics
+# plot_statistics
 
-Description goes here.
+This is a library originally designed to run Ripley's K analyses on Clam Plots.  The input is any number of tab separated files with an x and a y column like so:
+
+    21  23
+    4   45
+    32  99
+    32  32
+
+The output is a Tab separated file that shows the output of the Ripley's K analysis and then mean and upper and lower limits of a Monte Carlo simulation of the data.
+
+## Note on Patches/Pull Requests
 
-== 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
@@ -12,6 +19,6 @@ Description goes here.
   (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
 
 Copyright (c) 2010 Asa Wilson. See LICENSE for details.

data/Rakefile

@@ -5,8 +5,8 @@ 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.summary = %Q{This is a gem to do a Ripley's K analysis}
+    gem.description = %Q{This is a gem to do a Ripley's K analysis}
     gem.email = "acvwilson@gmail.com"
     gem.homepage = "http://github.com/acvwilson/plot_statistics"
     gem.authors = ["Asa Wilson"]

data/VERSION

@@ -1 +1 @@
-0.1.0
+0.2.0

data/lib/plot_statistics.rb

@@ -1,7 +1,8 @@
 class PlotStatistics
   require 'ostruct'
 
-  require File.dirname(__FILE__) + '/plot_statistics/clam.rb'
+  require File.dirname(__FILE__) + '/plot_statistics/circle'
+  require File.dirname(__FILE__) + '/plot_statistics/clam'
   require File.dirname(__FILE__) + '/plot_statistics/clam_plot'
   require File.dirname(__FILE__) + '/plot_statistics/monte_carlo'
 end

data/lib/plot_statistics/circle.rb

@@ -0,0 +1,71 @@
+class PlotStatistics
+  class Circle
+    attr_accessor :clam, :radius, :sample_points, :proportion_inside_plot
+
+    DEGREES = [15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180, 195, 210, 225, 240, 255, 270, 285, 300, 315, 330, 345, 360]
+    RADIANS_TO_DEGREES = 360.0 / (2.0 * Math::PI)
+
+    def initialize(params={})
+      @clam = params[:clam]
+      @radius = params[:radius]
+      @sample_points = { :out_of_bounds => 0.0, :in_bounds => 0.0 }
+      @proportion_inside_plot = out_of_bounds? ? estimate_proportion_inside_plot : 1.0
+    end
+
+    def create_samples
+      sample_circles = radius * 2
+      sample_radius = 0.5
+      sample_circles.times do
+        DEGREES.each do |degrees|
+          x = clam.x + sample_radius * Math.cos(degrees / RADIANS_TO_DEGREES)
+          y = clam.y + sample_radius * Math.sin(degrees / RADIANS_TO_DEGREES)
+
+          if point_out_of_bounds?(x, y)
+            sample_points[:out_of_bounds] += 1
+          else
+            sample_points[:in_bounds] += 1
+          end
+        end
+
+        sample_radius += 0.5
+      end
+    end
+
+    def estimate_proportion_inside_plot
+      create_samples
+      sample_points[:in_bounds] / (sample_points[:in_bounds] + sample_points[:out_of_bounds])
+    end
+
+    def point_out_of_bounds?(x, y)
+      [x, y].each do |coordinate|
+        return true unless coordinate > 0 && coordinate < 100
+      end
+      false
+    end
+
+    def out_of_bounds?
+      right_out_of_bounds?  ||
+      left_out_of_bounds?   ||
+      top_out_of_bounds?    ||
+      bottom_out_of_bounds?
+    end
+
+    def right_out_of_bounds?
+      clam.x + radius > 100
+    end
+
+    def left_out_of_bounds?
+      clam.x - radius < 0
+    end
+
+    def top_out_of_bounds?
+      clam.y + radius > 100
+    end
+
+    def bottom_out_of_bounds?
+      clam.y - radius < 0
+    end
+
+
+  end
+end

data/lib/plot_statistics/clam_plot.rb

@@ -23,7 +23,6 @@ class PlotStatistics
 
     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
@@ -38,13 +37,15 @@ class PlotStatistics
 
     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 }
 
+          circle_proportion = Circle.new(:clam => clam, :radius => radius).proportion_inside_plot
+          reciprocal_proportion = 1 / circle_proportion
+
           clams_inside_circle.inject(0) do |sum, inside_clam|
-            ( circle_proportion * 1.0 ) / ( number_of_clams ** 2 )
+            ( reciprocal_proportion * 1.0 ) / ( number_of_clams ** 2 )
           end
         end
 

data/plot_statistics.gemspec

@@ -5,28 +5,29 @@
 
 Gem::Specification.new do |s|
   s.name = %q{plot_statistics}
-  s.version = "0.1.0"
+  s.version = "0.2.0"
 
   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.date = %q{2010-03-16}
   s.default_executable = %q{plot_statistics}
-  s.description = %q{This is a gem I built for my wife to analyze various clam plots.}
+  s.description = %q{This is a gem to do a Ripley's K analysis}
   s.email = %q{acvwilson@gmail.com}
   s.executables = ["plot_statistics"]
   s.extra_rdoc_files = [
     "LICENSE",
-     "README.rdoc"
+     "README.markdown"
   ]
   s.files = [
     ".document",
      ".gitignore",
      "LICENSE",
-     "README.rdoc",
+     "README.markdown",
      "Rakefile",
      "VERSION",
      "bin/plot_statistics",
      "lib/plot_statistics.rb",
+     "lib/plot_statistics/circle.rb",
      "lib/plot_statistics/clam.rb",
      "lib/plot_statistics/clam_plot.rb",
      "lib/plot_statistics/monte_carlo.rb",
@@ -39,7 +40,7 @@ Gem::Specification.new do |s|
   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.summary = %q{This is a gem to do a Ripley's K analysis}
   s.test_files = [
     "spec/plot_statistics_spec.rb",
      "spec/spec_helper.rb"

metadata

@@ -4,9 +4,9 @@ version: !ruby/object:Gem::Version
   prerelease: false
   segments: 
   - 0
-  - 1
+  - 2
   - 0
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
 - Asa Wilson
@@ -14,7 +14,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-03-03 00:00:00 -05:00
+date: 2010-03-16 00:00:00 -04:00
 default_executable: plot_statistics
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -31,7 +31,7 @@ dependencies:
         version: 1.2.9
   type: :development
   version_requirements: *id001
-description: This is a gem I built for my wife to analyze various clam plots.
+description: This is a gem to do a Ripley's K analysis
 email: acvwilson@gmail.com
 executables: 
 - plot_statistics
@@ -39,16 +39,17 @@ extensions: []
 
 extra_rdoc_files: 
 - LICENSE
-- README.rdoc
+- README.markdown
 files: 
 - .document
 - .gitignore
 - LICENSE
-- README.rdoc
+- README.markdown
 - Rakefile
 - VERSION
 - bin/plot_statistics
 - lib/plot_statistics.rb
+- lib/plot_statistics/circle.rb
 - lib/plot_statistics/clam.rb
 - lib/plot_statistics/clam_plot.rb
 - lib/plot_statistics/monte_carlo.rb
@@ -85,7 +86,7 @@ rubyforge_project:
 rubygems_version: 1.3.6
 signing_key: 
 specification_version: 3
-summary: Statistics on clam plots
+summary: This is a gem to do a Ripley's K analysis
 test_files: 
 - spec/plot_statistics_spec.rb
 - spec/spec_helper.rb