feldtruby 0.2.2 → 0.3.0

data/.gitignore

@@ -0,0 +1,49 @@
+# rcov or simplecov generated
+coverage
+coverage.data
+
+# rdoc generated
+rdoc
+
+# yard generated
+doc
+.yardoc
+
+# bundler
+.bundle
+
+# jeweler generated
+pkg
+
+# Have editor/IDE/OS specific files you need to ignore? Consider using a global gitignore: 
+#
+# * Create a file at ~/.gitignore
+# * Include files you want ignored
+# * Run: git config --global core.excludesfile ~/.gitignore
+#
+# After doing this, these files will be ignored in all your git projects,
+# saving you from having to 'pollute' every project you touch with them
+#
+# Not sure what to needs to be ignored for particular editors/OSes? Here's some ideas to get you started. (Remember, remove the leading # of the line)
+#
+# For MacOS:
+#
+.DS_Store
+
+# For TextMate
+#*.tmproj
+#tmtags
+
+# For emacs:
+#*~
+#\#*
+#.\#*
+
+# For vim:
+#*.swp
+
+# For redcar:
+#.redcar
+
+# For rubinius:
+#*.rbc

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in feldtruby.gemspec
+gemspec

data/Rakefile

@@ -1,19 +1,26 @@
-# -*- ruby -*-
+require "bundler/gem_tasks"
 
-require 'rubygems'
-require 'hoe'
+require 'fileutils'
 
-# Hoe.plugin :compiler
-# Hoe.plugin :gem_prelude_sucks
-# Hoe.plugin :inline
-# Hoe.plugin :racc
-# Hoe.plugin :rcov
-# Hoe.plugin :rubyforge
+def psys(str)
+  puts str
+  system str
+end
 
-Hoe.plugin :gemcutter
+desc "Run all tests"
+task :test do
+  helper_files = Dir["test/**/*helper*.rb"]
+  test_files = Dir["test/**/test*.rb"]
+  require_files = (helper_files + test_files).map {|f| "require \"#{f}\""}.join('; ')
+  psys "ruby -Ilib:. -e '#{require_files}' --"
+end
 
-Hoe.spec 'feldtruby' do
-  developer 'Robert Feldt', 'robert.feldt@gmail.com'
+desc "Clean up intermediate/build files"
+task :clean do
+  FileUtils.rm_rf "pkg"
+end
 
-  license 'MIT' # this should match the license in the README
-end
+desc "Clean the repo of any files that should not be checked in"
+task :clobber => [:clean]
+
+task :default => :test

data/feldtruby.gemspec

@@ -0,0 +1,22 @@
+# -*- encoding: utf-8 -*-
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'feldtruby/version'
+
+Gem::Specification.new do |gem|
+  gem.name          = "feldtruby"
+  gem.version       = FeldtRuby::VERSION
+  gem.authors       = ["Robert Feldt"]
+  gem.email         = ["robert.feldt@gmail.com"]
+  gem.description   = %q{Robert Feldt's Common Ruby Code lib}
+  gem.summary       = %q{Robert Feldt's Common Ruby Code lib}
+  gem.homepage      = "https://github.com/robertfeldt/feldtruby"
+
+  gem.files         = `git ls-files`.split($/)
+  gem.executables   = gem.files.grep(%r{^bin/}).map{ |f| File.basename(f) }
+  gem.test_files    = gem.files.grep(%r{^(test|spec|features)/})
+  gem.require_paths = ["lib"]
+
+  gem.add_dependency('rinruby')
+  gem.add_dependency('json')
+end

data/lib/feldtruby/array.rb

@@ -37,4 +37,11 @@ class Array
 		self << element unless self.include?(element)
 		self
 	end
+
+	# Count elements in array and return as hash mapping elements to their counts.
+	def counts
+		count_hash = Hash.new(0)
+		self.each {|element| count_hash[element] += 1}
+		count_hash
+	end
 end

data/lib/feldtruby/minitest_extensions.rb

@@ -0,0 +1,16 @@
+require 'minitest/unit'
+require 'minitest/spec'
+require 'feldtruby/statistics'
+
+module MiniTest::Assertions
+  # Ensure that that are (statistically) the same number of each type
+  # of value in an array.
+  def assert_similar_proportions(values, msg = nil)
+    pvalue = FeldtRuby.probability_of_same_proportions(values)
+    assert(pvalue >= 0.95, msg || "Proportions differ! p-value that they are the same is #{pvalue} (<0.95)")
+  end
+end
+
+module MiniTest::Expectations
+  infect_an_assertion :assert_similar_proportions, :must_have_similar_proportions
+end

data/lib/feldtruby/statistics.rb

@@ -0,0 +1,109 @@
+require 'rinruby'
+require 'json'
+
+require 'feldtruby/array'
+require 'feldtruby/array/basic_stats'
+
+module FeldtRuby
+
+# RCommunicator uses RinRuby to communicate with an instance of R.
+# We extend the basic RinRuby by using json to tunnel back and forth.
+class RCommunicator
+  def initialize
+    # Will stay open until closed or the ruby interpreter exits.
+    # echo = false and interactive = false
+    @r = RinRuby.new(false, false)
+    setup_r()
+  end
+
+  # Include necessary libraries.
+  def setup_r
+    include_library("rjson")
+  end
+
+  # Include a library after ensuring it has been installed
+  def include_library(lib)
+    @r.eval "if(!library(#{lib}, logical.return=TRUE)) {install.packages(\"#{lib}\"); library(#{lib});}"
+  end
+
+  def eval(str)
+    @r.eval str
+  end
+
+  # This represents a hash returned as JSON from R but mapped to a
+  # Ruby object so we can more easily use it as if it was an R object.
+  class Rvalue
+    def initialize(hash)
+      @___h = hash
+      hash.to_a.each do |name, value|
+        ruby_name = ___ruby_name(name)
+        @___h[ruby_name] = @___h[name] if ruby_name != name
+        self.define_singleton_method(ruby_name) {@___h[name]}
+      end
+    end
+    def ___ruby_name(name)
+      name.gsub(".", "_")
+    end
+    def to_h; @___h; end
+  end
+
+  # Call an R method named rmethod with (Ruby) arguments. Returns
+  # an Integer, Float or an Rvalue (if the returned R value is complex).
+  def call(rmethod, *arguments)
+    str, args = "", []
+    arguments.each_with_index do |arg, index| 
+      args << (argname = arg_name(index))
+      str += "#{argname} <- fromJSON(\"#{arg.to_json}\");\n"
+    end
+    resname = res_name(1)
+    str += "#{resname} <- toJSON(#{rmethod.to_s}(#{args.join(', ')}));\n"
+    @r.eval str
+    pull_json_variable(resname)
+  end
+
+  # Get the JSON value from a variable in R and parse it back to a Ruby value.
+  def pull_json_variable(variableName)
+    res = @r.pull(variableName)
+    begin
+      Rvalue.new JSON.parse(res)
+    rescue JSON::ParserError
+      # First try to convert to Integer, then Float if it fails.
+      begin
+        Kernel::Integer(res)
+      rescue ArgumentError
+        Kernel::Float(res)
+      end
+    end
+  end
+
+  private
+
+  def res_name(index = 1)
+    arg_name(index, "res")
+  end
+
+  def arg_name(index, prefix = "arg")
+    "#{prefix}_#{index}_#{self.object_id}"
+  end
+end
+
+module Statistics
+  # Calc the probability that the unique values in array (or 
+  # hash of counts of the values) have (statistically) equal proportions.
+  def probability_of_same_proportions(aryOrHashOfCounts)
+    counts = (Hash === aryOrHashOfCounts) ? aryOrHashOfCounts : aryOrHashOfCounts.counts
+    vs = counts.values
+    res = RC.call("prop.test", vs, ([vs.sum] * vs.length))
+    res.p_value
+  end
+end
+
+# Make them available at top level
+extend Statistics
+
+end
+
+# Create one instance that people can use without having to instantiate.
+unless defined?(Kernel::RC)
+ Kernel::RC = FeldtRuby::RCommunicator.new
+end

data/lib/feldtruby/version.rb

@@ -0,0 +1,3 @@
+module FeldtRuby
+  VERSION = "0.3.0"
+end

data/test/test_array.rb

@@ -82,4 +82,22 @@ describe "Array extensions" do
 			[1,2,3].add_unless_there(3).must_equal [1,2,3]
 		end
 	end
+
+	describe "count_elements" do
+		it "counts elements when only two of them" do
+			counts = [2,1,2,2,1,1,2,1,2].counts
+			counts.keys.sort.must_equal [1,2]
+			counts[1].must_equal 4
+			counts[2].must_equal 5
+		end
+
+		it "counts elements when many different elements and of different types" do
+			counts = [:a, :b, :b, "c", "d", 5, "c", 5, "c", "d", 5, "d", 5, 5, "d"].counts
+			counts[:a].must_equal 1
+			counts[:b].must_equal 2
+			counts["c"].must_equal 3
+			counts["d"].must_equal 4
+			counts[5].must_equal 5
+		end
+	end
 end

data/test/test_statistics.rb

@@ -0,0 +1,86 @@
+require 'feldtruby/statistics'
+
+describe "RCommunicator" do
+  describe "RValue" do
+    it "can be used to access individual elements by their key/name" do
+      rv = FeldtRuby::RCommunicator::Rvalue.new({"a" => 1, "b" => "2"})
+      rv.a.must_equal 1
+      rv.b.must_equal "2"
+    end
+
+    it "maps non-ruby method names so they can be used as method names" do
+      rv = FeldtRuby::RCommunicator::Rvalue.new({"p.value" => 0.06})
+      rv.p_value.must_equal 0.06
+    end
+  end
+
+  describe "calling simple R functions that returns integers" do
+    it "can call sum, min, max etc" do
+      RC.call("sum", [1,2,3]).must_equal 6
+      RC.call("min", [1,2,3]).must_equal 1
+      RC.call("max", [1,2,3]).must_equal 3
+    end
+  end
+
+  describe "calling simple R functions that returns floats" do
+    it "can call sum, min, max etc" do
+      RC.call("sum", [1.2, 3.4]).must_equal 4.6
+      RC.call("min", [1.2, 3.4]).must_equal 1.2
+      RC.call("max", [1.2, 3.4]).must_equal 3.4
+    end
+
+    it "can call also with a symbol for the method name" do
+      RC.call(:mean, [1,2,3]).must_equal 2.0
+    end
+  end
+
+  describe "calling R functions that return complex objects" do
+    it "can call prop.test" do
+      res = RC.call("prop.test", [60, 40], [100, 100])
+      res.p_value.must_be_close_to 0.0072
+      cilow, cihigh = res.conf_int
+      cilow.must_be_close_to 0.0542
+      cihigh.must_be_close_to 0.3458
+    end
+  end
+end
+
+describe "Statistics" do
+  include FeldtRuby::Statistics
+  describe "Proportion testing for the count of values" do
+    it "works when counts are explicitly given" do
+      # A proportion test checks if the number/proportion of occurences of objects
+      # differ. It returns the probability that the proportions are the same
+      # given the actual counts.
+      probability_of_same_proportions({:a => 50, :b => 50}).must_be_close_to 1.0000
+      probability_of_same_proportions({:a => 51, :b => 49}).must_be_close_to 0.8875
+      probability_of_same_proportions({:a => 52, :b => 48}).must_be_close_to 0.6714
+      probability_of_same_proportions({:a => 53, :b => 47}).must_be_close_to 0.4795
+      probability_of_same_proportions({:a => 54, :b => 46}).must_be_close_to 0.3222
+      probability_of_same_proportions({:a => 55, :b => 45}).must_be_close_to 0.2031
+      probability_of_same_proportions({:a => 56, :b => 44}).must_be_close_to 0.1198
+      probability_of_same_proportions({:a => 57, :b => 43}).must_be_close_to 0.0659
+      probability_of_same_proportions({:a => 58, :b => 42}).must_be_close_to 0.0339
+      probability_of_same_proportions({:a => 59, :b => 41}).must_be_close_to 0.0162
+      probability_of_same_proportions({:a => 60, :b => 40}).must_be_close_to 0.0072
+    end
+
+    it "works when an array of the actual elements are given" do
+      probability_of_same_proportions(([:a] * 570) + ([:b] * 430)).must_be_close_to 5.091e-10
+    end
+  end
+end
+
+require 'feldtruby/minitest_extensions'
+
+describe "Test Statistics but with the extensions to MiniTest framework" do
+  it "can use assert_same_proportions" do
+    assert_similar_proportions [1,1,1,1,1, 2,2,2,2,2]
+    # This should fail but I found now way to test it since it uses the MiniTest framework itself...
+    # assert_similar_proportions( [1]*60 + [2]*40 )
+  end
+
+  it "can use must_have_similar_proportions" do
+    [1,1,1,1,1, 2,2,2,2,2].must_have_similar_proportions
+  end
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: feldtruby
 version: !ruby/object:Gem::Version
-  version: 0.2.2
+  version: 0.3.0
   prerelease: 
 platform: ruby
 authors:
@@ -9,64 +9,54 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-21 00:00:00.000000000 Z
+date: 2012-12-24 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: rinruby
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: '3.10'
-  type: :development
+        version: '0'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: '3.10'
+        version: '0'
 - !ruby/object:Gem::Dependency
-  name: hoe
+  name: json
   requirement: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: '3.4'
-  type: :development
+        version: '0'
+  type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     none: false
     requirements:
-    - - ~>
+    - - ! '>='
       - !ruby/object:Gem::Version
-        version: '3.4'
-description: ! 'Robert Feldt''s Common Ruby Code lib. I will gradually collect the
-  many generally useful Ruby tidbits I have laying around and clean them up into here.
-  Don''t want to rewrite these things again and again... So far this collects a number
-  of generally useful additions to the standard Ruby classes/libs and then includes
-  a simple optimization framework (FeldtRuby::Optimize).
-
-
-  email: robert.feldt ((a)) gmail.com'
+        version: '0'
+description: Robert Feldt's Common Ruby Code lib
 email:
 - robert.feldt@gmail.com
 executables: []
 extensions: []
-extra_rdoc_files:
-- History.txt
-- Manifest.txt
-- README.txt
+extra_rdoc_files: []
 files:
-- .autotest
+- .gitignore
+- Gemfile
 - History.txt
-- Manifest.txt
-- README.txt
 - README.md
 - Rakefile
 - TODO
+- feldtruby.gemspec
 - lib/feldtruby.rb
 - lib/feldtruby/array.rb
 - lib/feldtruby/array/basic_stats.rb
@@ -75,6 +65,7 @@ files:
 - lib/feldtruby/file/tempfile.rb
 - lib/feldtruby/float.rb
 - lib/feldtruby/math/rand.rb
+- lib/feldtruby/minitest_extensions.rb
 - lib/feldtruby/net/html_doc_getter.rb
 - lib/feldtruby/optimize.rb
 - lib/feldtruby/optimize/differential_evolution.rb
@@ -84,9 +75,11 @@ files:
 - lib/feldtruby/optimize/random_search.rb
 - lib/feldtruby/optimize/search_space.rb
 - lib/feldtruby/optimize/stdout_logger.rb
+- lib/feldtruby/statistics.rb
 - lib/feldtruby/string/to_iso.rb
 - lib/feldtruby/time.rb
 - lib/feldtruby/vector.rb
+- lib/feldtruby/version.rb
 - lib/feldtruby/visualization/circos.rb
 - lib/feldtruby/word_counter.rb
 - test/helper.rb
@@ -94,24 +87,21 @@ files:
 - test/test_array_basic_stats.rb
 - test/test_array_count_by.rb
 - test/test_float.rb
+- test/test_html_doc_getter.rb
 - test/test_optimize.rb
 - test/test_optimize_differential_evolution.rb
 - test/test_optimize_objective.rb
 - test/test_optimize_populationbasedoptimizer.rb
 - test/test_optimize_random_search.rb
 - test/test_optimize_search_space.rb
+- test/test_statistics.rb
 - test/test_time.rb
 - test/test_vector.rb
-- test/test_html_doc_getter.rb
 - test/test_word_counter.rb
-- .gemtest
 homepage: https://github.com/robertfeldt/feldtruby
-licenses:
-- MIT
+licenses: []
 post_install_message: 
-rdoc_options:
-- --main
-- README.txt
+rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
@@ -127,12 +117,13 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: feldtruby
+rubyforge_project: 
 rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: Robert Feldt's Common Ruby Code lib
 test_files:
+- test/helper.rb
 - test/test_array.rb
 - test/test_array_basic_stats.rb
 - test/test_array_count_by.rb
@@ -144,6 +135,7 @@ test_files:
 - test/test_optimize_populationbasedoptimizer.rb
 - test/test_optimize_random_search.rb
 - test/test_optimize_search_space.rb
+- test/test_statistics.rb
 - test/test_time.rb
 - test/test_vector.rb
 - test/test_word_counter.rb

data/.autotest

@@ -1,23 +0,0 @@
-# -*- ruby -*-
-
-require 'autotest/restart'
-
-# Autotest.add_hook :initialize do |at|
-#   at.extra_files << "../some/external/dependency.rb"
-#
-#   at.libs << ":../some/external"
-#
-#   at.add_exception 'vendor'
-#
-#   at.add_mapping(/dependency.rb/) do |f, _|
-#     at.files_matching(/test_.*rb$/)
-#   end
-#
-#   %w(TestA TestB).each do |klass|
-#     at.extra_class_map[klass] = "test/test_misc.rb"
-#   end
-# end
-
-# Autotest.add_hook :run_command do |at|
-#   system "rake build"
-# end

data/Manifest.txt

@@ -1,44 +0,0 @@
-.autotest
-History.txt
-Manifest.txt
-README.txt
-README.md
-Rakefile
-TODO
-lib/feldtruby.rb
-lib/feldtruby/array.rb
-lib/feldtruby/array/basic_stats.rb
-lib/feldtruby/array/count_by.rb
-lib/feldtruby/file/file_change_watcher.rb
-lib/feldtruby/file/tempfile.rb
-lib/feldtruby/float.rb
-lib/feldtruby/math/rand.rb
-lib/feldtruby/net/html_doc_getter.rb
-lib/feldtruby/optimize.rb
-lib/feldtruby/optimize/differential_evolution.rb
-lib/feldtruby/optimize/max_steps_termination_criterion.rb
-lib/feldtruby/optimize/objective.rb
-lib/feldtruby/optimize/optimizer.rb
-lib/feldtruby/optimize/random_search.rb
-lib/feldtruby/optimize/search_space.rb
-lib/feldtruby/optimize/stdout_logger.rb
-lib/feldtruby/string/to_iso.rb
-lib/feldtruby/time.rb
-lib/feldtruby/vector.rb
-lib/feldtruby/visualization/circos.rb
-lib/feldtruby/word_counter.rb
-test/helper.rb
-test/test_array.rb
-test/test_array_basic_stats.rb
-test/test_array_count_by.rb
-test/test_float.rb
-test/test_optimize.rb
-test/test_optimize_differential_evolution.rb
-test/test_optimize_objective.rb
-test/test_optimize_populationbasedoptimizer.rb
-test/test_optimize_random_search.rb
-test/test_optimize_search_space.rb
-test/test_time.rb
-test/test_vector.rb
-test/test_html_doc_getter.rb
-test/test_word_counter.rb

data/README.txt

@@ -1,59 +0,0 @@
-= feldtruby
-
-* https://github.com/robertfeldt/feldtruby
-
-== DESCRIPTION:
-
-Robert Feldt's Common Ruby Code lib. I will gradually collect the many generally useful Ruby tidbits I have laying around and clean them up into here. Don't want to rewrite these things again and again... So far this collects a number of generally useful additions to the standard Ruby classes/libs and then includes a simple optimization framework (FeldtRuby::Optimize).
-
-email: robert.feldt ((a)) gmail.com
-
-== FEATURES/PROBLEMS:
-
-* FIX (list of features or problems)
-
-== SYNOPSIS:
-
-  FIX (code sample of usage)
-
-== REQUIREMENTS:
-
-* FIX (list of requirements)
-
-== INSTALL:
-
-* FIX (sudo gem install, anything else)
-
-== DEVELOPERS:
-
-After checking out the source, run:
-
-  $ rake newb
-
-This task will install any missing dependencies, run the tests/specs,
-and generate the RDoc.
-
-== LICENSE:
-
-(The MIT License)
-
-Copyright (c) 2012 FIX
-
-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.