distribution 0.6.0 → 0.8.0

data/benchmark/factorial_hash.rb

@@ -1,4 +1,4 @@
-$:.unshift(File.expand_path(File.dirname(__FILE__)+"/../lib"))
+$LOAD_PATH.unshift(File.expand_path(File.dirname(__FILE__) + '/../lib'))
 require 'bench_press'
 require 'distribution'
 extend BenchPress
@@ -8,17 +8,16 @@ author 'Claudio Bustos'
 date '2011-01-31'
 summary "
 Is better create a lookup table for factorial or just calculate it?
-Distribution::MathExtension::SwingFactorial has a lookup table 
+Distribution::MathExtension::SwingFactorial has a lookup table
 for factorials n<20
 "
 
-reps 1000 #number of repetitions
+reps 1000 # number of repetitions
 
-measure "Lookup" do
-	Math.factorial(19)
+measure 'Lookup' do
+  Math.factorial(19)
 end
 
-measure "calculate" do
-	Distribution::MathExtension::SwingFactorial.naive_factorial(19)
+measure 'calculate' do
+  Distribution::MathExtension::SwingFactorial.naive_factorial(19)
 end
-

data/benchmark/factorial_method.rb

@@ -1,4 +1,4 @@
-$:.unshift(File.dirname(__FILE__)+"/../lib")
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../lib')
 require 'distribution'
 require 'bench_press'
 
@@ -10,19 +10,17 @@ date '2011-01-27'
 summary "
 Factorization requires a lot of processing, so approximation method could be  required. But for greats value, bigdecimal are required and things start to get harder.
 * Approximation (fast_factorial): Luschny f.3
-* Exact (factorial): Luschny Swing Prime 
+* Exact (factorial): Luschny Swing Prime
 "
 
-reps 10 #number of repetitions
+reps 10 # number of repetitions
 
-x=200
+x = 200
 
 measure "Math.factorial(#{x})" do
   Math.factorial(x)
 end
 
 measure "Math.fast_factorial(#{x})" do
-  
   Math.fast_factorial(x)
 end
-

data/benchmark/odd.rb

@@ -10,13 +10,12 @@ summary "
 Which is faster, n%1==1 or n%2==1
 "
 
-reps 10_000 #number of repetitions
-n=100000
-measure "Using &" do
-  n%1==1
+reps 10_000 # number of repetitions
+n = 100_000
+measure 'Using &' do
+  n % 1 == 1
 end
 
-measure "Using %" do
-  n%2==1
+measure 'Using %' do
+  n.odd?
 end
-

data/benchmark/power.rb

@@ -6,22 +6,22 @@ name 'Float vs Rational power'
 author 'Claudio Bustos'
 date '2011-02-02'
 summary "
-On ruby, the maximum size of a float is #{Float::MAX}. 
+On ruby, the maximum size of a float is #{Float::MAX}.
 With Rational, we can raise to integer numbers and surpass Float maximum.
 What is the speed reduction using Rational?"
 
-reps 1000 #number of repetitions
-int=10
-rat=10.quo(1)
-bd=BigDecimal("10")
-measure "Using float pow" do
-	int**307
+reps 1000 # number of repetitions
+int = 10
+rat = 10.quo(1)
+bd = BigDecimal('10')
+measure 'Using float pow' do
+  int**307
 end
 
-measure "Using rational" do
-	rat**307
+measure 'Using rational' do
+  rat**307
 end
 
-measure "Using big decimal pow" do
-	bd**307
+measure 'Using big decimal pow' do
+  bd**307
 end

data/bin/distribution

@@ -3,27 +3,27 @@
 require 'optparse'
 require 'fileutils'
 require 'erb'
-gem_base=File.expand_path(File.dirname(__FILE__)+"/..")
-require gem_base+"/lib/distribution"
+gem_base = File.expand_path(File.dirname(__FILE__) + '/..')
+require gem_base + '/lib/distribution'
 
-new=false
-parameters=""
+new = false
+parameters = ''
 OptionParser.new do |opts|
-  opts.banner="Usage: distribution [--new] [--params parameters] distribution"
-  opts.on("-n", "--new", "Create a new template for distribution") do
-    new=true
+  opts.banner = 'Usage: distribution [--new] [--params parameters] distribution'
+  opts.on('-n', '--new', 'Create a new template for distribution') do
+    new = true
   end
-  opts.on("-PMANDATORY", "--params MANDATORY", String, "Parameters for distribution") do |n_param|
-    parameters=", #{n_param}"
+  opts.on('-PMANDATORY', '--params MANDATORY', String, 'Parameters for distribution') do |n_param|
+    parameters = ", #{n_param}"
   end
-  
-  opts.on("-h", "--help", "Show this message") do
+
+  opts.on('-h', '--help', 'Show this message') do
     puts opts
     exit
   end
 
   begin
-    ARGV << "-h" if ARGV.empty?
+    ARGV << '-h' if ARGV.empty?
     opts.parse!(ARGV)
   rescue OptionParser::ParseError => e
     STDERR.puts e.message, "\n", opts
@@ -33,19 +33,19 @@ end
 
 ARGV.each do |distribution|
   if new
-    basename=distribution.downcase
-    raise "You should be inside distribution lib directory" unless File.exists? "../distribution.rb"
-    raise "Distribution already created" if File.exists? basename+".rb"
-    main=ERB.new(File.read(gem_base+"/data/template/distribution.erb"),)
-    ruby=ERB.new(File.read(gem_base+"/data/template/distribution/ruby.erb"))
-    gsl=ERB.new(File.read(gem_base+"/data/template/distribution/gsl.erb"))
-    spec=ERB.new(File.read(gem_base+"/data/template/spec.erb"))
-    
-    FileUtils.mkdir(basename) unless File.exists? basename
-    File.open(basename+".rb","w") {|fp| fp.write(main.result(binding))}
-    File.open(basename+"/ruby.rb","w") {|fp| fp.write(ruby.result(binding))}
-    File.open(basename+"/gsl.rb","w") {|fp| fp.write(gsl.result(binding))}
-    File.open("../../spec/#{basename}_spec.rb","w") {|fp| fp.write(spec.result(binding))}
-    
+    basename = distribution.downcase
+    fail 'You should be inside distribution lib directory' unless File.exist? '../distribution.rb'
+    fail 'Distribution already created' if File.exist? basename + '.rb'
+    main = ERB.new(File.read(gem_base + '/data/template/distribution.erb'))
+    ruby = ERB.new(File.read(gem_base + '/data/template/distribution/ruby.erb'))
+    gsl = ERB.new(File.read(gem_base + '/data/template/distribution/gsl.erb'))
+    spec = ERB.new(File.read(gem_base + '/data/template/spec.erb'))
+
+    FileUtils.mkdir(basename) unless File.exist? basename
+    File.open(basename + '.rb', 'w') { |fp| fp.write(main.result(binding)) }
+    File.open(basename + '/ruby.rb', 'w') { |fp| fp.write(ruby.result(binding)) }
+    File.open(basename + '/gsl.rb', 'w') { |fp| fp.write(gsl.result(binding)) }
+    File.open("../../spec/#{basename}_spec.rb", 'w') { |fp| fp.write(spec.result(binding)) }
+
   end
 end

data/data/template/spec.erb

@@ -41,13 +41,14 @@ describe Distribution::<%= distribution.capitalize %> do
     it_should_behave_like "<%= distribution %> engine"
     
   end
-    
-  describe Distribution::<%= distribution.capitalize %>::GSL_ do
-    before do
-      @engine=Distribution::<%= distribution.capitalize %>::GSL_
+  
+  if Distribution.has_gsl?
+    describe Distribution::<%= distribution.capitalize %>::GSL_ do
+      before do
+        @engine=Distribution::<%= distribution.capitalize %>::GSL_
+      end
+      it_should_behave_like "<%= distribution %> engine"
     end
-    it_should_behave_like "<%= distribution %> engine"
-    
   end
   
   

data/distribution.gemspec

@@ -0,0 +1,25 @@
+$LOAD_PATH.unshift File.expand_path('../lib', __FILE__)
+
+require 'date'
+require 'distribution/version'
+
+Gem::Specification.new do |s|
+  s.name = "distribution"
+  s.version = Distribution::VERSION
+  s.date = Date.today.to_s
+  s.homepage = "https://github.com/sciruby/distribution"
+
+  s.authors = ['Claudio Bustos', 'Carlos Agarie']
+  s.email = ['clbustos@gmail.com', 'carlos.agarie@gmail.com']
+  s.platform = Gem::Platform::RUBY
+  s.summary = "Distribution"
+  s.description = "Distribution is a gem with several probabilistic distributions. Pure Ruby is used by default, C (GSL) or Java extensions are used if available"
+
+  s.files = `git ls-files`.split("\n")
+  s.executables = `git ls-files`.split("\n").map{|f| f =~ /^bin\/(.*)/ ? $1 : nil}.compact
+  s.require_path = 'lib'
+
+  s.add_development_dependency 'bundler'
+  s.add_development_dependency 'rake'
+  s.add_development_dependency "rspec", '~> 3.2'
+end

data/lib/distribution.rb

@@ -1,157 +1,112 @@
-# = distribution.rb - 
+# = distribution.rb -
 # Distribution - Statistical Distributions package for Ruby
-# 
-# Copyright (C) 2011  Claudio Bustos
 #
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
+# Copyright (c) 2011-2012, Claudio Bustos
+# All rights reserved.
 #
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#     * Redistributions of source code must retain the above copyright
+#       notice, this list of conditions and the following disclaimer.
+#     * Redistributions in binary form must reproduce the above copyright
+#       notice, this list of conditions and the following disclaimer in the
+#       documentation and/or other materials provided with the distribution.
+#     * Neither the name of the copyright holder nor the
+#       names of its contributors may be used to endorse or promote products
+#       derived from this software without specific prior written permission.
+
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 #
 # == Other Sources
-# 
-# * Code of several Ruby engines came from statistics2.rb, 
+#
+# * Code of several Ruby engines came from statistics2.rb,
 #   created by Shin-ichiro HARA(sinara@blade.nagaokaut.ac.jp).
 #   Retrieve from http://blade.nagaokaut.ac.jp/~sinara/ruby/math/statistics2/
 # * Code of Beta and Gamma distribution came from GSL project.
 #   Ported by John O. Woods
 # Specific notices will be placed where there are appropiate
-# 
-if !respond_to? :define_singleton_method
-class Module
-  public :define_method
-end
+#
 
-class Object
-  def define_singleton_method(name,&block)
-    sc=class <<self;self;end
-    sc.define_method(name,&block)
-  end
-end
-end
 require 'distribution/math_extension'
-
+require 'distribution/shorthand'
+require 'distribution/distributable'
+require 'distribution/version'
 
 # Several distributions modules to calculate pdf, cdf, inverse cdf and generate
 # pseudo-random numbers for several statistical distributions
-# 
+#
 # == Usage:
 #    Distribution::Normal.cdf(1.96)
 #    => 0.97500210485178
 #    Distribution::Normal.p_value(0.95)
 #    => 1.64485364660836
 module Distribution
-  VERSION="0.6.0"
-  
-  module Shorthand
-    EQUIVALENCES={:p_value=>:p, :cdf=>:cdf, :pdf=>:pdf, :rng=>:r, :exact_pdf=>:epdf, :exact_cdf=>:ecdf, :exact_p_value=>:ep}
-    def self.add_shortcut(sh,m, &block)
-      if EQUIVALENCES.include? m.to_sym 
-        sh_name=sh+"_#{m}"
-        define_method(sh_name,&block)
-        sh_name=sh+"_#{EQUIVALENCES[m.to_sym]}"
-        define_method(sh_name,&block)
-        
-      end
-    end
-  end
-  
-  
   SQ2PI = Math.sqrt(2 * Math::PI)
 
-  # Create a method 'has_<library>' on Module
-  # which require a library and return true or false
-  # according to success of failure 
-  def self.create_has_library(library) #:nodoc:
-    define_singleton_method("has_#{library}?") do
-      cv="@@#{library}"
-      if !class_variable_defined? cv
-        begin 
-          require library.to_s
-          class_variable_set(cv, true)
-        rescue LoadError
-          class_variable_set(cv, false)
+  class << self
+    # Create a method 'has_<library>' on Module
+    # which require a library and return true or false
+    # according to success of failure
+    def create_has_library(library) #:nodoc:
+      define_singleton_method("has_#{library}?") do
+        cv = "@@#{library}"
+        unless class_variable_defined? cv
+          begin
+            require library.to_s
+            class_variable_set(cv, true)
+          rescue LoadError
+            class_variable_set(cv, false)
+          end
         end
+        class_variable_get(cv)
       end
-      class_variable_get(cv)
+    end
+
+    # Retrieves the libraries used to calculate
+    # distributions
+    def libraries_order
+      order = [:Ruby_]
+      order.unshift(:Statistics2_) if has_statistics2?
+      order.unshift(:GSL_) if has_gsl?
+      order.unshift(:Java_) if has_java?
+      order
+    end
+
+    def init_java
+      $LOAD_PATH.unshift File.expand_path('../../vendor/java', __FILE__)
+      require 'commons-math-2.2.jar'
+      java_import 'org.apache.commons.math.distribution.NormalDistributionImpl'
+      java_import 'org.apache.commons.math.distribution.PoissonDistributionImpl'
     end
   end
-  # Retrieves the libraries used to calculate 
-  # distributions
-  def self.libraries_order
-    order=[:Ruby_]
-    order.unshift(:Statistics2_) if has_statistics2?
-    order.unshift(:GSL_) if has_gsl?
-    order.unshift(:Java_) if has_java?
-    order
-  end
+
   create_has_library :gsl
   create_has_library :statistics2
   create_has_library :java
-  
-  # Magic module
-  module Distributable #:nodoc:
-    # Create methods for each module and add methods to 
-    # Distribution::Shorthand. 
-    # 
-    # Traverse Distribution.libraries_order adding
-    # methods availables for each engine module on
-    # the current library
-    #
-    # Kids: Metaprogramming trickery! Don't do at work.
-    # This section was created between a very long reunion
-    # and a 456 Km. travel
-    def create_distribution_methods()
-      
-      Distribution.libraries_order.each do |l_name|
-      if const_defined? l_name
-        l =const_get(l_name)
-        # Add methods from engine to base base, if not yet included
-        l.singleton_methods.each do |m|
-          if !singleton_methods.include? m
-            define_method(m) do |*args|
-              l.send(m,*args)
-            end
-            # Add method to Distribution::Shorthand
-            sh=const_get(:SHORTHAND)
-            Distribution::Shorthand.add_shortcut(sh,m) do |*args|
-              l.send(m,*args)
-            end
-            
-            module_function m
-          end
-        end 
-      end
-            
-    end
-    # create alias for common methods
-    alias_method :inverse_cdf, :p_value if singleton_methods.include? :p_value
-    end
 
-  end
+  require 'distribution/normal'
+  require 'distribution/chisquare'
+  require 'distribution/gamma'
+  require 'distribution/beta'
+  require 'distribution/t'
+  require 'distribution/f'
+  require 'distribution/bivariatenormal'
+  require 'distribution/binomial'
+  require 'distribution/hypergeometric'
+  require 'distribution/exponential'
+  require 'distribution/poisson'
+  require 'distribution/logistic'
+  require 'distribution/lognormal'
+  require 'distribution/weibull'
 
-  autoload(:Normal, 'distribution/normal')  
-  autoload(:ChiSquare, 'distribution/chisquare')
-  autoload(:Gamma, 'distribution/gamma')
-  autoload(:Beta, 'distribution/beta')
-  autoload(:T, 'distribution/t')
-  autoload(:F, 'distribution/f')
-  autoload(:BivariateNormal, 'distribution/bivariatenormal')
-  autoload(:Binomial, 'distribution/binomial')
-  autoload(:Hypergeometric, 'distribution/hypergeometric')
-  autoload(:Exponential, 'distribution/exponential')
-  autoload(:Poisson, 'distribution/poisson')
-  autoload(:Logistic, 'distribution/logistic')
+  init_java if has_java?
 end
-
-
-