distribution 0.7.3 → 0.8.0

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/distribution.gemspec

@@ -9,12 +9,11 @@ Gem::Specification.new do |s|
   s.date = Date.today.to_s
   s.homepage = "https://github.com/sciruby/distribution"
 
-  s.authors = ['Claudio Bustos']
-  s.email = ['clbustos@gmail.com']
-
+  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"
+  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

data/lib/distribution.rb

@@ -1,21 +1,30 @@
 # = distribution.rb -
 # Distribution - Statistical Distributions package for Ruby
 #
-# Copyright (C) 2011-2014  Claudio Bustos
+# Copyright (c) 2011-2012, Claudio Bustos
+# All rights reserved.
 #
-# 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.
-#
-# 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
 #
@@ -28,6 +37,8 @@
 #
 
 require 'distribution/math_extension'
+require 'distribution/shorthand'
+require 'distribution/distributable'
 require 'distribution/version'
 
 # Several distributions modules to calculate pdf, cdf, inverse cdf and generate
@@ -41,99 +52,47 @@ require 'distribution/version'
 module Distribution
   SQ2PI = Math.sqrt(2 * Math::PI)
 
-  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(shortcut, method, &block)
-      if EQUIVALENCES.include? method.to_sym
-        name = shortcut + "_#{method}"
-        define_method(name, &block)
-
-        name = shortcut + "_#{EQUIVALENCES[method.to_sym]}"
-        define_method(name, &block)
-
+  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
     end
-  end
 
-  # 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}"
-      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)
+    # 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
-  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
+    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
 
   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|
-            unless 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
-
-  def self.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
-
   require 'distribution/normal'
   require 'distribution/chisquare'
   require 'distribution/gamma'

data/lib/distribution/beta/gsl.rb

@@ -2,14 +2,11 @@ module Distribution
   module Beta
     module GSL_
       class << self
+        # PDF.
         def pdf(x, a, b)
           GSL::Ran.beta_pdf(x.to_f, a.to_f, b.to_f)
         end
-        # Return the P-value of the corresponding integral with
-        # k degrees of freedom
-        def p_value(pr, a, b)
-          GSL::Cdf.beta_Pinv(pr.to_f, a.to_f, b.to_f)
-        end
+
         # Beta cumulative distribution function (cdf).
         #
         # Returns the integral of Beta distribution
@@ -18,6 +15,14 @@ module Distribution
         def cdf(x, a, b)
           GSL::Cdf.beta_P(x.to_f, a.to_f, b.to_f)
         end
+
+        # Return the P-value of the corresponding integral with
+        # k degrees of freedom
+        def quantile(pr, a, b)
+          GSL::Cdf.beta_Pinv(pr.to_f, a.to_f, b.to_f)
+        end
+
+        alias_method :p_value, :quantile
       end
     end
   end

data/lib/distribution/beta/ruby.rb

@@ -35,7 +35,7 @@ module Distribution
         end
 
         # Inverse of the beta distribution function
-        def p_value(p, a, b, rmin = 0, rmax = 1)
+        def quantile(p, a, b, rmin = 0, rmax = 1)
           fail 'a <= 0' if a <= 0
           fail 'b <= 0' if b <= 0
           fail 'rmin == rmax' if rmin == rmax
@@ -68,6 +68,8 @@ module Distribution
 
           rmin + guess * (rmax - rmin)
         end
+
+        alias_method :p_value, :quantile
       end
     end
   end

data/lib/distribution/binomial/ruby.rb

@@ -6,6 +6,9 @@ module Distribution
           fail 'k>n' if k > n
           Math.binomial_coefficient(n, k) * (pr**k) * (1 - pr)**(n - k)
         end
+
+        alias_method :exact_pdf, :pdf
+
         # TODO: Use exact_regularized_beta for
         # small values and regularized_beta for bigger ones.
         def cdf(k, n, pr)
@@ -19,7 +22,7 @@ module Distribution
           out
         end
 
-        def p_value(prob, n, pr)
+        def quantile(prob, n, pr)
           ac = 0
           (0..n).each do |i|
             ac += pdf(i, n, pr)
@@ -27,7 +30,7 @@ module Distribution
           end
         end
 
-        alias_method :exact_pdf, :pdf
+        alias_method :p_value, :quantile
       end
     end
   end

data/lib/distribution/bivariatenormal.rb

@@ -7,21 +7,20 @@ module Distribution
   # Pdf if easy to calculate, but CDF is not trivial. Several papers
   # describe methods to calculate the integral.
   module BivariateNormal
-    SHORTHAND='bnor'
+    SHORTHAND = 'bnor'
 
     extend Distributable
     create_distribution_methods
-    
+
     ##
     # :singleton-method: pdf(k,n,prob)
     # Probability density function for exactly +k+ successes in +n+ trials
     # with success probability +prob+
-    # 
-    
+    #
+
     ##
     # :singleton-method: cdf(k,n,prob)
     # Cumulative density function for +k+ or less successes in +n+ trials
     # with success probability +prob+
-    
   end
 end

data/lib/distribution/bivariatenormal/gsl.rb

@@ -2,8 +2,8 @@ module Distribution
   module BivariateNormal
     module GSL_
       class <<self
-        def pdf(x,y,rho,s1=1.0,s2=1.0)
-          GSL::Ran::bivariate_gaussian_pdf(x, y, s1,s2,rho)
+        def pdf(x, y, rho, s1 = 1.0, s2 = 1.0)
+          GSL::Ran.bivariate_gaussian_pdf(x, y, s1, s2, rho)
         end
       end
     end

data/lib/distribution/bivariatenormal/java.rb

@@ -6,4 +6,4 @@ module Distribution
       end
     end
   end
-end
+end