distribution 0.7.3 → 0.8.0

data/lib/distribution/f/statistics2.rb

@@ -1,26 +1,29 @@
 module Distribution
   module F
     module Statistics2_
-    class << self
-      # Return the P-value of the corresponding integral with 
-      # k degrees of freedom
-      #
-      #   Distribution::F.p_value(0.95,1,2)
-      # Statistics2 have some problem with extreme values
-      def p_value(pr,k1,k2)
-        Statistics2.pfdist(k1,k2, pr)
+      class << self
+        # F cumulative distribution function (cdf).
+        #
+        # Returns the integral of F-distribution
+        # with k1 and k2 degrees of freedom
+        # over [0, x].
+        #   Distribution::F.cdf(20,3,2)
+        #
+        def cdf(x, k1, k2)
+          Statistics2.fdist(k1, k2, x)
+        end
+
+        # Return the P-value of the corresponding integral with
+        # k degrees of freedom
+        #
+        #   Distribution::F.p_value(0.95,1,2)
+        # Statistics2 have some problem with extreme values
+        def quantile(pr, k1, k2)
+          Statistics2.pfdist(k1, k2, pr)
+        end
+
+        alias_method :p_value, :quantile
       end
-      # F cumulative distribution function (cdf).
-      # 
-      # Returns the integral of F-distribution 
-      # with k1 and k2 degrees of freedom
-      # over [0, x].
-      #   Distribution::F.cdf(20,3,2)
-      # 
-      def cdf(x, k1, k2)
-        Statistics2.fdist(k1, k2,x)
-      end
-    end
     end
   end
 end

data/lib/distribution/gamma.rb

@@ -5,15 +5,15 @@ require 'distribution/gamma/java'
 
 module Distribution
   # From Wikipedia:
-  #    The gamma distribution is a two-parameter family of 
+  #    The gamma distribution is a two-parameter family of
   #    continuous probability distributions. It has a scale parameter a
   #    and a shape parameter b.
-  # 
+  #
   # Calculate pdf, cdf and inverse cdf for Gamma Distribution.
   #
   module Gamma
     extend Distributable
-    SHORTHAND='gamma'
+    SHORTHAND = 'gamma'
     create_distribution_methods
 
     ##
@@ -21,7 +21,6 @@ module Distribution
     # Returns PDF of of Gamma distribution with +a+ as scale
     # parameter and +b+ as shape parameter
 
-
     ##
     # :singleton-method: cdf(x,a,b)
     # Returns the integral of Gamma distribution with +a+ as scale
@@ -29,9 +28,8 @@ module Distribution
 
     ##
     # :singleton-method: p_value(qn,a,b)
-    # Return the upper limit for the integral of a 
-    # gamma distribution which returns +qn+ 
+    # Return the upper limit for the integral of a
+    # gamma distribution which returns +qn+
     # with scale +a+ and shape +b+
-
   end
 end

data/lib/distribution/gamma/gsl.rb

@@ -2,22 +2,26 @@ module Distribution
   module Gamma
     module GSL_
       class << self
-        def pdf(x,a,b)
-          GSL::Ran::gamma_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::gamma_Pinv(pr.to_f, a.to_f, b.to_f)
+        def pdf(x, a, b)
+          GSL::Ran.gamma_pdf(x.to_f, a.to_f, b.to_f)
         end
+
         # Chi-square cumulative distribution function (cdf).
         #
         # Returns the integral of Chi-squared distribution
         # with k degrees of freedom over [0, x]
         #
-        def cdf(x,a,b)
-          GSL::Cdf::gamma_P(x.to_f, a.to_f, b.to_f)
+        def cdf(x, a, b)
+          GSL::Cdf.gamma_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.gamma_Pinv(pr.to_f, a.to_f, b.to_f)
         end
+
+        alias_method :p_value, :quantile
       end
     end
   end

data/lib/distribution/gamma/java.rb

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

data/lib/distribution/gamma/ruby.rb

@@ -3,7 +3,6 @@ module Distribution
   module Gamma
     module Ruby_
       class << self
-
         include Math
         # Gamma distribution probability density function
         #
@@ -22,7 +21,7 @@ module Distribution
         # ==References
         # * http://www.gnu.org/software/gsl/manual/html_node/The-Gamma-Distribution.html
         # * http://en.wikipedia.org/wiki/Gamma_distribution
-        def pdf(x,a,b)
+        def pdf(x, a, b)
           return 0 if x < 0
           if x == 0
             return 1.quo(b) if a == 1
@@ -30,23 +29,18 @@ module Distribution
           elsif a == 1
             Math.exp(-x.quo(b)).quo(b)
           else
-            Math.exp((a-1)*Math.log(x.quo(b)) - x.quo(b) - Math.lgamma(a).first).quo(b)
+            Math.exp((a - 1) * Math.log(x.quo(b)) - x.quo(b) - Math.lgamma(a).first).quo(b)
           end
         end
 
         # Gamma cumulative distribution function
-        def cdf(x,a,b)
+        def cdf(x, a, b)
           return 0.0 if x <= 0.0
 
           y = x.quo(b)
-          return (1-Math::IncompleteGamma.q(a, y)) if y > a
-          return (Math::IncompleteGamma.p(a, y))
+          return (1 - Math::IncompleteGamma.q(a, y)) if y > a
+          (Math::IncompleteGamma.p(a, y))
         end
-
-        #def p_value(pr,a,b)
-        #  cdf(1.0-pr,a,b)
-        #end
-
       end
     end
   end

data/lib/distribution/hypergeometric.rb

@@ -2,38 +2,35 @@ require 'distribution/hypergeometric/ruby'
 require 'distribution/hypergeometric/gsl'
 require 'distribution/hypergeometric/java'
 
-
 module Distribution
   # From Wikipedia:
   #   In probability theory and statistics, the hypergeometric distribution is a discrete probability distribution that
   #   describes the number of successes in a sequence of n draws from a finite population without replacement, just as
   #   the binomial distribution describes the number of successes for draws with replacement.
   module Hypergeometric
-    SHORTHAND='hypg'
+    SHORTHAND = 'hypg'
     extend Distributable
 
     create_distribution_methods
 
     ##
     # :singleton-method: pdf(k,m,n,total)
-    # This function computes the probability p(k) of obtaining k 
-    # from a hypergeometric distribution with parameters 
+    # This function computes the probability p(k) of obtaining k
+    # from a hypergeometric distribution with parameters
     # m, n t.
     # * m: number of elements with desired attribute on population
-    # * n: sample size    
+    # * n: sample size
     # * t: population size
 
     ##
     # :singleton-method: cdf(k,m,n,total)
     # These functions compute the cumulative distribution function P(k)
-    # for the hypergeometric distribution with parameters m, n and t. 
+    # for the hypergeometric distribution with parameters m, n and t.
     # * m: number of elements with desired attribute on population
     # * n: sample size
     # * t: population size
-    
 
     ##
     # :singleton-method: p_value(k,m,n,total)
-
   end
 end

data/lib/distribution/hypergeometric/gsl.rb

@@ -3,14 +3,13 @@ module Distribution
     module GSL_
       class << self
         def pdf(k, m, n, total)  # :nodoc:
-          GSL::Ran::hypergeometric_pdf(k, m, total-m, n)
+          GSL::Ran.hypergeometric_pdf(k, m, total - m, n)
         end
-        # The GSL::Cdf function for hypergeometric 
-        #   
+        # The GSL::Cdf function for hypergeometric
+        #
         def cdf(k, m, n, total) # :nodoc:
-          GSL::Cdf::hypergeometric_P(k, m, total-m, n)
+          GSL::Cdf.hypergeometric_P(k, m, total - m, n)
         end
-        
       end
     end
   end

data/lib/distribution/hypergeometric/java.rb

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

data/lib/distribution/hypergeometric/ruby.rb

@@ -1,13 +1,14 @@
-# Added by John O. Woods, SciRuby project. 
+# Added by John O. Woods, SciRuby project.
 # Optimized by Claudio Bustos
 
 module Distribution
   module Hypergeometric
     module Ruby_
       class << self
-        def bc(n,k)
-          Math.binomial_coefficient(n,k)
+        def bc(n, k)
+          Math.binomial_coefficient(n, k)
         end
+
         # Hypergeometric probability density function
         #
         # Probability p(+k+, +m+, +n+, +total+) of drawing sets of size +m+ and +n+ with an intersection of size +k+
@@ -17,50 +18,48 @@ module Distribution
         # * http://www.gnu.org/software/gsl/manual/html_node/The-Hypergeometric-Distribution.html
         # * http://en.wikipedia.org/wiki/Hypergeometric_distribution
         def pdf(k, m, n, total)
-          min_m_n=m<n ? m : n
-          max_t=[0,m+n-total].max
-          return 0 if k>min_m_n or k<max_t
-          (bc(m,k) * bc(total-m,n-k)).quo(bc(total,n))
-        end
-        
-        
-        
-        def pdf_with_den(k,m,n,total,den)
-          (bc(m,k) * bc(total-m,n-k)).quo(den)
+          min_m_n = m < n ? m : n
+          max_t = [0, m + n - total].max
+          return 0 if k > min_m_n || k < max_t
+          (bc(m, k) * bc(total - m, n - k)).quo(bc(total, n))
         end
 
-        # p-value: 
-       
-        def p_value(pr, m, n, total)
-          ac=0
-          den=bc(total,n)
-          
-          (0..total).each do |i|
-            ac+=pdf_with_den(i,m,n,total,den)
-            return i if ac>=pr
-          end
+        alias_method :exact_pdf, :pdf
+
+        def pdf_with_den(k, m, n, total, den)
+          (bc(m, k) * bc(total - m, n - k)).quo(den)
         end
+
         # Cumulative distribution function.
         # The probability of obtain, from a sample of
         # size +n+, +k+ or less elements
         # in a population size +total+ with +m+ interesting elements.
-        # 
+        #
         # Slow, but secure
         def cdf(k, m, n, total)
-          raise(ArgumentError, "k>m") if k>m
-          raise(ArgumentError, "k>n") if k>n
+          fail(ArgumentError, 'k>m') if k > m
+          fail(ArgumentError, 'k>n') if k > n
           # Store the den
-          den=bc(total,n)
-          (0..k).collect { |ki| pdf_with_den(ki,m,n,total,den) }.inject { |sum,v| sum+v}
+          den = bc(total, n)
+          (0..k).collect { |ki| pdf_with_den(ki, m, n, total, den) }.inject { |sum, v| sum + v }
+        end
+
+        alias_method :exact_cdf, :cdf
+
+        # p-value:
+        def quantile(pr, m, n, total)
+          ac = 0
+          den = bc(total, n)
+
+          (0..total).each do |i|
+            ac += pdf_with_den(i, m, n, total, den)
+            return i if ac >= pr
+          end
         end
-        
-        
-        alias :exact_pdf :pdf 
-        alias :exact_p_value :p_value
-        alias :exact_cdf :cdf 
 
-        
+        alias_method :p_value, :quantile
+        alias_method :exact_p_value, :p_value
       end
     end
   end
-end
+end

data/lib/distribution/logistic.rb

@@ -1,13 +1,12 @@
 require 'distribution/logistic/ruby'
-#require 'distribution/logistic/gsl'
-#require 'distribution/logistic/java'
-
+# require 'distribution/logistic/gsl'
+# require 'distribution/logistic/java'
 
 module Distribution
   # From Wikipedia:
   # In probability theory and statistics, the logistic distribution is a continuous probability distribution. Its cumulative distribution function is the logistic function, which appears in logistic regression and feedforward neural networks. It resembles the normal distribution in shape but has heavier tails (higher kurtosis).
   module Logistic
-    SHORTHAND='logis'
+    SHORTHAND = 'logis'
     extend Distributable
     create_distribution_methods
     ##
@@ -21,7 +20,7 @@ module Distribution
     # Returns the pdf for logistic distribution (f(x,u,s))
     # * u: mean
     # * s: variance related parameter
-    
+
     ##
     # :singleton-method: cdf(x,u,s)
     # Returns the cdf for logistic distribution (F(x,u,s))
@@ -30,11 +29,9 @@ module Distribution
 
     ##
     # :singleton-method: p_value(pr , u,s)
-    # Returns the inverse cdf for logistic distribution 
+    # Returns the inverse cdf for logistic distribution
     # (F^-1(pr,u,s))
     # * u: mean
     # * s: variance related parameter
-    
-
   end
 end

data/lib/distribution/logistic/ruby.rb

@@ -2,18 +2,23 @@ module Distribution
   module Logistic
     module Ruby_
       class << self
-        def rng(u,s)
-          lambda {p_value(rand(),u,s)}
+        def rng(u, s)
+          -> { p_value(rand, u, s) }
         end
-        def pdf(x,u,s )
-          (Math.exp(-(x-u) / s)) / (s*(1+Math.exp(-(x-u) / s)**2))
+
+        def pdf(x, u, s)
+          (Math.exp(-(x - u) / s)) / (s * (1 + Math.exp(-(x - u) / s)**2))
         end
-        def cdf(x,u,s )
-          1/(1+Math.exp(-(x-u) / s))
+
+        def cdf(x, u, s)
+          1 / (1 + Math.exp(-(x - u) / s))
         end
-        def p_value(pr,u,s )
-          u+s*Math.log(pr/(1-pr))
+
+        def quantile(pr, u, s)
+          u + s * Math.log(pr / (1 - pr))
         end
+
+        alias_method :p_value, :quantile
       end
     end
   end

data/lib/distribution/lognormal.rb

@@ -12,28 +12,26 @@ module Distribution
   #    normally distributed, then so is logb(Y), for any two positive numbers
   #    a, b ≠ 1.)
   #
-  # This module calculate the pdf, cdf and inverse cdf for Beta Distribution.
+  # This module calculates the pdf, cdf and inverse cdf for the Lognormal distribution.
   #
   module LogNormal
     extend Distributable
-    SHORTHAND='lognormal'
+    SHORTHAND = 'lognormal'
     create_distribution_methods
 
     ##
     # :singleton-method: pdf(x,u,s)
-    # Returns PDF of of Lognormal distribution with parameters u (position) and
+    # Returns the PDF of the Lognormal distribution of x with parameters u (position) and
     # s (deviation)
 
-
     ##
     # :singleton-method: cdf(x,u,s)
-    # Returns the CDF of Lognormal distribution of x with parameters 
-    # u (position) and s(deviation)
+    # Returns the CDF of the Lognormal distribution of x with parameters u (position) and
+    # s(deviation)
 
     ##
     # :singleton-method: p_value(pr,u,s)
     # Return the quantile of the corresponding integral +pr+
     # on a lognormal distribution's cdf with parameters z and s
-
   end
 end