rust 0.7 → 0.9

data/lib/{rust-plots.rb → rust/plots/core.rb}

@@ -1,5 +1,4 @@
-require_relative 'rust-core'
-require_relative 'rust-calls'
+require_relative '../core'
 
 module Rust::Plots
     class BasePlot
@@ -134,173 +133,6 @@ module Rust::Plots
         end
     end
     
-    class ScatterPlot < BasePlot
-        def initialize(x = nil, y = nil, **options)
-            super()
-            @series = []
-            if x && y
-                self.series(x, y, options)
-            end
-        end
-        
-        def series(x, y, **options)
-            @series << [x, y, options]
-            
-            return self
-        end
-        
-        def thickness(t)
-            self['lwd'] = t
-            
-            return self
-        end
-        
-        def lines()
-            self['type'] = "l"
-            
-            return self
-        end
-        
-        def points()
-            self['type'] = "p"
-            
-            return self
-        end
-        
-        def lines_and_points()
-            self['type'] = "b"
-            
-            return self
-        end
-        
-        protected
-        def _show()
-            first = true
-            palette = self.palette(@series.size)
-            i = 0
-            
-            base_options = {}
-            unless @options['xlim']
-                x_values = @series.map { |v| v[0] }.flatten
-                y_values = @series.map { |v| v[1] }.flatten
-                
-                base_options[:xlim] = [x_values.min, x_values.max]
-                base_options[:ylim] = [y_values.min, y_values.max]
-            end
-            
-            @series.each do |x, y, options|
-                options = options.merge(base_options)
-                Rust["plotter.x"] = x
-                Rust["plotter.y"] = y
-                
-                function = nil
-                if first
-                    function = Rust::Function.new("plot")
-                    first = false
-                else
-                    function = Rust::Function.new("lines")
-                end
-                
-                augmented_options = {}
-                augmented_options['col'] = options[:color] || palette[i]
-                augmented_options['xlim'] = options[:xlim] if options[:xlim]
-                augmented_options['ylim'] = options[:ylim] if options[:ylim]
-                
-                function.options = self._augmented_options(augmented_options)
-                function.arguments << Rust::Variable.new("plotter.x")
-                function.arguments << Rust::Variable.new("plotter.y")
-                
-                function.call
-                
-                i += 1
-            end
-            
-            return self
-        end
-    end
-    
-    class BarPlot < BasePlot
-        def initialize(bars)
-            super()
-            @bars = bars
-        end
-        
-        protected
-        def _show()
-            Rust["plotter.bars"] = @bars.values
-            Rust["plotter.labels"] = @bars.keys
-            
-            Rust._eval("names(plotter.bars) <- plotter.labels")
-            
-            function = Rust::Function.new("barplot")
-            function.options = self._augmented_options
-            function.arguments << Rust::Variable.new("plotter.bars")
-            
-            function.call
-            
-            return self
-        end
-    end
-    
-    class DistributionPlot < BasePlot
-        def initialize
-            super()
-            @series = []
-        end
-        
-        def series(data, **options)
-            @series << [data, options]
-            
-            return self
-        end
-    end
-    
-    class DensityPlot < DistributionPlot
-        protected
-        def _show()
-            first = true
-            @series.each do |data, options|
-                Rust["plotter.series"] = data
-                
-                if first
-                    first = false
-                    command = "plot"
-                else
-                    command = "lines"
-                end
-                
-                function = Rust::Function.new(command)
-                function.options = self._augmented_options({"col" => options[:color]})
-                function.arguments << Rust::Variable.new("density(plotter.series)")
-                function.call
-            end
-            
-            return self
-        end
-    end
-    
-    class BoxPlot < DistributionPlot
-        protected
-        def _show()
-            function = Rust::Function.new("boxplot")
-            
-            names = []
-            @series.each_with_index do |data, i|
-                series, options = *data
-                varname = "plotter.series#{i}"
-                Rust[varname] = series
-                function.arguments << Rust::Variable.new(varname)
-                names << (options[:name] || (i+1).to_s)
-            end
-            
-            function.options = self._augmented_options({'names' => names})
-            
-            function.call
-            
-            return self
-        end
-    end
-    
     class Renderable
         def initialize
             @options = Rust::Options.new

data/lib/rust/plots/distribution-plots.rb

@@ -0,0 +1,62 @@
+require_relative 'core'
+
+module Rust::Plots
+    class DistributionPlot < BasePlot
+        def initialize
+            super()
+            @series = []
+        end
+        
+        def series(data, **options)
+            @series << [data, options]
+            
+            return self
+        end
+    end
+    
+    class DensityPlot < DistributionPlot
+        protected
+        def _show()
+            first = true
+            @series.each do |data, options|
+                Rust["plotter.series"] = data
+                
+                if first
+                    first = false
+                    command = "plot"
+                else
+                    command = "lines"
+                end
+                
+                function = Rust::Function.new(command)
+                function.options = self._augmented_options({"col" => options[:color]})
+                function.arguments << Rust::Variable.new("density(plotter.series)")
+                function.call
+            end
+            
+            return self
+        end
+    end
+    
+    class BoxPlot < DistributionPlot
+        protected
+        def _show()
+            function = Rust::Function.new("boxplot")
+            
+            names = []
+            @series.each_with_index do |data, i|
+                series, options = *data
+                varname = "plotter.series#{i}"
+                Rust[varname] = series
+                function.arguments << Rust::Variable.new(varname)
+                names << (options[:name] || (i+1).to_s)
+            end
+            
+            function.options = self._augmented_options({'names' => names})
+            
+            function.call
+            
+            return self
+        end
+    end
+end

data/lib/rust/stats/all.rb

@@ -0,0 +1,4 @@
+self_path = File.expand_path(__FILE__)
+Dir.glob(File.dirname(self_path) + "/*.rb").each do |lib|
+    require_relative lib unless lib == self_path
+end

data/lib/{rust-basics.rb → rust/stats/correlation.rb}

@@ -1,4 +1,4 @@
-require_relative 'rust-core'
+require_relative '../core'
 
 module Rust::Correlation
     class Pearson
@@ -64,7 +64,7 @@ module Rust::Correlation
                 Rust['correlation.a'] = d1
                 Rust['correlation.b'] = d2
                 
-                _, warnings = Rust._eval("correlation.result <- cor.test(correlation.a, correlation.b, method='p')", true)
+                _, warnings = Rust._eval("correlation.result <- cor.test(correlation.a, correlation.b, method='k')", true)
                 
                 result = Result.new
                 result.name             = "Kendall's rank correlation tau"

data/lib/{rust-descriptive.rb → rust/stats/descriptive.rb}

@@ -1,6 +1,4 @@
-require 'code-assertions'
-
-require_relative 'rust-core'
+require_relative '../core'
 
 module Rust::Descriptive
     class << self
@@ -47,7 +45,7 @@ module Rust::Descriptive
             return data.sum
         end
         
-        def quantile(data, percentiles=[0.0, 0.25, 0.5, 0.75, 1.0])
+        def quantile(data, percentiles = [0.0, 0.25, 0.5, 0.75, 1.0])
             raise TypeError, "Expecting Array of numerics" if !data.is_a?(Array) || !data.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !percentiles.is_a?(Array) || !percentiles.all? { |e| e.is_a?(Numeric) }
             raise "Percentiles outside the range: #{percentiles}" if percentiles.any? { |e| !e.between?(0, 1) }
@@ -106,3 +104,25 @@ module Rust::Descriptive
         end
     end
 end
+
+module Rust::RBindings
+    def mean(series)
+        Rust::Descriptive.mean(series)
+    end
+    
+    def median(series)
+        Rust::Descriptive.median(series)
+    end
+    
+    def var(series)
+        Rust::Descriptive.variance(series)
+    end
+    
+    def sd(series)
+        Rust::Descriptive.standard_deviation(series)
+    end
+    
+    def quantile(series, percentiles = [0.0, 0.25, 0.5, 0.75, 1.0])
+        Rust::Descriptive.quantile(series, percentiles)
+    end
+end

data/lib/{rust-effsize.rb → rust/stats/effsize.rb}

@@ -1,8 +1,6 @@
-require 'code-assertions'
+require_relative '../core'
 
-Rust.exclusive do
-    Rust._eval("library(effsize)")
-end
+Rust.prerequisite('effsize')
 
 module Rust::EffectSize
     class Result
@@ -16,11 +14,9 @@ module Rust::EffectSize
             return "#{name} = #{estimate} (#{magnitude}) [#{confidence_interval.min}, #{confidence_interval.max}]"
         end
     end
-end
 
-module Rust::EffectSize::CliffDelta
-    class << self
-        def compute(d1, d2)
+    class CliffDelta
+        def self.compute(d1, d2)
             raise TypeError, "Expecting Array of numerics" if !d1.is_a?(Array) || !d1.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !d2.is_a?(Array) || !d2.all? { |e| e.is_a?(Numeric) }
             
@@ -45,11 +41,9 @@ module Rust::EffectSize::CliffDelta
             end
         end
     end
-end
-
-module Rust::EffectSize::CohenD
-    class << self
-        def compute(d1, d2)
+    
+    class CohenD
+        def self.compute(d1, d2)
             raise TypeError, "Expecting Array of numerics" if !d1.is_a?(Array) || !d1.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !d2.is_a?(Array) || !d2.all? { |e| e.is_a?(Numeric) }
             

data/lib/{rust-probabilities.rb → rust/stats/probabilities.rb}

@@ -1,4 +1,4 @@
-require_relative 'rust-core'
+require_relative '../core'
 
 class Numeric
     def distance(other)

data/lib/{rust-tests.rb → rust/stats/tests.rb}

@@ -1,4 +1,4 @@
-require_relative 'rust-core'
+require_relative '../core'
 
 module Rust::StatisticalTests
     class Result
@@ -85,85 +85,9 @@ module Rust::StatisticalTests
             end
         end
     end
-end
 
-module Rust::StatisticalTests::PValueAdjustment
-    def self.method(name)
-        name = name.to_s
-        case name.downcase
-        when "bonferroni", "b"
-            return Bonferroni
-        when "holm", "h"
-            return Holm
-        when "hochberg"
-            return Hochberg
-        when "hommel"
-            return Hommel
-        when "benjaminihochberg", "bh"
-            return BenjaminiHochberg
-        when "benjaminiyekutieli", "by"
-            return BenjaminiYekutieli
-        end
-    end
-    
-    class Bonferroni
-        def self.adjust(*p_values)
-            Rust.exclusive do
-                Rust['adjustment.p'] = p_values
-                return Rust._pull("p.adjust(adjustment.p, method=\"bonferroni\")")
-            end
-        end
-    end
-    
-    class Holm
-        def self.adjust(*p_values)
-            Rust.exclusive do
-                Rust['adjustment.p'] = p_values
-                return Rust._pull("p.adjust(adjustment.p, method=\"holm\")")
-            end
-        end
-    end
-    
-    class Hochberg
-        def self.adjust(*p_values)
-            Rust.exclusive do
-                Rust['adjustment.p'] = p_values
-                return Rust._pull("p.adjust(adjustment.p, method=\"hochberg\")")
-            end
-        end
-    end
-    
-    class Hommel
-        def self.adjust(*p_values)
-            Rust.exclusive do
-                Rust['adjustment.p'] = p_values
-                return Rust._pull("p.adjust(adjustment.p, method=\"hommel\")")
-            end
-        end
-    end
-    
-    class BenjaminiHochberg
-        def self.adjust(*p_values)
-            Rust.exclusive do
-                Rust['adjustment.p'] = p_values
-                return Rust._pull("p.adjust(adjustment.p, method=\"BH\")")
-            end
-        end
-    end
-    
-    class BenjaminiYekutieli
-        def self.adjust(*p_values)
-            Rust.exclusive do
-                Rust['adjustment.p'] = p_values
-                return Rust._pull("p.adjust(adjustment.p, method=\"BY\")")
-            end
-        end
-    end
-end
-
-module Rust::StatisticalTests::Wilcoxon
-    class << self
-         def paired(d1, d2, alpha = 0.05, **options)
+    class Wilcoxon
+         def self.paired(d1, d2, alpha = 0.05, **options)
             raise TypeError, "Expecting Array of numerics" if !d1.is_a?(Array) || !d1.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !d2.is_a?(Array) || !d2.all? { |e| e.is_a?(Numeric) }
             raise "The two distributions have different size" if d1.size != d2.size
@@ -185,7 +109,7 @@ module Rust::StatisticalTests::Wilcoxon
             end
         end
         
-        def unpaired(d1, d2, alpha = 0.05, **options)
+        def self.unpaired(d1, d2, alpha = 0.05, **options)
             raise TypeError, "Expecting Array of numerics" if !d1.is_a?(Array) || !d1.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !d2.is_a?(Array) || !d2.all? { |e| e.is_a?(Numeric) }
             
@@ -206,11 +130,9 @@ module Rust::StatisticalTests::Wilcoxon
             end
         end
     end
-end
-    
-module Rust::StatisticalTests::T
-    class << self
-        def paired(d1, d2, alpha = 0.05, **options)
+
+    class T
+        def self.paired(d1, d2, alpha = 0.05, **options)
             raise TypeError, "Expecting Array of numerics" if !d1.is_a?(Array) || !d1.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !d2.is_a?(Array) || !d2.all? { |e| e.is_a?(Numeric) }
             raise "The two distributions have different size" if d1.size != d2.size
@@ -232,7 +154,7 @@ module Rust::StatisticalTests::T
             end
         end
         
-        def unpaired(d1, d2, alpha = 0.05, **options)
+        def self.unpaired(d1, d2, alpha = 0.05, **options)
             raise TypeError, "Expecting Array of numerics" if !d1.is_a?(Array) || !d1.all? { |e| e.is_a?(Numeric) }
             raise TypeError, "Expecting Array of numerics" if !d2.is_a?(Array) || !d2.all? { |e| e.is_a?(Numeric) }
             
@@ -253,11 +175,9 @@ module Rust::StatisticalTests::T
             end
         end
     end
-end
 
-module Rust::StatisticalTests::Shapiro
-    class << self
-        def compute(vector, alpha = 0.05, **options)
+    class Shapiro
+        def self.compute(vector, alpha = 0.05, **options)
             raise TypeError, "Expecting Array of numerics" if !vector.is_a?(Array) || !vector.all? { |e| e.is_a?(Numeric) }
             Rust.exclusive do
                 Rust['shapiro.v'] = vector
@@ -275,6 +195,80 @@ module Rust::StatisticalTests::Shapiro
             end
         end
     end
+    
+    module PValueAdjustment
+        def self.method(name)
+            name = name.to_s
+            case name.downcase
+            when "bonferroni", "b"
+                return Bonferroni
+            when "holm", "h"
+                return Holm
+            when "hochberg"
+                return Hochberg
+            when "hommel"
+                return Hommel
+            when "benjaminihochberg", "bh"
+                return BenjaminiHochberg
+            when "benjaminiyekutieli", "by"
+                return BenjaminiYekutieli
+            end
+        end
+        
+        class Bonferroni
+            def self.adjust(*p_values)
+                Rust.exclusive do
+                    Rust['adjustment.p'] = p_values
+                    return Rust._pull("p.adjust(adjustment.p, method=\"bonferroni\")")
+                end
+            end
+        end
+        
+        class Holm
+            def self.adjust(*p_values)
+                Rust.exclusive do
+                    Rust['adjustment.p'] = p_values
+                    return Rust._pull("p.adjust(adjustment.p, method=\"holm\")")
+                end
+            end
+        end
+        
+        class Hochberg
+            def self.adjust(*p_values)
+                Rust.exclusive do
+                    Rust['adjustment.p'] = p_values
+                    return Rust._pull("p.adjust(adjustment.p, method=\"hochberg\")")
+                end
+            end
+        end
+        
+        class Hommel
+            def self.adjust(*p_values)
+                Rust.exclusive do
+                    Rust['adjustment.p'] = p_values
+                    return Rust._pull("p.adjust(adjustment.p, method=\"hommel\")")
+                end
+            end
+        end
+        
+        class BenjaminiHochberg
+            def self.adjust(*p_values)
+                Rust.exclusive do
+                    Rust['adjustment.p'] = p_values
+                    return Rust._pull("p.adjust(adjustment.p, method=\"BH\")")
+                end
+            end
+        end
+        
+        class BenjaminiYekutieli
+            def self.adjust(*p_values)
+                Rust.exclusive do
+                    Rust['adjustment.p'] = p_values
+                    return Rust._pull("p.adjust(adjustment.p, method=\"BY\")")
+                end
+            end
+        end
+    end
 end
 
 module Rust::RBindings

data/lib/rust.rb

@@ -1,9 +1,4 @@
-require_relative 'rust-core'
-require_relative 'rust-basics'
-require_relative 'rust-csv'
-require_relative 'rust-tests'
-require_relative 'rust-effsize'
-require_relative 'rust-descriptive'
-require_relative 'rust-plots'
-require_relative 'rust-calls'
-require_relative 'rust-probabilities'
+require_relative 'rust/core'
+require_relative 'rust/models/all'
+require_relative 'rust/plots/all'
+require_relative 'rust/stats/all'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rust
 version: !ruby/object:Gem::Version
-  version: '0.7'
+  version: '0.9'
 platform: ruby
 authors:
 - Simone Scalabrino
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-02-16 00:00:00.000000000 Z
+date: 2022-08-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rinruby
@@ -52,20 +52,38 @@ dependencies:
         version: 1.1.2
 description: Ruby advanced statistical library based on RinRuby
 email: s.scalabrino9@gmail.com
-executables: []
+executables:
+- ruby-rust
 extensions: []
 extra_rdoc_files: []
 files:
-- lib/rust-basics.rb
-- lib/rust-calls.rb
-- lib/rust-core.rb
-- lib/rust-csv.rb
-- lib/rust-descriptive.rb
-- lib/rust-effsize.rb
-- lib/rust-plots.rb
-- lib/rust-probabilities.rb
-- lib/rust-tests.rb
+- bin/ruby-rust
 - lib/rust.rb
+- lib/rust/core.rb
+- lib/rust/core/csv.rb
+- lib/rust/core/rust.rb
+- lib/rust/core/types/all.rb
+- lib/rust/core/types/dataframe.rb
+- lib/rust/core/types/datatype.rb
+- lib/rust/core/types/factor.rb
+- lib/rust/core/types/language.rb
+- lib/rust/core/types/list.rb
+- lib/rust/core/types/matrix.rb
+- lib/rust/core/types/s4class.rb
+- lib/rust/core/types/utils.rb
+- lib/rust/models/all.rb
+- lib/rust/models/anova.rb
+- lib/rust/models/regression.rb
+- lib/rust/plots/all.rb
+- lib/rust/plots/basic-plots.rb
+- lib/rust/plots/core.rb
+- lib/rust/plots/distribution-plots.rb
+- lib/rust/stats/all.rb
+- lib/rust/stats/correlation.rb
+- lib/rust/stats/descriptive.rb
+- lib/rust/stats/effsize.rb
+- lib/rust/stats/probabilities.rb
+- lib/rust/stats/tests.rb
 homepage: https://github.com/intersimone999/ruby-rust
 licenses:
 - GPL-3.0-only
@@ -85,7 +103,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.7
+rubygems_version: 3.3.15
 signing_key:
 specification_version: 4
 summary: Ruby advanced statistical library