galaaz 0.4.0

data/r_requires/ggplot.rb

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+# coding: utf-8
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+# check if packages are already installed and if not intall them
+R.install_rlibs('ggplot2', 'grid', 'gridExtra', 'ggplotify')
+
+# Load plotting libraries
+R.library('ggplot2')
+R.library('grid')
+R.library('gridExtra')
+R.library('ggplotify')

data/specs/all.rb

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+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2013 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require_relative 'r_eval.spec'
+
+# Specification for R::Vector
+require_relative 'r_vector_creation.spec'
+require_relative 'r_vector_object.spec'
+require_relative 'r_vector_subsetting.spec'
+require_relative 'r_vector_functions.spec'
+require_relative 'r_vector_operators.spec'
+
+# Specification for R::Lists
+require_relative 'r_list.spec'
+require_relative 'r_list_apply.spec'
+
+# Specification for R::Matrix
+require_relative 'r_matrix.spec'
+
+# Specification for R::Dataframes
+require_relative 'r_dataframe.spec'
+
+# Specification for language features
+require_relative 'r_function.spec'
+require_relative 'r_language.spec'

data/specs/r_dataframe.spec.rb

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+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+
+describe R::DataFrame do
+
+  #----------------------------------------------------------------------------------------
+  context "Create DataFrame" do
+
+    it "should create a dataframe from a vector" do
+      vec = R.seq(6)
+      vec.dim = R.c(2, 3)
+      
+      # create a DataFrame from a vector
+      df = R.as__data__frame(vec)
+      expect(df[1, "V1"]).to eq 1
+      expect df[1, 'V2'] == 3
+      expect df[1, :all] == R.c(V1: 1, V2: 3, V3: 5)
+      
+    end
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  context "Subsetting" do
+    
+    it "should do integer subsetting" do
+      grades = R.c(1.0, 2.0, 2.0, 3.0, 1.0)
+      
+      info = R.data__frame(
+        grade: (3..1),
+        desc: R.c("Excellent", "Good", "Poor"),
+        fail: R.c(false, false, true)
+      )
+      
+      id = R.match(grades, info.grade)
+      table = info[id, :all]
+      
+      expect(table.grade[1]).to eq 1
+      expect(table.desc.levels[2]).to eq "Good"
+      expect(table.fail[4]).to eq false
+      
+      info.rownames = info.grade
+      table2 = info[grades.as__character, :all]
+      
+      expect(table2.grade[2]).to eq 2
+      expect(table2.desc.levels[1]).to eq "Excellent"
+      expect(table2.fail[4]).to eq true
+      
+    end
+    
+    it "should do 'each_column'" do
+      
+      mtcars = ~:mtcars
+      
+      mtcars.each_column do |col, col_name|
+        # col_name is an R::Vector with one string element.
+        # Extract the 'native' value by indexing with '<< 0'
+        case col_name << 0
+        when "mpg"
+          expect col[1] == 21
+          expect col[9] == 22.8
+          expect col[32] == 21.4
+        when "cyl"
+          expect col[1] == 6
+          expect col[10] == 6
+          expect col[32] == 4
+        when "disp"
+          expect col[1] == 160
+          expect col[32] == 121
+        end
+        
+      end
+      
+    end
+
+    it "should do 'each_row'" do
+
+      mtcars = ~:mtcars
+      
+      mtcars.each_row do |row, row_name|
+        case row_name << 0
+        when "Mazda RX4"
+          expect row['mpg'] == 21
+          expect row.qsec == 16.46
+        when "Hornet Sportabout"
+          expect row['cyl'] == 8
+          expect row['wt'] == 3.44
+        when "Merc 240D"
+          expect row['hp'] == 62
+          expect row.drat == 3.69
+        when "Volvo 142E"
+          expect row.hp == 109
+          expect row.am == 1
+          expect row.carb == 2
+        end
+        
+      end
+      
+    end
+    
+  end
+  
+  #----------------------------------------------------------------------------------------
+  context "Boostraping" do
+    
+    before(:each) do
+      @df = R.data__frame(x: R.rep((1..3), each: 2), y: (6..1), z: (~:letters)[(1..6)])
+      R.set__seed(10)
+    end
+    
+    it "should do reordering with integer subsetting" do
+      
+      table = @df[R.sample(@df.nrow), :all]
+      expect(table.x[3]).to eq 3
+      expect(table.y[2]).to eq 5
+      expect(table.z.levels[6]).to eq "f"
+      
+    end
+    
+    it "should select random rows with integer subsetting" do
+      table = @df[R.sample(@df.nrow, 3), :all]
+      
+      expect(table.x[3]).to eq 3
+      expect(table.y[1]).to eq 3
+      expect(table.z.levels[table.z[2]]).to eq "b"
+    end
+    
+    it "should randomly reorder a dataframe" do
+      df2 = @df[R.sample(@df.nrow), (3..1)]
+      
+      expect(df2.z.levels[df2.z[4]]).to eq "c"
+      expect(df2.y[2]).to eq 5
+      expect(df2.x[5]).to eq 1
+    end
+    
+    it "should reorder by a given variable" do
+      df2 = @df[R.sample(@df.nrow), (3..1)]
+      df2 = df2[df2.x.order, :all]
+      
+      expect(df2.x[1]).to eq 1
+      expect(df2.y[1]).to eq 5
+      expect(df2.z.levels[df2.z[1]]).to eq "b"
+    end
+    
+    it "should reorder variables" do
+      df2 = @df[R.sample(@df.nrow), (3..1)]
+      df2 = df2[df2.x.order, :all]
+      
+      df2 = df2[:all, df2.names.order]
+      
+      expect(df2.names.all__equal R.c("x", "y", "z")).to eq true
+    end
+    
+  end
+
+  # df = R.tibble::tibble(x = 1:3, y = 3:1, z = letters[1:3])
+  
+end
+

data/specs/r_eval.spec.rb

@@ -0,0 +1,164 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+
+describe R do
+
+  context "Accessing R through R::Support.eval" do
+
+    before(:each) do
+      R::Support.eval(<<-R)
+        # x is a "double" vector
+        x <- c(1, 2, 3)
+        hyp <- function(x, y) { sqrt(x^2 + y^2) };
+      R
+    end
+
+    it "Integer values in R are automatically unboxed as float" do
+      var = R::Support.eval("5L")
+      # although var is an Interop, it is automatically unboxed, when it is a vector of length
+      # one, and can thus be compared with a number.
+      expect(5).to eq var
+      expect(5.0).to eq var
+    end
+
+    it "Interop pointers can be operated through eval" do
+      var = R::Support.eval("5L")
+      # calling method 'class' on var returns a vector of size one with a string that
+      # contains the class of the object
+      expect("integer").to eq R::Support.eval("class").call(var).to_s
+    end
+    
+    it "A number evaluated in R is automatically unboxed as float in Ruby" do
+      var = R::Support.eval("4")
+      expect(4.0).to eq var
+      expect("numeric").to eq R::Support.eval("class").call(var).to_s
+    end
+
+    it "R vectors can be indexed by the indexing method of the host language" do
+      var = R::Support.eval("'Hello'")
+      expect(var[0]).to eq "Hello"
+    end
+
+    it "should retrieve named R objects to Ruby variables using eval. Returned value should be an Interop" do
+      # retrieve x and hyp from R and attribute it to local Ruby variables
+      x = R::Support.eval("x")
+      # hyp is an R function and works like a named function in Ruby
+      hyp = R::Support.eval("hyp")
+
+      # is is a foreign object
+      expect(Truffle::Interop.foreign?(x)).to be true
+      # we can index the object starting at 0.  This is a property offered by
+      # Interop API
+      expect(x[0]).to eq 1.0
+
+      # calling a named function or block is done by use of the 'call' method
+      expect(hyp.call(3, 4)).to eq 5.0
+    end
+
+  end
+
+  context "Basic access to R without R::Support" do
+    
+    it "should retrieve named R objects to Ruby variables by using '~' " do
+      # retrieve x and hyp from R and attribute it to local Ruby variables
+      x = ~:x
+
+      expect(x.is_a? R::Vector).to eq true
+      expect(x.length).to eq 3
+      # it is not a foreign object. It's an R::Vectors
+      expect(Truffle::Interop.foreign?(x)).to be false
+      # Values are indexed starting with 1, the same as R notation
+      expect(x[1]).to eq 1.0
+    end
+
+    it "should return a String Vector" do
+      # Interop will take a one dimensional array and return the value of the first
+      # element.  This might change on a future release. At the present moment, var
+      # becomes a character array with 5 elements
+      var = R.c("Hello")
+      
+      expect(var.length).to eq 1
+      expect(var.typeof).to eq "character"
+      expect(var.is_a? R::Vector).to eq true
+      expect(var[1]).to eq "Hello"
+    end
+    
+    it "shoud access named objects in R" do
+      # to create a double vector through the Ruby interface, we need that at least
+      # one element of the vector is a 'float'
+      double = R.c(1.0, 2, 3)
+      expect((~:x).identical double).to eq true
+      expect(R.hyp(3, 4)).to eq 5
+    end
+
+    it "should box R functions in R::Closure Ruby class" do
+      # hyp is an R function and works like a named function in Ruby
+      hyp = ~:hyp
+      
+      # calling a named function or block is done by use of the 'call' method
+      expect(hyp.call(3, 4)).to eq 5.0
+      expect(hyp.typeof).to eq "closure"
+      expect(hyp.is_a? R::Closure).to eq true
+    end
+    
+    it "should print values the same way as R" do
+      # retrieve x and hyp from R and attribute it to local Ruby variables
+      x = ~:x
+      
+      # Converting to string (to_s) will print as an R vector would
+      expect(x[1].to_s).to eq ("[1] 1")
+      expect(x.to_s).to eq ("[1] 1 2 3")
+    end
+
+    it "should allow logical comparison using R::Objects" do
+      # retrieve x and hyp from R and attribute it to local Ruby variables
+      x = ~:x
+
+      expect(x[1] == 1).to eq true
+      expect(x[2] == 1).to eq false
+    end
+    
+    it "should have NA" do
+      expect(R.is__na R::NA).to eq true
+    end
+    
+  end
+
+  context "Call Non-standard Evaluation methods" do
+
+    it "should pass delayed evaluation parameters to methods" do
+      # call the subset method filtering by 'cyl == 8 & carb > 3'
+      # In order to convert a Ruby symbol to an R symbol we use the '.r' method on the
+      # Ruby symbol.  Ruby bitwise operators '&' and '|' are overloaded and used as 
+      # the equivalent R operators and not as bitwise operators.
+      mt_subset = (~:mtcars).subset((:cyl == 8) & (:carb > 3))
+      expect(mt_subset.mpg == R.c(14.3, 10.4, 10.4, 14.7, 13.3, 15.8, 15.0)).to eq true
+      expect((mt_subset.cyl == 8).all).to eq true
+      expect((mt_subset.carb > 3).all).to eq true
+    end
+    
+  end
+  
+end

data/specs/r_function.spec.rb

@@ -0,0 +1,105 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+require 'galaaz'
+
+describe R do
+
+  #----------------------------------------------------------------------------------------
+  context "When calling R functions" do
+
+    # Let's call a function passing named parameters
+    it "should pass named parameters" do
+      # Named parameters are in Ruby are converted to named parameters in R
+      m = R.matrix(R.seq(1, 10), nrow: 2,
+                   dimnames: R.list(R.c("1", "2"),
+                                    R.c("a", "b", "c", "d", "e")))
+      expect(m.dimnames[[1]].identical(R.c("1", "2"))).to eq true
+      expect(m.dimnames[[2]].identical(R.c("a", "b", "c", "d", "e"))).to eq true
+    end
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  context "Using Ruby Procs as parameters to R functions and expressions" do
+
+    before(:each) do
+      @x = @y = R.seq(-~:pi, ~:pi, length: 10)
+    end
+    
+    it "should accept a Proc as parameter" do
+      # call R outer function passing in a Proc
+      # note that x and y are Ruby objects that were received from an
+      # R function, so they are R::Vectors or another type of R::Object. We
+      # can operate on them with R functions: for instance, R.cos(y)
+      f = R.outer(@x, @y,
+                  lambda { |x, y|
+                    R.cos(y) / (x**2 + 1)})
+      expect(f[1, 1] == -0.09199967).to eq true
+      expect(f[7, 6] == -0.04599983).to eq true
+    end
+
+    it "should accept a Method as parameter" do
+
+      module Calculation
+        # note that x and y are Ruby objects that were received from an
+        # R function, so they are R::Vectors or another type of R::Object.  We
+        # can operate on them with R functions: for instance, R.cos(y)
+        def self.func(x, y)
+          R.cos(y) / (x**2 + 1)
+        end
+      end
+
+      f = R.outer(@x, @y, Calculation.method(:func))
+      expect(f[1, 1] == -0.09199967).to eq true
+      expect(f[7, 6] == -0.04599983).to eq true
+      
+    end
+    
+    it "should accept Procs in Expressions" do
+      
+      df = R.data__frame(x: @x, y: @y)
+      # create a quoted function f that takes 3 parameters :x, :y and a Proc
+      # we want to evaluate f in the scope of the dataframe 'df'
+      f = E.outer(:x, :y, lambda { |x, y| R.cos(y) / (1 + x**2) })
+      
+      # now lets evaluate f in the scope of df, where :x and :y are defined
+      res = f.eval(df)
+      expect(res[1, 1] == -0.09199967).to eq true
+      expect(res[10, 10] == -0.09199967).to eq true
+    end
+
+    it "Should be able to 'eval' a Proc in expression" do
+      
+      df = R.data__frame(x: R.c(1, 2, 3), y: R.c(4, 5, 6))
+      f = E.outer(:x, :y, Proc.new { |x, y| x + y })
+      
+      res = f.eval(df)
+      expect(res[1, :all] == R.c(5, 6, 7)).to eq true
+      expect(res[3, :all] == R.c(7, 8, 9)).to eq true
+
+    end
+      
+  end
+  
+end