galaaz 0.4.0

data/lib/expression.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.
+##########################################################################################
+
+module E
+
+  #----------------------------------------------------------------------------------------
+  # @param symbol [Symbol]
+  # @param args [Array] arguments to the missing method
+  #----------------------------------------------------------------------------------------
+  
+  def self.method_missing(symbol, *args)
+    name = R::Support.convert_symbol2r(symbol)
+    R::Language.build(name, *args)
+  end
+
+  #--------------------------------------------------------------------------------------
+  #
+  #--------------------------------------------------------------------------------------
+
+  def self.[](executable)
+    R::RubyCallback.build(executable)
+  end
+
+end
+

data/lib/galaaz.rb

@@ -0,0 +1,27 @@
+# -*- 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_relative 'r'
+
+$LOAD_PATH << File.dirname(File.expand_path('..', __FILE__)) + "/r_requires"
+

data/lib/r.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_relative 'robject'
+require_relative 'rsupport'
+
+module R
+
+  RCONSTANTS = ["LETTERS", "letters", "month.abb", "month.name", "pi"]
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def self.method_missing(symbol, *args, &block)
+    
+    if (block_given?)
+      val = R::Support.process_missing(symbol, false, *args)
+      return R::Support.new_scope(symbol, val, *args, &block)
+    end
+
+    R::Support.process_missing(symbol, false, *args)
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def self.internal_eval(symbol, *args)
+    R::Support.process_missing(symbol, true, *args)
+  end
+
+  #----------------------------------------------------------------------------------------
+  # Checks to see if the given libs are installed in R and if not, install them
+  # @param libs [Array] Array of strings with the names of the libraries to check and
+  # install
+  #----------------------------------------------------------------------------------------
+
+  def self.install_rlibs(*libs)
+
+    packages = R.c(libs)
+
+    new_packages = packages[!(packages._ :in, R.installed__packages[:all, "Package"])]
+    if(new_packages.size > 0)
+      puts "The following packages are missing and will be installed:\n #{new_packages}"
+      R.install__packages(new_packages)
+    end
+    
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def self.install_and_loads(*libs)
+    R.install_rlibs(*libs)
+    libs.each { |lib| R.require lib }
+  end
+  
+end
+
+# define methods for accessing indexed object: Vector, Lists
+require_relative 'rindexed_object'
+# define methods for accessing multi dimensional indexed objects: Matrix, DataFrames
+require_relative 'rmd_indexed_object'
+# Binary operators: '+', '-', etc
+require_relative 'rbinary_operators'
+# Unary operators: '!', '@-', etc
+require_relative 'runary_operators'
+# Definition of R Vector
+require_relative 'rvector'
+# Definition of R Lists
+require_relative 'rlist'
+# Definition of R Matrix
+require_relative 'rmatrix'
+# Definition of R DataFrame
+require_relative 'rdata_frame'
+# Definition of R Closure (functions)
+require_relative 'rclosure'
+# Definition of R Expression
+require_relative 'rexpression'
+# Definition of R Environment
+require_relative 'renvironment'
+# Definition of R Language
+require_relative 'rlanguage'
+# Definition of R Symbol
+require_relative 'rsymbol'
+# Access to package symbols
+require_relative 'rpkg'
+
+# Defines the E module for creating R expressions
+require_relative 'expression'
+# Ruby class extensions.  Extends Symbol to allow the creation of
+# expressions using Symbol: (:x > 10)
+require_relative 'ruby_extensions'
+# Class to allow R calling back into Ruby
+require_relative 'ruby_callback'

data/lib/r_methods.rb

@@ -0,0 +1,89 @@
+# -*- 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.
+##########################################################################################
+
+module R
+
+  module Support
+    
+    #--------------------------------------------------------------------------------------
+    # Captures the R output to a variable and returns it. 
+    #--------------------------------------------------------------------------------------
+    
+    def self.capture
+      
+      Polyglot.eval("R", <<-R)
+        function(obj, ...) {
+          sink(tt <- textConnection("results","w"), split=FALSE);
+          print(obj, ...);
+          sink();
+          close(tt);
+          results
+        }
+      R
+      
+    end 
+    
+    #--------------------------------------------------------------------------------------
+    # multi-dimensional indexing
+    #--------------------------------------------------------------------------------------
+    
+    def self.md_index
+      Polyglot.eval("R", <<-R)
+        function(mdobject, ...) { 
+          mdobject[...];
+        }
+      R
+    end
+
+    #--------------------------------------------------------------------------------------
+    # R function that returns another R function that calls back a Ruby Method or Proc
+    # Some R functions that receive a function as argument will test to see if their
+    # parameters is a function or a symbol, so the Ruby method needs to be wrapped inside
+    # an R function in order for it to pass this test.
+    #--------------------------------------------------------------------------------------
+
+    def self.ruby_callback_method
+      Polyglot.eval("R", <<-R)
+        function(rb_method) {
+          function(...) {
+          rb_method(...)
+          }
+        }
+      R
+    end
+
+    #--------------------------------------------------------------------------------------
+    # @bug Needed to create method row__names because dispatch is not working properly
+    #--------------------------------------------------------------------------------------
+
+    def self.set_row_names
+      Polyglot.eval("R", "function(object, x) row.names(object) <- x")
+    end
+
+    def self.get_row_names
+      Polyglot.eval("R", "function(x) row.names(x)")
+    end
+
+  end
+  
+end

data/lib/rbinary_operators.rb

@@ -0,0 +1,226 @@
+# -*- 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.
+##########################################################################################
+
+module R
+
+  #--------------------------------------------------------------------------------------
+  # Module for binary operators with normal elements: matrix, vector, etc.
+  #--------------------------------------------------------------------------------------
+
+  module ExecBinOp
+    
+    #--------------------------------------------------------------------------------------
+    # 
+    #--------------------------------------------------------------------------------------
+
+    def exec_oper(operator, other_object)
+      R::Support.exec_function_name(operator, @r_interop, other_object)
+    end
+
+  end
+
+  #--------------------------------------------------------------------------------------
+  # Module for binary operators when creating an expression (call)
+  #--------------------------------------------------------------------------------------
+
+  module CallBinOp
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+    
+    def exec_oper(operator, other_object)
+      R::Language.build(operator, self, other_object)
+    end
+
+  end
+
+  #--------------------------------------------------------------------------------------
+  # Module for binary operators when creating formulas
+  #--------------------------------------------------------------------------------------
+
+  module FormulaBinOp
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def prep_object(object)
+      
+      case object
+      when :all
+        '.'
+      when R::RSymbol, Symbol
+        object.to_s
+      when R::Language
+        R.deparse(object).substring(2)
+      when String
+        object
+      end
+      
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+    
+    def exec_oper(operator, other_object, response = false)
+
+      o1 = prep_object(self)
+      o2 = prep_object(other_object)
+
+      response ? R.reformulate(o2, response: o1) :
+         R.reformulate(R.paste0(o1, operator.delete("`"), o2))
+      
+    end
+
+  end
+
+  #--------------------------------------------------------------------------------------
+  # Note that binary operators work on vectors and matrices as well as scalars. 
+  #--------------------------------------------------------------------------------------
+  
+  module BinaryOperators
+
+    #--------------------------------------------------------------------------------------
+    # @param other_object
+    #--------------------------------------------------------------------------------------
+
+    def +(other_object)
+      exec_oper("`+`", other_object)
+    end
+    
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def -(other_object)
+      exec_oper("`-`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def *(other_object)
+      exec_oper("`*`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def /(other_object)
+      exec_oper("`/`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def **(other_object)
+      exec_oper("`^`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def %(other_object)
+      exec_oper("`%%`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def ==(other_object)
+      exec_oper("`==`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def <(other_object)
+      exec_oper("`<`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def <=(other_object)
+      exec_oper("`<=`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def >(other_object)
+      exec_oper("`>`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def >=(other_object)
+      exec_oper("`>=`", other_object)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def !=(other_object)
+      exec_oper("`!=`", other_object)
+    end
+    
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def &(other_object)
+      R::Support.exec_function_name("`&`", @r_interop, other_object.r_interop)
+    end
+    
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def |(other_object)
+      R::Support.exec_function_name("`|`", @r_interop, other_object.r_interop)
+    end
+
+    #--------------------------------------------------------------------------------------
+    #
+    #--------------------------------------------------------------------------------------
+
+    def coerce(numeric)
+      [R.c(numeric), self]
+    end
+    
+  end
+
+end