Module: R::Support

Defined in:
lib/R_interface/rsupport.rb,
lib/R_interface/r_methods.rb,
lib/R_interface/rsupport_scope.rb

Overview

This is a support module for evaluating R functions

Constant Summary collapse

@@exec_counter = 
0
@@exec_from_ruby =

Using this method gives us more control over what happens when calling do.call and allows for debugging. Use it in exec_function when debugging is needed.

Polyglot.eval("R", <<-R)
  function(build_method, ...) {
    # function 'invoke' from package rlang should do a cleaner than
    # do.call (this is what the documentation says).
    # res = do.call(...);
    res = invoke(...);
    res2 = build_method(res);
    res2
  }
R

Class Method Summary collapse

Class Method Details

.capture ⇒ Object

Captures the R output to a variable and returns it. 



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# File 'lib/R_interface/r_methods.rb', line 32

def self.capture
  Polyglot.eval("R", <<-R)
    function(obj, ...) {
      sink(tt <- textConnection("results","w"), split=FALSE, type = c("output", "message"));
      print(obj, ...);
      sink();
      close(tt);
      results
    }
  R
end

.capture2 ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 44

def self.capture2
  Polyglot.eval("R", <<-R)
    function(obj, ...) {
      tryCatch({
        sink(tt <- textConnection("results","w"), split=FALSE, type = c("output", "message"));
        print(obj, ...);
        sink();
        results
      }, finally = {
        close(tt);
      })
    }
  R
end

.convert_symbol2r(symbol) ⇒ Object

Converts a Ruby symbol onto an R symbol. Converts ‘__’ to ‘.’ and ‘rclass’ to class

Parameters:

  • symbol (Symbol) —

    A Ruby symbol to convert to R



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# File 'lib/R_interface/rsupport.rb', line 200

def self.convert_symbol2r(symbol)
  name = symbol.to_s
  # convert '__' to '.'
  name.gsub!(/__/,".")
  # Method 'rclass' is a substitute for R method 'class'.  Needed, as 'class' is also
  # a Ruby method on an object
  name.gsub!("rclass", "class")
  name
end

.create_bin_expr(operator) ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 152

def self.create_bin_expr(operator)
  is_formula = (operator == "`~`")? 'TRUE' : 'FALSE'
  Polyglot.eval("R", <<-R)
    function(op1, op2) {
      o1 = enexpr(op1)
      o2 = enexpr(op2)
      if (typeof(o1) == 'symbol' && o1 == expr(`__`)) {
        o1 = expr(.)
      }
      if (typeof(o2) == 'symbol' && o2 == expr(`__`)) {
        o2 = expr(.)
      }
      exp = expr(#{operator}(!!o1, !!o2))
      if (#{is_formula}) {
        as.formula(exp)
      } else {
        exp
      }
    }
    R
end

.dbk_index ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 81

def self.dbk_index
  Polyglot.eval("R", <<-R)
    function(obj, ...) {
      obj[[...]]
    }
  R
end

.enquo ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 122

def self.enquo
  Polyglot.eval("R", <<-R)
    function(x, ...) {
      enquo(x)          
    } 
  R
end

.eval(string) ⇒ Object

@TODO: Fix the ‘rescue’ clause and open issue with fastR Evaluates an R code

Parameters:

  • string (String) —

    A string of R code that can be correctly parsed by R



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# File 'lib/R_interface/rsupport.rb', line 86

def self.eval(string)
  begin
    Polyglot.eval("R", string)
  rescue RuntimeError
    raise NoMethodError.new("Method #{string} not found in R environment")
  end
end

.exec_function(function, *args) ⇒ Object

Parameters:

  • function (R function (Interop)) —

    R function to execute



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# File 'lib/R_interface/rsupport.rb', line 215

def self.exec_function(function, *args)

  begin
    
    # If the execution counter is 0, function was not recursively called
    # Starts capturing output
    if (@@exec_counter == 0)
      R::Support.eval("unlockBinding('r_capture', globalenv())")
      @@con = R::Support.start_capture.call("r_capture")
    end
    
    @@exec_counter = @@exec_counter + 1
    
    # function has no arguments, call it directly
    if (args.length == 0)
      res = R::Object.build(function.call)
    else
      pl = R::Support.parse2list(*args)
      res = @@exec_from_ruby.call(R::Object.method(:build), function, pl)
      # R::Object.build(R::Support.eval("do.call").call(function, pl))
    end

    @@exec_counter = @@exec_counter - 1
    
    # When execution counter back to 0, print the captured output if the length
    # of the output is greater than 0
    if (@@exec_counter == 0)
      R::Support.stop_capture.call(@@con)
      if (R::Support.eval("length(r_capture) > 0")[0])
        cap = R::Object.build(R::Support.eval("r_capture"))
        (0...cap.size).each do |i|
          puts cap >> i
        end
      end
    end

  rescue StandardError => e
    R::Support.stop_capture.call(@@con) if (@@exec_counter == 0)
    raise e
  end

  res
  
end

.exec_function_i(function, *args) ⇒ Object

Executes the given R function with the given arguments.



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# File 'lib/R_interface/rsupport.rb', line 276

def self.exec_function_i(function, *args)
  pl = R::Support.parse2list(*args)
  R::Support.eval("invoke").call(function, pl)
end

.exec_function_name(function_name, *args) ⇒ Object

Parameters:

  • function_name (String) —

    Name of the R function to execute



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# File 'lib/R_interface/rsupport.rb', line 265

def self.exec_function_name(function_name, *args)
  # @TODO: should check all that can go wrong when calling eval(function_name) to
  # raise the proper exception      
  f = R::Support.eval(function_name)
  R::Support.exec_function(f, *args)
end

.interop(object) ⇒ Object

Parameters:

  • object (Object) —

    Any Ruby object

Returns:

  • boolean if the object is an interop or not



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# File 'lib/R_interface/rsupport.rb', line 99

def self.interop(object)
  Truffle::Interop.foreign?(object)
end

.md_index ⇒ Object

multi-dimensional indexing



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# File 'lib/R_interface/r_methods.rb', line 93

def self.md_index
  Polyglot.eval("R", <<-R)
    function(mdobject, ...) { 
      mdobject[...];
    }
  R
end

.new_scope(symbol, *args, &block) ⇒ Object 



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# File 'lib/R_interface/rsupport_scope.rb', line 68

def self.new_scope(symbol, *args, &block)
  executionScope = Scope.with(symbol, *args)
  scope = executionScope.new
  scope.instance_eval(&block)
  # scope
end

.parse2list(*args) ⇒ Object

Parses the Ruby arguments into a R list of R objects

Parameters:

  • args (Ruby Parameter list) 


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# File 'lib/R_interface/rsupport.rb', line 171

def self.parse2list(*args)
  
  params = Polyglot.eval("R", "list()")
  
  args.each_with_index do |arg, i|
    if (arg.is_a? Hash)
      params = parse_hash(arg, params)
    elsif (arg.is_a? NotAvailable)
      params = R::Support.eval("c").call(params, arg.r_interop)
    elsif (arg.is_a? NilClass)
      params = R::Support.eval("`length<-`").call(params, i+1)
    else
      params = R::Support.eval("`[[<-`").
                 call(params, i+1, R::Support.parse_arg(arg))
    end
  end
  
  # if the parameter is an empty list, then add the element NULL to the list
  (Polyglot.eval("R", "length").call(params) == 0) ?
    Polyglot.eval("R", "list").call(nil) : params
  
end

.parse_arg(arg) ⇒ Object

whatever needs it

Parameters:

  • arg (Object) —

    A Ruby object to be converted to R to be used by an R function, or

Returns:

  • Object that can be used in R



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# File 'lib/R_interface/rsupport.rb', line 109

def self.parse_arg(arg)

  case(arg)
  when -> (arg) { interop(arg) }
    arg
  when R::Object
    arg.r_interop
  when Numeric
    R::Support.eval('c').call(arg)
  when NegRange
    final_value = (arg.exclude_end?)? (arg.last - 1) : arg.last
    R::Support.eval('seq').call(arg.first, final_value)
  when Range
    final_value = (arg.exclude_end?)? (arg.last - 1) : arg.last
    R::Support.eval('seq').call(arg.first, final_value)
  when :all
    R.empty_symbol
  when Symbol
    arg = R::Support.eval('as.name').call(arg.to_s.gsub(/__/,"."))
  when Proc, Method
    R::RubyCallback.build(arg)
  # This is a Ruby argument that will be automatically converted
  # by the low level Polyglot interface to R
  else 
    arg
  end

end

.parse_hash(hsh, lst) ⇒ Object

Given a hash, convert it to an R argument list



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# File 'lib/R_interface/rsupport.rb', line 142

def self.parse_hash(hsh, lst)

  hsh.each_pair do |key, value|
    k = key.to_s.gsub(/__/,".")
    
    case 
    when (value.is_a? NotAvailable)
      na_named = R::Support.eval("`names<-`").call(value.r_interop, k)
      lst = R::Support.eval("c").call(lst, na_named)
    when (k == 'all')
      lst = R::Support.eval("`[[<-`").
              call(lst, R::Support.eval('`+`').
                          call(R::Support.eval('length').call(lst), 1),
                   R::Support.parse_arg(value))
    else
      lst = R::Support.eval("`[[<-`").
              call(lst, k, R::Support.parse_arg(value))
    end
  end
  
  lst
  
end

.print_foreign(interop) ⇒ Object Also known as: pf

Prints a foreign R interop pointer. Used for debug.



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# File 'lib/R_interface/rsupport.rb', line 352

def self.print_foreign(interop)
  puts "===External value==="
  R::Support.eval("print").call(interop)
  puts "===end external value==="
end

.print_str(obj) ⇒ Object 



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# File 'lib/R_interface/rsupport.rb', line 337

def self.print_str(obj)
  
  lst = obj.as__list
  puts lst
=begin      
  (1..lst.length >> 0).each do |i|
    puts lst[[i]]
  end
=end      
end

.process_missing(symbol, internal, *args) ⇒ Object

Process the missing method it should not wrap the return value inside an R::Object it is not applied to an object

Parameters:

  • symbol (Symbol)
  • internal (Boolean) —

    true if the method will return to an internal method, i.e.,

  • object (Ruby Object) —

    the ruby object to which the method is applied, false if



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# File 'lib/R_interface/rsupport.rb', line 314

def self.process_missing(symbol, internal, *args)

  name = R::Support.convert_symbol2r(symbol)
  
  case name
  # when missing method has an '=' sign in it...
  when ->(x) { x =~ /(.*)=$/ }
    R::Support.set_symbol($1, *args)
  # when missing method is 'eval'... needs special treatment
  when "eval"
    R::Support.r_evaluate(*args)
  else
    function = R::Support.eval(name)
    internal ? R::Support.exec_function_i(function, *args) :
      R::Support.exec_function(function, *args)
  end

end

.r_evaluate(*args) ⇒ Object

Calls the R ‘eval’ function. This requires some special semantics R function ‘eval’ needs to be called in a special way, since it expects the second argument to be an environment. If the arguments are packed into a list, then there is no second argument and the function fails to use the second argument as environment



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# File 'lib/R_interface/rsupport.rb', line 300

def self.r_evaluate(*args)
  r_args = args.map { |arg| R::Support.parse_arg(arg) }
  R::Object.build(R::Support.eval("eval").call(*r_args))
end

.range ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 134

def self.range
  Polyglot.eval("R", <<-R)
    function(x, y, neg = FALSE) {
      e1 = enexpr(x)
      e2 = enexpr(y)
      if (neg) {
        expr(-(!!e1:!!e2))
      } else {
        expr(!!e1:!!e2)
      }
    }
  R
end

.ruby_callback_method ⇒ Object

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.



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# File 'lib/R_interface/r_methods.rb', line 108

def self.ruby_callback_method
  Polyglot.eval("R", <<-R)
    function(rb_method) {
      function(...) {
      rb_method(...)
      }
    }
  R
end

.set_symbol(name, *args) ⇒ Object

sets the R symbol <name> to the given value

Parameters:

  • name (String) —

    String representation of the R symbol that needs to be assigned

  • args (Array) —

    Array with one object to be set to the symbol



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# File 'lib/R_interface/rsupport.rb', line 287

def self.set_symbol(name, *args)
  args << R::Support.eval("globalenv").call()
  R::Support.exec_function_name("assign", name, *args)
end

.start_capture ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 59

def self.start_capture
  Polyglot.eval("R", <<-R)
    function(cap_variable) {
      sink(con <- textConnection(cap_variable,"w"), split=FALSE, type = c("output"));
      con
    }
  R
end

.stop_capture ⇒ Object 



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# File 'lib/R_interface/r_methods.rb', line 68

def self.stop_capture
  Polyglot.eval("R", <<-R)
    function(con) {
      sink();
      close(con);
    }
  R
end