Class: FeldtRuby::RCommunicator

Inherits:
Object
  • Object
show all
Includes:
Statistics::DesignOfExperiments, Statistics::Plotting
Defined in:
lib/feldtruby/statistics.rb,
lib/feldtruby/statistics.rb,
lib/feldtruby/statistics/design_of_experiments.rb

Overview

RCommunicator uses RinRuby to communicate with an instance of R. We extend the basic RinRuby by using json to tunnel back and forth.

Defined Under Namespace

Classes: Rvalue

Constant Summary

Constants included from Statistics::Plotting

Statistics::Plotting::GfxFormatToGfxParams

Instance Method Summary collapse

Methods included from Statistics::DesignOfExperiments

#latin_hypercube_sample_of_parameters, #parameters_to_R_data_frame

Methods included from Statistics::Plotting

#density_tile2d, #filled_contour, #gfx_device, #ggplot2_setup_and_theme, #hash_to_R_params, #hexbin_heatmap, #load_csv_files_as_data, #overlaid_densities, #overlaid_densities_from_csv_files, #plot_2dims, #save_graph, #scatter_plot, #smooth_scatter_plot

Constructor Details

#initialize ⇒ RCommunicator

Returns a new instance of RCommunicator.



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# File 'lib/feldtruby/statistics.rb', line 12

def initialize
  # Will stay open until closed or the ruby interpreter exits.
  # echo = false and interactive = false
  @r = RinRuby.new(false, false)

  @installed_libraries = []

  setup_r()

end

Instance Method Details

#call(rmethod, *arguments) ⇒ Object

Call an R method named rmethod with (Ruby) arguments. Returns an Integer, Float or an Rvalue (if the returned R value is complex).



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# File 'lib/feldtruby/statistics.rb', line 86

def call(rmethod, *arguments)
  str, args = "", []
  arguments.each_with_index do |arg, index| 
    args << (argname = arg_name(index))
    str += "#{argname} <- fromJSON(\"#{arg.to_json}\");\n"
  end
  resname = res_name(1)
  str += "#{resname} <- toJSON(#{rmethod.to_s}(#{args.join(', ')}));\n"
  @r.eval str
  pull_json_variable(resname)
end

#eval(str) ⇒ Object 



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# File 'lib/feldtruby/statistics.rb', line 48

def eval(str)
  @r.eval str
end

#include_library(lib) ⇒ Object

Include a library after ensuring it has been installed



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# File 'lib/feldtruby/statistics.rb', line 29

def include_library(lib)

  return if @installed_libraries.include?(lib)

  @installed_libraries << lib

  @r.eval "if(!library(#{lib}, logical.return=TRUE)) {install.packages(\"#{lib}\"); library(#{lib});}"

end

#load_feldtruby_r_script(scriptName, reload = false) ⇒ Object

Load R scripts in the feldtruby/R directory.



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# File 'lib/feldtruby/statistics.rb', line 40

def load_feldtruby_r_script(scriptName, reload = false)
  @loaded_scripts ||= Array.new # Ensure there is an empty array for loaded script names, if this is first call here.
  return if reload == false && @loaded_scripts.include?(scriptName)
  @loaded_scripts << scriptName
  path = File.join(FeldtRuby::TopDirectory, "R", scriptName)
  @r.eval "source(\"#{path}\")"
end

#pull_json_variable(variableName) ⇒ Object

Get the JSON value from a variable in R and parse it back to a Ruby value.



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# File 'lib/feldtruby/statistics.rb', line 99

def pull_json_variable(variableName)
  res = @r.pull(variableName)
  begin
    Rvalue.new JSON.parse(res)
  rescue JSON::ParserError
    # First try to convert to Integer, then Float if it fails.
    begin
      Kernel::Integer(res)
    rescue ArgumentError
      Kernel::Float(res)
    end
  end
end

#pull_matrix_variable_to_hash_with_column_names(variableName, columnNames) ⇒ Object

Pull a matrix variable into a hash and name the columns according to values in columnNames.



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# File 'lib/feldtruby/statistics.rb', line 115

def pull_matrix_variable_to_hash_with_column_names(variableName, columnNames)
  var = arg_name(rand(1e5), variableName)
  RC.eval "#{var} <- toJSON(data.frame(#{variableName}));"
  hash = pull_json_variable(var).to_h

  # Now convert back to the proper parameter names and delete the ones generated by lhs.
  index = 0
  columnNames.each do |p|
    name_of_column = "X#{index += 1}"
    hash[p] = hash[name_of_column]
    hash.delete(name_of_column)
  end
  hash
end

#ruby_object_to_R_string(o) ⇒ Object

Convert a Ruby object of one of the types String, Symbol, Array, Integer or Float to a String that can be used in R code/scripts to represent the object.



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# File 'lib/feldtruby/statistics.rb', line 133

def ruby_object_to_R_string(o)

    case o

    when String
      return o.inspect

    when Symbol
      return o.to_s

    when Array
      elems = o.map {|e| ruby_object_to_R_string(e)}.join(", ")
      return "c(#{elems})"

    when Integer
      return o.to_s

    when Float
      return o.to_s

    else
      raise "Cannot represent object #{o} in valid R code"

    end

end

#setup_r ⇒ Object

Include necessary libraries.



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# File 'lib/feldtruby/statistics.rb', line 24

def setup_r
  include_library("rjson")
end

#subst_eval(script, scriptNameToRubyValues) ⇒ Object

Given a script that has variable references in the form “name” insert the ruby objects mapped from these names in scriptNameToRubyValues



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# File 'lib/feldtruby/statistics.rb', line 54

def subst_eval(script, scriptNameToRubyValues)

  scriptNameToRubyValues.each do |key, value|

    script = script.gsub("_#{key.to_s}_", ruby_object_to_R_string(value))

  end

  #puts "Eval'ing script:\n#{script}"
  eval script

end