Class: RSRuby

Inherits:
Object
  • Object
show all
Includes:
Singleton
Defined in:
lib/rsruby.rb,
ext/rsruby.c

Overview

Synopsis

This class represents the embedded R interpreter. The Singleton module is mixed in to ensure that only one R interpreter is running in a script at any one time and that the interpreter can always be easily accessed without using a global variable.

The R interpreter is started by calling RSRuby.instance. The returned object represents the R interpreter and R functions are called by calling methods on this object:

r = RSRuby.instance
r.sum(1,2,3)
puts r.t_test(1,2,3)['p-value']

See the manual for more details on calling functions and the conversion system for passing data between Ruby and R. If no suitable conversion from R to Ruby is found, an RObj is returned (all R functions are returned as instances of RObj). –

Copyright © 2006 Alex Gutteridge

The Original Code is the RPy python module.

The Initial Developer of the Original Code is Walter Moreira. Portions created by the Initial Developer are Copyright © 2002 the Initial Developer. All Rights Reserved.

Contributor(s): Gregory R. Warnes <[email protected]> (RPy Maintainer)

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA ++

Constant Summary collapse

VERSION = 
'0.4.3'
TOP_CONVERSION =

Constants for conversion modes

4
PROC_CONVERSION = 
4
CLASS_CONVERSION = 
3
BASIC_CONVERSION = 
2
VECTOR_CONVERSION = 
1
NO_CONVERSION = 
0
NO_DEFAULT = 
-1

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Object

Starts the R interpreter.



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# File 'lib/rsruby.rb', line 74

def initialize()

  #Initialize in C
  c_initialize

  @@default_mode = NO_DEFAULT

  @@class_table = {}
  @@proc_table  = {}

  #Setup R object cache
  @@cache = {}
  @@cache['get'] = self.get_fun('get')

  #Get constants
  @@cache['TRUE']  = self.__getitem__('T')
  @@cache['FALSE'] = self.__getitem__('F')
  @@cache['NA']    = self.eval_R('NA')
  # @@cache['NAN']   = self.eval_R('as.double(NA)')
  @@cache['NaN']   = self.eval_R('NaN')
  
  #help!
  @@cache['helpfun'] = self.with_mode(NO_CONVERSION, self.__getitem__('help'))

  #Catch errors
  self.eval_R("options(error=expression(NULL))")
  #disable errors
  self.options('show.error.messages' => false)

end

Dynamic Method Handling

This class handles dynamic methods through the method_missing method

#method_missing(r_id, *args) ⇒ Object

Handles method name conversion and calling of R functions If called without args the R function/varialbe is returned rather than called.



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# File 'lib/rsruby.rb', line 108

def method_missing(r_id,*args)

  #Translate Ruby method call to R
  robj_name = RSRuby.convert_method_name(r_id.to_s)

  #Retrieve it
  robj = self.__getitem__(robj_name)

  #TODO perhaps this is not neccessary - always call these methods
  #use the [] syntax for variables etc...
  if args.length > 0

    #convert arguments to lcall format
    lcall_args = RSRuby.convert_args_to_lcall(args)
    
    #Return result of calling object with lcall 
    #formatted args
    return robj.lcall(lcall_args)

  end

  return robj

end

Class Method Details

.convert_args_to_lcall(args) ⇒ Object

Converts an Array of function arguments into lcall format. If the last element of the array is a Hash then the contents of the Hash are interpreted as named arguments.

The returned value is an Array of tuples (Arrays of length two). Each tupple corresponds to a name/argument pair.

For example:

convert_args_to_lcall([1,2,3,{:a=>4,:b=>5}) 
=> [['',1],['',2],['',3],['a',4],['b',5]]



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# File 'lib/rsruby.rb', line 176

def RSRuby.convert_args_to_lcall(args)

  lcall_args = []
  
  args.each_with_index do |arg,i|
    unless arg.kind_of?(Hash) and i == args.length-1
      lcall_args.push(['',arg])
    else
      arg.each do |k,v|
        lcall_args.push([k.to_s,v])
      end
    end
  end

  return lcall_args

end

.convert_method_name(name) ⇒ Object

Converts a String representing a ‘Ruby-style’ R function name into a String with the real R name according to the rules given in the manual.



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# File 'lib/rsruby.rb', line 157

def RSRuby.convert_method_name(name)
  if name.length > 1 and name[-1].chr == '_' and name[-2].chr != '_'
    name = name[0..-2]
  end
  name.gsub!(/__/,'<-')
  name.gsub!(/_/, '.')
  return name
end

.get_default_mode ⇒ Object

Returns the current default conversion mode as an Integer.



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# File 'lib/rsruby.rb', line 203

def RSRuby.get_default_mode
  @@default_mode
end

.get_rsruby_input ⇒ Object

TODO - not implemented



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# File 'lib/rsruby.rb', line 213

def RSRuby.get_rsruby_input
  @@rsruby_input
end

.get_rsruby_output ⇒ Object

TODO - not implemented



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# File 'lib/rsruby.rb', line 223

def RSRuby.get_rsruby_output
  @@rsruby_output
end

.get_rsruby_showfiles ⇒ Object

TODO - not implemented



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# File 'lib/rsruby.rb', line 233

def RSRuby.get_rsruby_showfiles
  @@rsruby_showfiles
end

.set_default_mode(m) ⇒ Object

Sets the default conversion mode for RSRuby. The constants defined in #RSRuby should be used



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# File 'lib/rsruby.rb', line 196

def RSRuby.set_default_mode(m)
  if m < -1 or m > TOP_CONVERSION
    raise ArgumentError, "Invalid mode requested"
  end
  @@default_mode = m
end

.set_rsruby_input(m) ⇒ Object

TODO - not implemented



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# File 'lib/rsruby.rb', line 208

def RSRuby.set_rsruby_input(m)
  @@rsruby_input = m
end

.set_rsruby_output(m) ⇒ Object

TODO - not implemented



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# File 'lib/rsruby.rb', line 218

def RSRuby.set_rsruby_output(m)
  @@rsruby_output = m
end

.set_rsruby_showfiles(m) ⇒ Object

TODO - not implemented



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# File 'lib/rsruby.rb', line 228

def RSRuby.set_rsruby_showfiles(m)
  @@rsruby_showfiles = m
end

Instance Method Details

#[](r_id) ⇒ Object

The same as method_missing, but only returns the R function/object, does not call it.



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# File 'lib/rsruby.rb', line 135

def [](r_id)

  #Translate Ruby method call to R
  robj_name = RSRuby.convert_method_name(r_id.to_s)
  
  #Retrieve it
  robj = self.__getitem__(robj_name)
  
  #And return it
  return robj

end

#__getitem__(name) ⇒ Object 



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# File 'lib/rsruby.rb', line 268

def __getitem__(name)

  #Find the identifier and cache (unless already cached)
  unless @@cache.has_key?(name)
    @@cache[name] = @@cache['get'].lcall([['',name]])
  end

  #Retrieve object from cache
  robj = @@cache[name]

  return robj

end

#c_initialize ⇒ Object 



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# File 'lib/rsruby.rb', line 69

alias c_initialize initialize

#class_table ⇒ Object

Returns the current class table Hash for RSRuby.



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# File 'lib/rsruby.rb', line 238

def class_table
  @@class_table
end

#class_table=(h) ⇒ Object

Sets the RSRuby class table Hash.



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# File 'lib/rsruby.rb', line 243

def class_table=(h)
  @@class_table = h
end

#eval_R(s) ⇒ Object

Evaluates the given string in R. Returns the result of the evaluation.



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# File 'lib/rsruby.rb', line 258

def eval_R(s)
  self.eval(self.parse(:text => s))
end

#get_fun(name) ⇒ Object

Obtain an R object via its name. This is only used to get the ‘get’ function. All subsequent calls go via the ‘get’ function itself



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# File 'ext/rsruby.c', line 70

VALUE get_fun(VALUE self, VALUE name){

  VALUE str;
  int conversion=TOP_MODE;
  SEXP robj;
  VALUE  rubyobj;
  //VALUE  params[2];
  char* cstr_name;

  str = StringValue(name);

  cstr_name = RSTRING(str)->ptr;

  robj = (SEXP)get_fun_from_name(cstr_name);
  if (!robj)
    return Qnil;

  /* Wrap the returned R object as a ruby Object */
  rubyobj = Data_Wrap_Struct(rb_const_get(rb_cObject, 
					  rb_intern("RObj")), 0, 0, robj);
  rb_iv_set(rubyobj,"@conversion",INT2FIX(conversion));
  rb_iv_set(rubyobj,"@wrap",Qfalse);

  return rubyobj;

}

#help(*args) ⇒ Object

Wraps the R help function.



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# File 'lib/rsruby.rb', line 263

def help(*args)
  helpobj = @@cache['helpfun'].call(args)
  self.print(helpobj)
end

#proc_table ⇒ Object

Returns the current proc table Hash for RSRuby.



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# File 'lib/rsruby.rb', line 248

def proc_table
  @@proc_table
end

#proc_table=(h) ⇒ Object

Sets the RSRuby proc table Hash.



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# File 'lib/rsruby.rb', line 253

def proc_table=(h)
  @@proc_table = h
end

#shutdown ⇒ Object

Shutdown the R interpreter



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# File 'ext/rsruby.c', line 119

VALUE cShutdown(VALUE self){

  r_finalize();
  return Qtrue;

}

#with_mode(mode, func) ⇒ Object

Takes an #RObj representing an R function and sets the ‘wrapping’ mode for that function. Implemented for compatibility with RPy.



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# File 'lib/rsruby.rb', line 150

def with_mode(mode,func)
  func.wrap = mode
  return func
end