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

Copyright (C) 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 (C) 2002 the Initial Developer. All Rights Reserved.

Contributor(s): Gregory R. Warnes <greg@warnes.net> (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

VERSION =
'0.5.1'
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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initializeRSRuby

Create a new RSRuby interpreter instance. The Singleton design pattern ensures that only one instance can be running in a script. Further calls to RSRuby.instance will return the original instance.



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

def initialize()

  #Initialize R
  r_init

  @default_mode = NO_DEFAULT

  @class_table = {}
  @proc_table  = {}
  
  @caching = true
  reset_cache
  
  #Catch errors
  self.__init_eval_R__("options(error=expression(NULL))")
  #disable errors
  self.__init_eval_R__("options(show.error.messages=F)")

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 131

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

Instance Attribute Details

#cachingObject

Returns the value of attribute caching



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

def caching
  @caching
end

#class_tableObject

Returns the value of attribute class_table



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

def class_table
  @class_table
end

#default_modeObject

Returns the value of attribute default_mode



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

def default_mode
  @default_mode
end

#proc_tableObject

Returns the value of attribute proc_table



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

def proc_table
  @proc_table
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 199

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 180

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_modeObject

Returns the current default conversion mode as an Integer. DEPRECATED: Use the accessor on the RSRuby instance isntead



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

def RSRuby.get_default_mode
  RSRuby.instance.default_mode
end

.get_rsruby_inputObject

TODO - not implemented



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

def RSRuby.get_rsruby_input
  @@rsruby_input
end

.get_rsruby_outputObject

TODO - not implemented



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

def RSRuby.get_rsruby_output
  @@rsruby_output
end

.get_rsruby_showfilesObject

TODO - not implemented



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

def RSRuby.get_rsruby_showfiles
  @@rsruby_showfiles
end

.img(filename, args = {}) {|r| ... } ⇒ Object

Yields:

  • (r)

Raises:

  • (ArgumentError)


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# File 'lib/rsruby.rb', line 119

def self.img(filename,args={})
  format = File.extname(filename).gsub(".","").to_sym
  r = RSRuby.instance
  raise ArgumentError, "Format #{format.to_s} is not supported" unless [:pdf].include? format
  r.pdf(filename,args)
  yield(r)
  r.dev_off.call
end

.set_default_mode(m) ⇒ Object

Sets the default conversion mode for RSRuby. The constants defined in #RSRuby should be used DEPRECATED: Use the accessor instead



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# File 'lib/rsruby.rb', line 220

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

.set_rsruby_input(m) ⇒ Object

TODO - not implemented



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

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 243

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 253

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 158

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, init = false) ⇒ Object



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# File 'lib/rsruby.rb', line 280

def __getitem__(name,init=false)

  #Find the identifier and cache (unless already cached)
  unless @cache.has_key?(name) && @caching
    if init
      robj = @cache['get'].__init_lcall__([['',name]])
    else
      robj = @cache['get'].lcall([['',name]])
    end
    @cache[name] = robj if @caching
  end

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

  return robj

end

#__init_eval_R__(s) ⇒ Object



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# File 'lib/rsruby.rb', line 275

def __init_eval_R__(s)
  parsed = self.parse.__init_lcall__([['text',s]])
  self.eval.__init_lcall__([['',parsed]])
end

#crashObject

This method is for testing catching of segfaults



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# File 'ext/rsruby.c', line 154

VALUE crash(){
  int* ptr = (int*)0;
  *ptr = 1;
  return Qtrue; 
}

#delete_from_cache(x) ⇒ Object

Delete an R object from the cache. Use R-style function naming, not ruby style.



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# File 'lib/rsruby.rb', line 115

def delete_from_cache(x)
  @cache.delete(x)
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 263

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 69

VALUE get_fun(VALUE self, VALUE name){

  VALUE str;
  int conversion=TOP_MODE;
  SEXP robj;
  VALUE  rubyobj;
  char* cstr_name;

  str = StringValue(name);

  cstr_name = RSTRING_PTR(str);

  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 269

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

#r_initObject

Starts the R interpreter.



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# File 'ext/rsruby.c', line 129

VALUE rr_init(VALUE self){

  SEXP R_References;

  init_R(0,NULL);
  // Initialize the list of protected objects
  R_References = R_NilValue;
  SET_SYMVALUE(install("R.References"), R_References);

  return self;

}

#reset_cacheObject



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# File 'lib/rsruby.rb', line 94

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

  #Get constants
  @cache['TRUE']  = self.__getitem__('T',true)
  @cache['FALSE'] = self.__getitem__('F',true)

  @cache['parse'] = self.__getitem__('parse',true)
  @cache['eval']  = self.__getitem__('eval',true)

  @cache['NA']    = self.__init_eval_R__('NA')
  @cache['NaN']   = self.__init_eval_R__('NaN')
  # @cache['NAN']   = self.eval_R('as.double(NA)')
  
  #help!
  @cache['helpfun'] = self.with_mode(NO_CONVERSION, self.__getitem__('help',true))
end

#shutdownObject

Shutdown the R interpreter



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# File 'ext/rsruby.c', line 118

VALUE rs_shutdown(VALUE self){

  r_finalize();
  Rf_endEmbeddedR(0);
  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 173

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