rinruby 0.99.3 → 1.0.0

data/lib/rinruby.rb

@@ -55,37 +55,38 @@
 #++
 #
 #
-#The required files java and readline are used when present at functionality.
+#The files "java" and "readline" are used when available to add functionality.
 
 class RinRuby
 
-  VERSION = '0.99.3'
+  VERSION = '1.0.0'
 
   require 'socket'
 
   attr_reader :interactive
   attr_reader :readline
 
-#RinRuby is invoked within a Ruby script (or the interactive 'irb' prompt denoted >>) using:
+#RinRuby is invoked within a Ruby script (or the interactive "irb" prompt denoted >>) using:
 #
 #      >> require "rinruby"
 #
-#This reads the definition of the RinRuby class into the current Ruby interpreter and creates an instance of the RinRuby class named R. There is a second method for starting an instance of R which allows the user to use any name for the instance, in this case myr:
+#The previous statement reads the definition of the RinRuby class into the current Ruby interpreter and creates an instance of the RinRuby class named R. There is a second method for starting an instance of R which allows the user to use any name for the instance, in this case myr:
 #
 #      >> require "rinruby"
 #      >> myr = RinRuby.new
 #      >> myr.eval "rnorm(1)"
+#
 #Any number of independent instances of R can be created in this way.
 #
-#<b>Parameters that can be passed to the new method</b>
+#<b>Parameters that can be passed to the new method:</b>
 #
 #* echo: By setting the echo to false, output from R is suppressed, although warnings are still printed. This option can be changed later by using the echo method. The default is true.
-#* interactive: When interactive is false, R is run in non-interaction mode, resulting in plots without an explicit device being written to Rplots.pdf. Otherwise, when interactive is true, such plots are shown on the screen. The default is true.
-#* executable: The path of the R executable (which is R in Linux and Mac OSX, or Rterm.exe in Windows) can be set with the executable argument. The default is nil, which on Windows uses the registry keys to find the path, or on linux and Mac OS X uses the path defined by $PATH.
+#* interactive: When interactive is false, R is run in non-interactive mode, resulting in plots without an explicit device being written to Rplots.pdf. Otherwise (i.e., interactive is true), plots are shown on the screen. The default is true.
+#* executable: The path of the R executable (which is "R" in Linux and Mac OSX, or "Rterm.exe" in Windows) can be set with the executable argument. The default is nil which makes RinRuby use the registry keys to find the path (on Windows) or use the path defined by $PATH (on Linux and Mac OS X).
 #* port_number: This is the smallest port number on the local host that could be used to pass data between Ruby and R. The actual port number used depends on port_width.
-#* port_width: RinRuby will randomly select a uniform number between port_number and port_number + port_width - 1, (inclusive), to pass data between Ruby and R. If the randomly selected port is not available, RinRuby will continue selecting random ports until it finds one that is available. By setting port_width to 1, RinRuby will wait until port_number is available. The default port_width is 1000.
+#* port_width: RinRuby will randomly select a uniform number between port_number and port_number + port_width - 1 (inclusive) to pass data between Ruby and R. If the randomly selected port is not available, RinRuby will continue selecting random ports until it finds one that is available. By setting port_width to 1, RinRuby will wait until port_number is available. The default port_width is 1000.
 #
-#It may be desirable to change the parameters to the instance of R, but still call it by the name of R. In that case the old instance of R which was created with the require rinruby statement should be closed first using the quit method which is explained below. Unless the previous instance is killed, it will continue to use system resources until exiting Ruby. The following shows an example by changing the parameter echo:
+#It may be desirable to change the parameters to the instance of R, but still call it by the name of R. In that case the old instance of R which was created with the 'require "rinruby"' statement should be closed first using the quit method which is explained below. Unless the previous instance is killed, it will continue to use system resources until exiting Ruby. The following shows an example by changing the parameter echo:
 #
 #      >> require "rinruby"
 #      >> R.quit
@@ -149,7 +150,7 @@ class RinRuby
     @socket = @server_socket.accept
   end
 
-#The method quit will gracefully close the bridge between Ruby and R, freeing up system resources. This method is automatically run when a Ruby script ends.
+#The quit method will properly close the bridge between Ruby and R, freeing up system resources. This method does not need to be run when a Ruby script ends.
 
   def quit
     @writer.puts "q(save='no')"
@@ -175,6 +176,7 @@ class RinRuby
 #      -1.88900 -0.84930 -0.45220 -0.49290 -0.06069          0.78160
 #      [1] 0.7327981
 #This example used a string substitution to make the argument to first eval method equivalent to x <- rnorm(10). This example used three invocations of the eval method, but a single invoke is possible using a here document:
+#
 #      >> R.eval <<EOF
 #              x <- rnorm(#{sample_size})
 #              summary(x)
@@ -183,7 +185,7 @@ class RinRuby
 #
 #<b>Parameters that can be passed to the eval method</b>
 #
-#* string: The string parameter is the code which is to be passed to R, for example, string = "hist(gamma(1000,5,3))". The string can also span a large chunk of code by use of a here document, as shown:
+#* string: The string parameter is the code which is to be passed to R, for example, string = "hist(gamma(1000,5,3))". The string can also span several lines of code by use of a here document, as shown:
 #      R.eval <<EOF
 #         x<-rgamma(1000,5,3)
 #         hist(x)
@@ -230,7 +232,7 @@ class RinRuby
     true
   end
 
-#When using sending code to Ruby using an interactive prompt, this method will change the prompt to an R prompt. From the R prompt commands can be sent to R exactly as if the R program was actually running. When the user is ready to return to Ruby, then the command exit() will return the prompt to Ruby. This is the ideal situation for the explorative programmer who needs to run several lines of code in R, and see the results after each command. This is also an easy way to execute loops without the use of a here document. It should be noted that the prompt command does not work in a script, just Ruby's interaction irb.
+#When sending code to Ruby using an interactive prompt, this method will change the prompt to an R prompt. From the R prompt commands can be sent to R exactly as if the R program was actually running. When the user is ready to return to Ruby, then the command exit() will return the prompt to Ruby. This is the ideal situation for the explorative programmer who needs to run several lines of code in R, and see the results after each command. This is also an easy way to execute loops without the use of a here document. It should be noted that the prompt command does not work in a script, just Ruby's interactive irb.
 #
 #<b>Parameters that can be passed to the prompt method:</b>
 #
@@ -274,23 +276,22 @@ class RinRuby
     true
   end
 
-#If a method is called which is not defined, then it is assumed that the user is attempting to either pull or assign a variable to R.  This allows the user to do a simplified notation.  When an undefined method is followed by an equals sign, then it is assumed to be an assignment.  Thus
+#If a method is called which is not defined, then it is assumed that the user is attempting to either pull or assign a variable to R.  This allows for the short-hand equivalents to the pull and assign methods.  For example:
 #
 #      >> R.x = 2
 #
-#is the same as
+#is the same as:
 #
 #      >> R.assign("x",2)
 #
-#If an equals sign does not follow the method, then it is assumed to be a pull.  Thus
+#Also:
 #
 #      >> n = R.x
 #
-#is the same as
+#is the same as:
 #
 #      >> n = R.pull("x")
 #
-#This is also the reason is it not recommended that any variables be named after a method already defined, since this simplified notation would not work for that variable.
 #The parameters passed to method_missing are those used for the pull or assign depending on the context.
 
   def method_missing(symbol, *args)
@@ -334,7 +335,7 @@ class RinRuby
 #
 #      >> R.test = 144
 #
-#is the same as
+#is the same as:
 #
 #      >> R.assign("test",144)
 #
@@ -427,7 +428,7 @@ class RinRuby
 #      >> summary_of_x = R.pull "as.numeric(summary(x))"
 #      >> puts summary_of_x
 #
-#produces the following :
+#produces the following:
 #
 #      -1.889
 #      -0.8493
@@ -444,11 +445,11 @@ class RinRuby
 #
 #* singletons: R represents a single number as a vector of length one, but in Ruby it is often more convenient to use a number rather than an array of length one. Setting singleton=false will cause the pull method to shed the array, while singletons=true will return the number of string within an array.  The default is false.
 #
-#The pull method is an alternative to the simplified form where the parameters are automatically used, in other words:
+#The pull method is an alternative to the simplified form where the parameters are automatically used.  For example:
 #
 #      >> puts R.test
 #
-#is the same as
+#is the same as:
 #
 #      >> puts R.pull("test")
 
@@ -515,7 +516,7 @@ class RinRuby
     result
   end
 
-#The eval method displays the output from R by default, but this can be turned off by using the echo method. This method is useful when the output behavior needs to be changed
+#The echo method controls whether the eval method displays output from R.
 #
 #<b>Parameters that can be passed to the eval method</b>
 #

metadata

@@ -1,47 +1,47 @@
---- !ruby/object:Gem::Specification
-required_ruby_version: !ruby/object:Gem::Requirement
-  requirements: 
-  - - '>='
-    - !ruby/object:Gem::Version
-      version: !str 0
-  version: 
-email: rinruby@ddahl.org
-cert_chain: []
+--- !ruby/object:Gem::Specification 
+rubygems_version: 0.9.2
+specification_version: 1
+name: rinruby
+version: !ruby/object:Gem::Version 
+  version: 1.0.0
+date: 2008-07-03 00:00:00 -05:00
 summary: Accessing the R interpreter from pure Ruby
-post_install_message: 
-extra_rdoc_files: []
+require_paths: 
+- lib
+email: rinruby@ddahl.org
 homepage: http://rinruby.ddahl.org
-signing_key: 
-name: rinruby
-rdoc_options: []
-autorequire: 
 rubyforge_project: rinruby
-executables: []
 description: 
-specification_version: 2
+autorequire: 
 default_executable: 
+bindir: bin
+has_rdoc: true
+required_ruby_version: !ruby/object:Gem::Version::Requirement 
+  requirements: 
+  - - ">"
+    - !ruby/object:Gem::Version 
+      version: 0.0.0
+  version: 
+platform: ruby
+signing_key: 
+cert_chain: 
+post_install_message: 
+authors: 
+- David B. Dahl
 files: 
 - lib/rinruby.rb
 - README.txt
-required_rubygems_version: !ruby/object:Gem::Requirement
-  requirements: 
-  - - '>='
-    - !ruby/object:Gem::Version
-      version: !str 0
-  version: 
+test_files: []
+
+rdoc_options: []
+
+extra_rdoc_files: []
+
+executables: []
+
 extensions: []
-rubygems_version: 1.1.0
+
 requirements: 
 - R (http://www.r-project.org), an environment for statistical computing and graphics
-authors: 
-- David B. Dahl
-date: 2008-07-02 05:00:00 +00:00
-platform: ruby
-test_files: []
-version: !ruby/object:Gem::Version
-  version: 0.99.3
-require_paths: 
-- lib
 dependencies: []
-bindir: bin
-has_rdoc: true
+