simpler 0.0.1

data/.document

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+README.rdoc
+lib/**/*.rb
+bin/*
+features/**/*.feature
+LICENSE

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC
+.RData
+.Rhistory
+Rplots.pdf

data/History

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+== 0.0.1 / 2010-07-09
+
+* initial release
+* supporting array -> vector and dataframe .to_r methods

data/LICENSE

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+Copyright (c) 2009 John Prince
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.rdoc

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+= simpler
+
+simpler ("simple R") is a lightweight wrapper that calls R (really Rscript)
+from within ruby.  It is designed to favor R in syntax.
+
+=== Why use this rather than rsruby?  
+
+You should probably be using rsruby--it's a fantastic gem.  However, if you
+want to code using more of an R code sytax (e.g., to cut and paste R code and
+have it just work), or if you can't get rsruby working, this gem may be useful
+to you.
+
+== Examples
+
+require 'simpler'
+
+Basic execution (Raw input in, raw input out)
+
+    sr = Simpler.new
+    sr.execute!("mean(c(1,2,3))") # -> "[1] 2\n"  (a Simpler::Reply object)
+
+Using ruby variables (calculating correlation coefficient):
+
+    xv = [1,2,7]
+    yv = [3,4,8]
+    reply = sr.go(xv,yv) do |x,y|
+      "cor(#{x},#{y})"
+    end
+    reply # -> "[1] 0.9994238\n"
+
+For plotting on the fly (RScript)
+
+== Credit
+
+Simpler is loosely inspired by the original gnuplot and, of course, the excellent rsruby. 
+
+==Casting
+
+All replies are of class Simpler::String, so casting can be done in a way that works for you by defining your own methods.
+
+== Copyright
+
+Copyright (c) 2010 John Prince. See LICENSE for details.

data/Rakefile

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+require 'rubygems'
+require 'rake'
+require 'jeweler'
+require 'rake/testtask'
+require 'rake/rdoctask'
+require 'rcov/rcovtask'
+
+Jeweler::Tasks.new do |gem|
+  gem.name = "simpler"
+  gem.summary = %Q{simpler ("simple R")- A low-tech method to run R scripts.  Allows you to basically copy and paste R code and run it.}
+  gem.description = %Q{you should check out rsruby first.  This is a very low-tech way to run R.  It does have the advantage of being able to run R code essentially unchanged.}
+  gem.email = "jtprince@gmail.com"
+  gem.homepage = "http://github.com/jtprince/simpler"
+  gem.authors = ["John Prince"]
+  gem.add_development_dependency "spec-more", ">= 0"
+end
+
+Rake::TestTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+Rcov::RcovTask.new do |spec|
+  spec.libs << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+task :default => :spec
+
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "simpler #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/simpler/data_frame.rb

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+
+class Simpler
+  # This is an R-centric container for storing data
+  class DataFrame
+    # this is necessary for
+    attr_accessor :col_names
+    attr_accessor :row_names
+    attr_accessor :hash
+    # takes a hash, where the col_name is the key and the data rows are an
+    # array of values.  The default ordering of the hash keys will be used,
+    # unless overridden with col_names.  The row_names can be used to specify
+    # the names of the rows (remains nil if no values specified)
+    def initialize(hash, row_names=nil, col_names=nil)
+      @hash = hash
+      @row_names = row_names
+      @col_names = col_names || @hash.keys
+    end
+
+    # creates the code to transform the object into R code.  If usefile is
+    # specified, the dataframe is written as a table and the code generated
+    # will read in the table as a data frame.
+    def to_r(usefile=nil)
+      if usefile
+        raise NotImplementedError, "not implemented just yet"
+      else
+        # build the vectors
+        lines = @col_names.map do |name| 
+          val = @hash[name]
+          "#{Simpler.varname(val)} <- c(#{val.join(',')})"
+        end
+        args = @col_names.map do |name|
+          "#{name}=#{Simpler.varname(@hash[name])}"
+        end
+        if @row_names
+          varname = Simpler.varname(@row_names)
+          lines << "#{varname} <- c(#{@row_names.map {|v| "\"#{v}\""}.join(',')})"
+          args.push("row.names=#{varname}")
+        end
+        lines << "#{Simpler.varname(self)} <- data.frame(#{args.join(', ')})"
+        lines.join("\n") << "\n"
+      end
+    end
+
+  end
+end

data/lib/simpler/plot.rb

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+
+class Simpler
+  module Plot
+
+    def plot(file_w_extension, opts={}, &block)
+      device = self.class.filename_to_plottype(file_w_extension)
+      opts_as_ropts = opts.map {|k,v| "#{k}=#{r_format(v)}"}
+      string = "#{device}(#{file_w_extension.inspect}, #{opts_as_ropts.join(', ')})\n"
+      string << block.call << "\n"
+      string << "dev.off()\n"
+      string
+    end
+
+  end
+end
+

data/lib/simpler/reply.rb

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+
+class Simpler
+  class Reply < String
+
+    # removes the [1] from the line
+    def rm_leader
+      gsub(/^\[\d+\] /,'')
+    end
+
+    def array_cast
+      self.chomp.split("\n").rm_leader.split(" ")
+    end
+
+    def to_f
+    end
+
+    def to_i
+      rm_leader.to_f
+    end
+
+  end
+end

data/lib/simpler.rb

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+require 'open3'
+require 'simpler/data_frame'
+require 'simpler/plot'
+require 'simpler/reply'
+
+class Array
+  def to_r(varname=nil)
+    varname ||= Simpler.varname(self)
+    "#{varname} <- c(#{self.join(',')})\n"
+  end
+end
+
+class Simpler
+  include Plot
+
+  RPLOTS_FILE = "Rplots.pdf"
+  PDF_VIEWER = "evince"
+
+  # returns the variable name of the object
+  def self.varname(obj)
+    "rb#{obj.object_id}"
+  end
+
+  # returns it as a symbol, currently recognizes pdf, png, svg
+  def self.filename_to_plottype(name)
+    name.match(/\.([^\.]+)$/)[1].downcase.to_sym
+  end
+
+  attr_accessor :commands
+  attr_accessor :pdf_viewer
+
+  def initialize(commands=[], opts={:pdf_viewer => PDF_VIEWER})
+    @pdf_viewer = opts[:pdf_viewer]
+    @commands = commands
+  end
+
+  def r_format(object)
+    case object
+    when String
+      object.inspect
+    when Numeric
+      object.to_s
+    else
+      object.to_s
+    end
+  end
+
+  # displays the Rplots.pdf file at the end of execution
+  def show!(string=nil)
+    if File.exist?(RPLOTS_FILE)
+      original_mtime = File.mtime(RPLOTS_FILE)
+    end
+    reply = run!(string)
+    system "#{@pdf_viewer} #{RPLOTS_FILE} &"
+    reply
+  end
+
+  # pushes string onto command array (if given), executes all commands, and
+  # clears the command array.
+  def run!(string=nil)
+    @commands.push(string) if string
+    reply = nil
+    Open3.popen3("Rscript -") do |stdin, stdout, stderr|
+      stdin.puts @commands.map {|v| v + "\n"}.join
+      stdin.close_write
+      reply = stdout.read 
+    end
+    @commands.clear
+    Simpler::Reply.new(reply)
+  end
+
+  # pushes string onto command array (if given), executes all commands, and
+  # clears the command array.
+  def run!(string=nil)
+    @commands.push(string) if string
+    reply = nil
+    Open3.popen3("Rscript -") do |stdin, stdout, stderr|
+      stdin.puts @commands.map {|v| v + "\n"}.join
+      stdin.close_write
+      reply = stdout.read 
+    end
+    @commands.clear
+    Simpler::Reply.new(reply)
+  end
+
+  # returns self for chaining
+  def with(*objects, &block)
+    var_names = objects.map {|v| Simpler.varname(v) }
+    conversion_code = objects.map {|v| v.to_r }
+    @commands.push(*conversion_code)
+    @commands << block.call(*var_names)
+    self
+  end
+ 
+  def go(*objects, &block)
+    with(*objects, &block).run!
+  end
+
+end

data/spec/simpler_spec.rb

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+require 'spec_helper'
+
+require 'simpler'
+
+describe "Simpler" do
+  before do
+    @typos = [2,3,0,3,1,0,0,1]
+    @rate = [2,4,0,3,1,3,0,0]
+    @r = Simpler.new
+  end
+
+  it "can create valid commands" do
+    @r.with(@typos) {|t| "mean(#{t})" }
+    @r.commands.first.matches /rb\d+ <- c\(2,3,0,3,1,0,0,1\)/
+    @r.commands.last.matches /mean\(rb\d+\)/ 
+  end
+
+  it 'can get a reply' do
+    reply = @r.run!("typos = c(2,3,0,3,1,0,0,1)\nmean(typos)\nhist(typos)")
+    reply.chomp.is "[1] 1.25"
+  end
+
+end
+
+describe 'making data frames' do
+  before do
+    @hash = {
+      :one => [1,2,6,7],
+      :two => [3,4,2,9],
+      :three => [3,1,1,7],
+    }
+    @col_names = %w(one two three).map(&:to_sym)
+    @row_names = ['spicy', 'cool', 'wetness', 'relative humidity']
+  end
+  it 'makes data frames with row names' do
+    expected =  %Q{                  one two three
+spicy               1   3     3
+cool                2   4     1
+wetness             6   2     1
+relative humidity   7   9     7
+}
+    df = Simpler::DataFrame.new(@hash, @row_names, @col_names)
+    as_data_frame = Simpler.new.with(df) {|df| df }.run!
+    as_data_frame.is expected
+  end
+
+  it 'makes data frames with no row names' do
+    expected = %Q{  one two three
+1   1   3     3
+2   2   4     1
+3   6   2     1
+4   7   9     7
+}
+    df = Simpler::DataFrame.new(@hash, nil, @col_names)
+    as_data_frame = Simpler.new.with(df) {|df| df }.run!
+    as_data_frame.is expected
+  end
+end
+
+describe 'making plots' do
+
+  before do
+    @x = [1,2,3,4,5,6]
+    @y = [3,5,4,7,8,2]
+    @file = "plot"
+    @exts = %w(svg pdf png).map(&:to_sym)
+    @r = Simpler.new
+  end
+
+  it 'has convenience wrappers for plotting to file' do
+    @exts.each do |ext|
+      file = @file + "." + ext
+      @r.with(@x, @y) do |x,y|
+        @r.plot(file) do
+          %Q{
+            plot(#{x},#{y}, main="#{ext} scatterplot example", col=rgb(0,100,0,50,maxColorValue=255), pch=16)
+          }
+        end
+      end.run!
+      File.exist?(file).is true
+      IO.read(@file + ".svg").matches(/svg/) if ext == :svg
+      File.unlink(file)
+    end
+    # pdf and png matching giving: "ArgumentError: invalid byte sequence in UTF-8"
+  end
+end
+
+describe 'showing plots' do
+  before do
+    module ::Kernel
+      alias_method :old_system, :system
+      def system(string) ; $SYSTEM_CALL = string end
+    end
+    @x = [1,2,3,4,5,6]
+    @y = [3,5,4,7,8,2]
+    @r = Simpler.new
+  end
+
+  after do
+    module ::Kernel
+      alias_method :system, :old_system
+    end
+  end
+
+  it 'can disply plots' do
+    ok $SYSTEM_CALL.nil?
+
+    @r.with(@x, @y) do |x,y| 
+      "plot(#{x}, #{y})"
+    end.show!
+
+    # this shows that we've made a system call to visualize the data
+    ok !$SYSTEM_CALL.nil?
+  end
+end
+
+describe 'ancillary functions' do
+  it 'can get the device from the filename' do
+    Simpler.filename_to_plottype("bob.the.pdf").is :pdf
+    Simpler.filename_to_plottype("larry.the.svg").is :svg
+  end
+end

data/spec/spec_helper.rb

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+require 'rubygems'
+require 'spec/more'
+
+Bacon.summary_on_exit

metadata

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+--- !ruby/object:Gem::Specification 
+name: simpler
+version: !ruby/object:Gem::Version 
+  prerelease: false
+  segments: 
+  - 0
+  - 0
+  - 1
+  version: 0.0.1
+platform: ruby
+authors: 
+- John Prince
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2010-07-09 00:00:00 -06:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: spec-more
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        segments: 
+        - 0
+        version: "0"
+  type: :development
+  version_requirements: *id001
+description: you should check out rsruby first.  This is a very low-tech way to run R.  It does have the advantage of being able to run R code essentially unchanged.
+email: jtprince@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE
+- README.rdoc
+files: 
+- .document
+- .gitignore
+- History
+- LICENSE
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/simpler.rb
+- lib/simpler/data_frame.rb
+- lib/simpler/plot.rb
+- lib/simpler/reply.rb
+- spec/simpler_spec.rb
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/jtprince/simpler
+licenses: []
+
+post_install_message: 
+rdoc_options: 
+- --charset=UTF-8
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      segments: 
+      - 0
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.3.6
+signing_key: 
+specification_version: 3
+summary: simpler ("simple R")- A low-tech method to run R scripts.  Allows you to basically copy and paste R code and run it.
+test_files: 
+- spec/simpler_spec.rb
+- spec/spec_helper.rb