sciruby 0.1.0 → 0.1.3

data/.autotest

@@ -0,0 +1,23 @@
+# -*- ruby -*-
+
+require 'autotest/restart'
+
+# Autotest.add_hook :initialize do |at|
+#   at.extra_files << "../some/external/dependency.rb"
+#
+#   at.libs << ":../some/external"
+#
+#   at.add_exception 'vendor'
+#
+#   at.add_mapping(/dependency.rb/) do |f, _|
+#     at.files_matching(/test_.*rb$/)
+#   end
+#
+#   %w(TestA TestB).each do |klass|
+#     at.extra_class_map[klass] = "test/test_misc.rb"
+#   end
+# end
+
+# Autotest.add_hook :run_command do |at|
+#   system "rake build"
+# end

data/History.txt

@@ -0,0 +1,6 @@
+=== 1.0.0 / 2011-01-31
+
+* 1 major enhancement
+
+  * Birthday!
+

data/Manifest.txt

@@ -0,0 +1,119 @@
+.autotest
+History.txt
+Manifest.txt
+readme.md
+Rakefile
+lib/sciruby.rb
+lib/sciruby/validation.rb
+lib/sciruby/recommend.rb
+lib/sciruby/plotter.rb
+lib/sciruby/editor.rb
+lib/sciruby/config.rb
+lib/sciruby/analysis.rb
+lib/sciruby/analysis/suite.rb
+lib/sciruby/analysis/suite_report_builder.rb
+lib/sciruby/data.rb
+lib/sciruby/data/guardian.rb
+lib/sciruby/data/r.rb
+lib/sciruby/data/r/base.rb
+lib/sciruby/data/r/data_frame.rb
+lib/sciruby/data/r/grouped_data.rb
+lib/sciruby/data/r/list.rb
+lib/sciruby/data/r/multi_time_series.rb
+lib/sciruby/data/r/r_matrix.rb
+lib/sciruby/data/r/time_series.rb
+lib/sciruby/data/r/time_series_base.rb
+lib/sciruby/data/r/vector.rb
+lib/ext/shoes.rb
+lib/ext/csv.rb
+lib/ext/string.rb
+bin/sciruby-plotter
+static/sciruby-icon.png
+test/test_recommend.rb
+test/helpers_tests.rb
+data/r/man/ability.cov.Rd
+data/r/man/airmiles.Rd
+data/r/man/AirPassengers.Rd
+data/r/man/airquality.Rd
+data/r/man/anscombe.Rd
+data/r/man/attenu.Rd
+data/r/man/attitude.Rd
+data/r/man/austres.Rd
+data/r/man/beavers.Rd
+data/r/man/BJsales.Rd
+data/r/man/BOD.Rd
+data/r/man/cars.Rd
+data/r/man/ChickWeight.Rd
+data/r/man/chickwts.Rd
+data/r/man/co2.Rd
+data/r/man/crimtab.Rd
+data/r/man/datasets-package.Rd
+data/r/man/discoveries.Rd
+data/r/man/DNase.Rd
+data/r/man/esoph.Rd
+data/r/man/eurodist.Rd
+data/r/man/euro.Rd
+data/r/man/EuStockMarkets.Rd
+data/r/man/faithful.Rd
+data/r/man/Formaldehyde.Rd
+data/r/man/freeny.Rd
+data/r/man/HairEyeColor.Rd
+data/r/man/Harman23.cor.Rd
+data/r/man/Harman74.cor.Rd
+data/r/man/Indometh.Rd
+data/r/man/infert.Rd
+data/r/man/InsectSprays.Rd
+data/r/man/iris.Rd
+data/r/man/islands.Rd
+data/r/man/JohnsonJohnson.Rd
+data/r/man/LakeHuron.Rd
+data/r/man/lh.Rd
+data/r/man/LifeCycleSavings.Rd
+data/r/man/Loblolly.Rd
+data/r/man/longley.Rd
+data/r/man/lynx.Rd
+data/r/man/morley.Rd
+data/r/man/mtcars.Rd
+data/r/man/nhtemp.Rd
+data/r/man/Nile.Rd
+data/r/man/nottem.Rd
+data/r/man/occupationalStatus.Rd
+data/r/man/Orange.Rd
+data/r/man/OrchardSprays.Rd
+data/r/man/PlantGrowth.Rd
+data/r/man/precip.Rd
+data/r/man/presidents.Rd
+data/r/man/pressure.Rd
+data/r/man/Puromycin.Rd
+data/r/man/quakes.Rd
+data/r/man/randu.Rd
+data/r/man/rivers.Rd
+data/r/man/rock.Rd
+data/r/man/sleep.Rd
+data/r/man/stackloss.Rd
+data/r/man/state.Rd
+data/r/man/sunspot.month.Rd
+data/r/man/sunspots.Rd
+data/r/man/sunspot.year.Rd
+data/r/man/swiss.Rd
+data/r/man/Theoph.Rd
+data/r/man/Titanic.Rd
+data/r/man/ToothGrowth.Rd
+data/r/man/treering.Rd
+data/r/man/trees.Rd
+data/r/man/UCBAdmissions.Rd
+data/r/man/UKDriverDeaths.Rd
+data/r/man/UKgas.Rd
+data/r/man/UKLungDeaths.Rd
+data/r/man/USAccDeaths.Rd
+data/r/man/USArrests.Rd
+data/r/man/USJudgeRatings.Rd
+data/r/man/USPersonalExpenditure.Rd
+data/r/man/uspop.Rd
+data/r/man/VADeaths.Rd
+data/r/man/volcano.Rd
+data/r/man/warpbreaks.Rd
+data/r/man/women.Rd
+data/r/man/WorldPhones.Rd
+data/r/man/WWWusage.Rd
+data/r/man/zCO2.Rd

data/Rakefile

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+#!/usr/bin/ruby
+# -*- ruby -*-
+# -*- coding: utf-8 -*-
+$:.unshift(File.dirname(__FILE__)+'/lib/')
+
+require 'rubygems'
+require 'rdoc/task'
+require 'sciruby'
+require 'hoe'
+
+# Hoe.plugin :compiler
+# Hoe.plugin :cucumberfeatures
+# Hoe.plugin :gem_prelude_sucks
+Hoe.plugin :git
+Hoe.plugin :gemspec
+Hoe.plugin :bundler
+# Hoe.plugin :inline
+# Hoe.plugin :manifest
+# Hoe.plugin :newgem
+# Hoe.plugin :racc
+# Hoe.plugin :rubyforge
+# Hoe.plugin :website
+
+desc "Ruby Lint"
+task :lint do
+  executable=Config::CONFIG['RUBY_INSTALL_NAME']
+  Dir.glob("lib/**/*.rb") {|f|
+    if !system %{#{executable} -w -c "#{f}"}
+        puts "Error on: #{f}"
+    end
+  }
+end
+
+desc "Open an irb session preloaded with sciruby"
+task :console do
+  sh "irb -rubygems -I lib -r sciruby.rb"
+end
+
+desc "Start the plotter without the console"
+task :plotter, [:script] => [] do |t,args|
+  if args.script.empty?
+    raise ArgumentError, "Need a script, e.g.: rake plotter[script.rb]"
+  else
+    sh "ruby -rubygems -I lib -r sciruby.rb -e 'SciRuby::Plotter.new(\"#{args.script}\")'"
+  end
+end
+
+desc "Start the plotter without the console"
+task :editor do
+  sh "ruby -rubygems -I lib -r sciruby.rb -e 'SciRuby::Editor.new'"
+end
+
+task :release do
+  system %{git push origin master}
+end
+
+h = Hoe.spec 'sciruby' do
+  self.version = SciRuby::VERSION
+  self.require_ruby_version ">=1.9"
+  self.developer('SciRuby Development Team', 'sciruby-dev@googlegroups.com')
+  self.extra_deps = {'distribution' => ">=0.4.0",
+                     'green_shoes' => ">=1.0.282",
+                     'statsample' => ">=1.1.0",
+                     'integration' => ">= 0",
+                     'minimization' => ">= 0",
+                     'gsl' => "~> 1.14.5",
+                     'rsvg2' => '~> 1.0.0',
+                     'simpler' => '>=0.1.0',
+                     'rubyvis' => '>=0.4.0'        }.to_a
+
+
+  self.extra_dev_deps = {'hoe' => "~> 2.12",
+                         'rdoc' => ">=0",
+                         'rspec' => ">=2.0",
+                         'haml' => ">=0", # for Rubyvis
+                         'coderay' => ">=0", # for Rubyvis
+                         'nokogiri' => ">=0", # for Rubyvis
+                         'RedCloth' => ">=0", # for Rubyvis
+                         'gtksourceview2' => ">=0", # for editor
+                         'shoulda' => "~> 2.11",
+                         'hoe-gemspec' => "~> 1.0",
+                         'hoe-bundler' => "~> 1.1",
+                         'minitest' => "~> 2.0" }.to_a
+
+  #self.executables = `git ls-files -- bin/*`.split("\n").map { |f| File.basename(f) }
+
+  self.post_install_message = <<-EOF
+***********************************************************
+Welcome to SciRuby: Tools for Scientific Computing in Ruby!
+
+                     *** WARNING ***
+Please be aware that SciRuby is in ALPHA status. If you're
+thinking of using SciRuby to write mission critical code,
+such as for driving a car or flying a space shuttle, you
+may wish to choose other software (for now).
+
+In order to leverage the GUI features, you will need to
+install gtk2 and optionally gtksourceview2:
+
+  $ gem install gtk2 gtksourceview2
+
+You will probably first need to install the headers for
+a number of required packages. In Ubuntu, use:
+
+  $ sudo apt-get install libgtk2.0-dev libgtksourceview2-dev \\
+      librsvg2-dev libcairo2-dev
+
+If you have trouble with Green Shoes, you should look at
+the Green Shoes wiki:
+
+* http://github.com/ashbb/green_shoes/wiki
+
+For Mac OSX Green Shoes:
+
+* https://github.com/ashbb/green_shoes/wiki/Building-Green-Shoes-on-OSX
+
+More explicit instructions for SciRuby should be available
+at our website, sciruby.com, or through our mailing list
+(which can also be found on our website).
+
+Thanks for installing SciRuby! Happy hypothesis testing!
+
+***********************************************************
+  EOF
+
+  self.need_rdoc = false
+
+end
+
+RDoc::Task.new(:docs) do |rd|
+  rd.main = h.readme_file
+  rd.options << '-d' if (`which dot` =~ /\/dot/) unless
+    ENV['NODOT'] || Hoe::WINDOZE
+  rd.rdoc_dir = 'doc'
+
+  rd.rdoc_files.include("lib/**/*.rb")
+  rd.rdoc_files += h.spec.extra_rdoc_files
+  rd.rdoc_files.reject! {|f| f=="Manifest.txt"}
+  title = h.spec.rdoc_options.grep(/^(-t|--title)=?$/).first
+  if title then
+    rd.options << title
+
+    unless title =~ /\=/ then # for ['-t', 'title here']
+    title_index = spec.rdoc_options.index(title)
+    rd.options << spec.rdoc_options[title_index + 1]
+    end
+  else
+    title = "#{h.name}-#{h.version} Documentation"
+    title = "#{h.rubyforge_name}'s " + title if h.rubyforge_name != h.name
+    rd.options << '--title' << title
+  end
+end
+
+desc 'Publish rdocs with analytics support'
+task :publish_docs => [:clean, :docs] do
+  ruby %{aggregate_adsense_to_doc.rb}
+  path = File.expand_path("~/.rubyforge/user-config.yml")
+  config = YAML.load(File.read(path))
+  host = "#{config["username"]}@rubyforge.org"
+
+  remote_dir = "/var/www/gforge-projects/#{h.rubyforge_name}/#{h.remote_rdoc_dir
+  }"
+  local_dir = h.local_rdoc_dir
+  Dir.glob(local_dir+"/**/*") {|file|
+    sh %{chmod 755 #{file}}
+  }
+  sh %{rsync #{h.rsync_args} #{local_dir}/ #{host}:#{remote_dir}}
+end
+
+require 'rspec/core/rake_task'
+namespace :spec do
+  desc "Run all specs"
+  RSpec::Core::RakeTask.new
+  # options in .rspec in package root
+end
+
+
+# vim: syntax=ruby

data/bin/sciruby-plotter

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+#!/usr/bin/env ruby
+
+require 'rubygems'
+require 'sciruby'
+
+if ARGV.size == 0
+  STDERR.puts "sciruby-plotter: missing plot script"
+  STDERR.puts "Usage: sciruby-plotter myscript.rb"
+  exit false
+end
+
+SciRuby::Plotter.new ARGV.first

data/data/r/man/AirPassengers.Rd

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+% File src/library/datasets/man/AirPassengers.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{AirPassengers}
+\docType{data}
+\alias{AirPassengers}
+\title{Monthly Airline Passenger Numbers 1949-1960}
+\description{
+ The classic Box & Jenkins airline data.  Monthly totals of
+ international airline passengers, 1949 to 1960.
+}
+\usage{AirPassengers}
+\format{
+  A monthly time series, in thousands.
+}
+\source{
+  Box, G. E. P., Jenkins, G. M. and Reinsel, G. C. (1976)
+  \emph{Time Series Analysis, Forecasting and Control.}
+  Third Edition. Holden-Day. Series G.
+}
+ \examples{
+\dontrun{
+## These are quite slow and so not run by example(AirPassengers)
+
+## The classic 'airline model', by full ML
+(fit <- arima(log10(AirPassengers), c(0, 1, 1),
+              seasonal = list(order=c(0, 1 ,1), period=12)))
+update(fit, method = "CSS")
+update(fit, x=window(log10(AirPassengers), start = 1954))
+pred <- predict(fit, n.ahead = 24)
+tl <- pred$pred - 1.96 * pred$se
+tu <- pred$pred + 1.96 * pred$se
+ts.plot(AirPassengers, 10^tl, 10^tu, log = "y", lty = c(1,2,2))
+
+## full ML fit is the same if the series is reversed, CSS fit is not
+ap0 <- rev(log10(AirPassengers))
+attributes(ap0) <- attributes(AirPassengers)
+arima(ap0, c(0, 1, 1), seasonal = list(order=c(0, 1 ,1), period=12))
+arima(ap0, c(0, 1, 1), seasonal = list(order=c(0, 1 ,1), period=12),
+      method = "CSS")
+
+## Structural Time Series
+ap <- log10(AirPassengers) - 2
+(fit <- StructTS(ap, type= "BSM"))
+par(mfrow=c(1,2))
+plot(cbind(ap, fitted(fit)), plot.type = "single")
+plot(cbind(ap, tsSmooth(fit)), plot.type = "single")
+}}
+\keyword{datasets}

data/data/r/man/BJsales.Rd

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+% File src/library/datasets/man/BJsales.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2007 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{BJsales}
+\docType{data}
+\alias{BJsales}
+\alias{BJsales.lead}
+\title{Sales Data with Leading Indicator}
+\description{
+  The sales time series \code{BJsales} and leading indicator
+  \code{BJsales.lead} each contain 150 observations.
+  The objects are of class \code{"ts"}.
+}
+\usage{
+BJsales
+BJsales.lead
+}
+\source{
+  The data are given in Box & Jenkins (1976).
+  Obtained from the Time Series Data Library at
+  \url{http://www-personal.buseco.monash.edu.au/~hyndman/TSDL/}
+}
+\references{
+  G. E. P. Box and G. M. Jenkins (1976):
+  \emph{Time Series Analysis, Forecasting and Control},
+  Holden-Day, San Francisco, p. 537.
+
+  P. J. Brockwell and R. A. Davis (1991):
+  \emph{Time Series: Theory and Methods},
+  Second edition, Springer Verlag, NY, pp. 414.
+}
+\keyword{datasets}

data/data/r/man/BOD.Rd

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+% File src/library/datasets/man/BOD.Rd
+% Part of the R package, http://www.R-project.org
+% Copyright 1995-2010 R Core Development Team
+% Distributed under GPL 2 or later
+
+\name{BOD}
+\docType{data}
+\alias{BOD}
+\title{ Biochemical Oxygen Demand }
+\description{
+  The \code{BOD} data frame has 6 rows and 2 columns giving the
+  biochemical oxygen demand versus time in an evaluation of water
+  quality.
+}
+\usage{BOD}
+\format{
+  This data frame contains the following columns:
+  \describe{
+    \item{Time}{
+      A numeric vector giving the time of the measurement (days).
+    }
+    \item{demand}{
+      A numeric vector giving the biochemical oxygen demand (mg/l).
+    }
+  }
+}
+\source{
+  Bates, D.M. and Watts, D.G. (1988),
+  \emph{Nonlinear Regression Analysis and Its Applications},
+  Wiley, Appendix A1.4.
+
+  Originally from Marske (1967), \emph{Biochemical
+    Oxygen Demand Data Interpretation Using Sum of Squares Surface}
+  M.Sc. Thesis, University of Wisconsin -- Madison.
+}
+\examples{
+\testonly{options(show.nls.convergence=FALSE)
+old <- options(digits = 5)}
+require(stats)
+# simplest form of fitting a first-order model to these data
+fm1 <- nls(demand ~ A*(1-exp(-exp(lrc)*Time)), data = BOD,
+   start = c(A = 20, lrc = log(.35)))
+coef(fm1)
+fm1
+# using the plinear algorithm
+fm2 <- nls(demand ~ (1-exp(-exp(lrc)*Time)), data = BOD,
+   start = c(lrc = log(.35)), algorithm = "plinear", trace = TRUE)
+# using a self-starting model
+fm3 <- nls(demand ~ SSasympOrig(Time, A, lrc), data = BOD)
+summary(fm3)
+\testonly{options(old)}
+}
+\keyword{datasets}