bio-statsample-timeseries 0.1.1

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

@@ -0,0 +1,13 @@
+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - 2.0.0
+  - jruby-19mode # JRuby in 1.9 mode
+  - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,21 @@
+source "http://rubygems.org"
+
+gem 'statsample', '=1.2.0'
+
+# Add dependencies required to use your gem here.
+# Example:
+   gem "activesupport", "= 3.2.10"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "minitest", "~> 4.7.5"
+  gem "cucumber", ">= 0"
+  gem "bundler", "~> 1.3.5"
+  gem "jeweler", "~> 1.8.4"
+  gem "bio", ">= 1.4.2"
+  gem "rdoc", "~> 3.12"
+  gem 'mocha', '~> 0.14.0'
+end

data/LICENSE.txt

@@ -0,0 +1,20 @@
+Copyright (c) 2013 Ankur Goel
+
+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.md

@@ -0,0 +1,47 @@
+# bio-statsample-timeseries
+
+[![Build Status](https://secure.travis-ci.org/AnkurGel/bioruby-statsample-timeseries.png)](http://travis-ci.org/ankurgel/bioruby-statsample-timeseries)
+
+Full description goes here
+
+Note: this software is under active development!
+
+## Installation
+
+```sh
+    gem install bio-statsample-timeseries
+```
+
+## Usage
+
+```ruby
+    require 'bio-statsample-timeseries'
+```
+
+The API doc is online. For more code examples see the test files in
+the source tree.
+        
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/ankurgel/bioruby-statsample-timeseries
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Cite
+
+If you use this software, please cite one of
+  
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+## Biogems.info
+
+This Biogem is published at [#bio-statsample-timeseries](http://biogems.info/index.html)
+
+## Copyright
+
+Copyright (c) 2013 Ankur Goel. See LICENSE.txt for further details.
+

data/README.rdoc

@@ -0,0 +1,48 @@
+= bio-statsample-timeseries
+
+{<img
+src="https://secure.travis-ci.org/ankurgel/bioruby-statsample-timeseries.png"
+/>}[http://travis-ci.org/#!/ankurgel/bioruby-statsample-timeseries]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-statsample-timeseries
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-statsample-timeseries'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/ankurgel/bioruby-statsample-timeseries
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-statsample-timeseries
+
+== Copyright
+
+Copyright (c) 2013 Ankur Goel. See LICENSE.txt for further details.
+

data/Rakefile

@@ -0,0 +1,48 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-statsample-timeseries"
+  gem.homepage = "http://github.com/ankurgel/bioruby-statsample-timeseries"
+  gem.license = "MIT"
+  gem.summary = %Q{TimeSeries modules for Statsample}
+  gem.description = %Q{Statsample-timeseries is an extension to Statsample. It incorporates helpful timeseries functions and modules like ARMA, ARIMA, acf, pacf, lags etc.}
+  gem.email = "ankurgel@gmail.com"
+  gem.authors = ["Ankur Goel", "Claudio Bustos"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+require 'cucumber/rake/task'
+Cucumber::Rake::Task.new(:features)
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-statsample-timeseries #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

@@ -0,0 +1 @@
+0.1.1

data/bin/bio-statsample-timeseries

@@ -0,0 +1,74 @@
+#!/usr/bin/env ruby
+#
+# BioRuby bio-statsample-timeseries Plugin BioStatsampleTimeseries
+# Author:: Ankur Goel
+# Copyright:: 2013
+
+ USAGE = "Describe bio-statsample-timeseries"
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'bio-statsample-timeseries'
+require 'optparse'
+
+# Uncomment when using the bio-logger 
+# require 'bio-logger'
+# Bio::Log::CLI.logger('stderr')
+# Bio::Log::CLI.trace('info')
+
+options = {:example_switch=>false,:show_help=>false}
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
+
+  o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
+    # TODO: your logic here, below an example
+    options[:example_parameter] = 'this is a parameter'
+  end
+  
+  o.separator ""
+  o.on("--switch-example", 'TODO: put a description for the SWITCH') do
+    # TODO: your logic here, below an example
+    self[:example_switch] = true
+  end
+
+  # Uncomment the following when using the bio-logger 
+  # o.separator ""
+  # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
+  #   Bio::Log::CLI.logger(name)
+  # end
+  #
+  # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
+  #   Bio::Log::CLI.trace(s)
+  # end
+  # 
+  # o.on("-q", "--quiet", "Run quietly") do |q|
+  #   Bio::Log::CLI.trace('error')
+  # end
+  # 
+  # o.on("-v", "--verbose", "Run verbosely") do |v|
+  #   Bio::Log::CLI.trace('info')
+  # end
+  # 
+  # o.on("--debug", "Show debug messages") do |v|
+  #   Bio::Log::CLI.trace('debug')
+  # end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  # Uncomment the following when using the bio-logger 
+  # Bio::Log::CLI.configure('bio-statsample-timeseries')
+
+  # TODO: your code here
+  # use options for your logic
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end

data/features/acf.feature

@@ -0,0 +1,31 @@
+Feature: ACF
+
+  As a statistician
+  So that I can evaluate autocorrelation of a series
+  I want to evaluate acf
+
+Background: a timeseries
+
+  Given the following values in a timeseries:
+    | timeseries |
+    | 10  20  30  40  50  60  70  80  90  100 |
+    | 110 120 130 140 150 160 170 180 190 200 |
+
+Scenario: cross-check acf for 10 lags
+  When I provide 10 lags for acf
+  And I calculate acf
+  Then I should get 11 values in resultant acf
+  And I should see "1.0, 0.85, 0.7015037593984963, 0.556015037593985, 0.4150375939849624, 0.2800751879699248, 0.15263157894736842, 0.034210526315789476, -0.07368421052631578, -0.16954887218045114, -0.2518796992481203" as complete series 
+
+Scenario: cross-check acf for 5 lags
+  When I provide 5 lags for acf
+  And I calculate acf
+  Then I should get 6 values in resultant acf
+  And I should see "1.0, 0.85, 0.7015037593984963, 0.556015037593985, 0.4150375939849624, 0.2800751879699248" as complete series
+
+Scenario: first value should be 1.0
+  When I provide 2 lags for acf
+  And I calculate acf
+  Then I should get 3 values in resultant acf
+  And I should see 1.0 as first value
+

data/features/pacf.feature

@@ -0,0 +1,42 @@
+Feature: PACF
+
+  As a statistician
+  So that I can quickly evaluate partial autocorrelation of a series
+  I want to evaluate pacf
+
+Background: a timeseries
+
+  Given the following values in a timeseries:
+    | timeseries |
+    | 10  20  30  40  50  60  70  80  90  100 |
+    | 110 120 130 140 150 160 170 180 190 200 |
+
+Scenario: check pacf for 10 lags with unbiased
+  When I provide 10 lags for pacf
+  When I provide yw yule walker as method
+  Then I should get Array as resultant output
+  Then I should get 11 values in resultant pacf
+
+Scenario: check pacf for 5 lags with mle
+  When I provide 5 lags for pacf
+  When I provide mle yule walker as method
+  Then I should get Array as resultant output
+  Then I should get 6 values in resultant pacf
+
+Scenario: check first value of pacf
+  When I provide 5 lags for pacf
+  When I provide yw yule walker as method
+  Then I should get Array as resultant output
+  And I should see 1.0 as first value
+
+Scenario: check all values in pacf for 5 lags with mle
+  When I provide 5 lags for pacf
+  When I provide mle yule walker as method
+  Then I should get Array as resultant output
+  And I should see "1.0, 0.85, -0.07566212829370711, -0.07635069706072706, -0.07698628638512295, -0.07747034005560738" as complete series 
+
+Scenario: check all values in pacf for 5 lags with unbiased
+  When I provide 5 lags for pacf
+  When I provide yw yule walker as method
+  Then I should get Array as resultant output
+  And I should see "1.0, 0.8947368421052632, -0.10582010582010604, -0.11350188273265083, -0.12357534824820737, -0.13686534216335522" as complete series 

data/features/step_definitions/step_definitions.rb

@@ -0,0 +1,37 @@
+require 'statsample'
+include Statsample::TimeSeries
+
+Given /^the following values in a timeseries:$/ do |series|
+  arr = []
+  series.hashes.each do |sequence|
+    arr += sequence['timeseries'].split(' ').map(&:to_i).to_ts
+  end
+  @timeseries = arr.to_ts
+end
+
+When /^I provide (\d+) lags for p?acf$/ do |lags|
+  @lags = lags.to_i
+end
+
+When /^I provide (\w+) yule walker as method$/ do |method|
+  @method = method
+end
+
+Then /^I should get (\w+) as resultant output$/ do |klass|
+  @result = @timeseries.pacf(@lags, @method)
+  assert_equal @result.class.to_s, klass
+end
+
+Then /^I should get (\w+) values in resultant p?acf$/ do |values_count|
+  assert_equal @result.size, values_count.to_i
+end
+
+And /^I should see (\d+\.\d) as first value$/ do |first_value|
+  assert_equal @result.first, first_value.to_f
+end
+
+And /^I should see \"(.+)\" as complete series$/ do |series|
+  series = series.split(',').map(&:to_f)
+  assert_equal @result, series
+end
+

data/features/step_definitions/step_definitions_acf.rb

@@ -0,0 +1,8 @@
+require 'statsample'
+include Statsample::TimeSeries
+
+#all instance variable and cucumber DSL s DRYed up in step_definitions.rb
+And /^I calculate acf$/ do
+  @result = @timeseries.acf(@lags)
+end
+

data/features/support/env.rb

@@ -0,0 +1,15 @@
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
+require 'bio-statsample-timeseries'
+
+require 'test/unit/assertions'
+
+World(Test::Unit::Assertions)

data/lib/bio-statsample-timeseries.rb

@@ -0,0 +1,16 @@
+# Please require your code below, respecting the naming conventions in the
+# bioruby directory tree.
+#
+# For example, say you have a plugin named bio-plugin, the only uncommented
+# line in this file would be 
+#
+#   require 'bio/bio-plugin/plugin'
+#
+# In this file only require other files. Avoid other source code.
+
+require 'bio-statsample-timeseries/statsample-timeseries.rb'
+require 'statsample'
+require_relative 'bio-statsample-timeseries/timeseries.rb'
+require_relative 'bio-statsample-timeseries/arima.rb'
+
+