fastout 0.0.1

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Files changed (51) hide show
  1. data/.gitignore +4 -0
  2. data/.rspec +2 -0
  3. data/Gemfile +4 -0
  4. data/Gemfile.lock +38 -0
  5. data/MIT-LICENSE +20 -0
  6. data/README.md +8 -0
  7. data/Rakefile +2 -0
  8. data/doc/classes/Fastout.html +105 -0
  9. data/doc/classes/Ranker.html +468 -0
  10. data/doc/classes/Ranker.src/M000001.html +18 -0
  11. data/doc/classes/Ranker.src/M000002.html +22 -0
  12. data/doc/classes/Ranker.src/M000003.html +42 -0
  13. data/doc/classes/Ranker.src/M000004.html +21 -0
  14. data/doc/classes/Ranker.src/M000005.html +28 -0
  15. data/doc/classes/Ranker.src/M000006.html +35 -0
  16. data/doc/classes/Ranker.src/M000007.html +18 -0
  17. data/doc/classes/Ranker.src/M000008.html +18 -0
  18. data/doc/classes/Ranker.src/M000009.html +33 -0
  19. data/doc/classes/Ranker.src/M000010.html +18 -0
  20. data/doc/classes/Ranker.src/M000011.html +22 -0
  21. data/doc/classes/Ranker.src/M000012.html +24 -0
  22. data/doc/classes/Ranker.src/M000013.html +28 -0
  23. data/doc/classes/Ranker.src/M000014.html +20 -0
  24. data/doc/classes/Ranker.src/M000015.html +19 -0
  25. data/doc/classes/Ranker/Point.html +262 -0
  26. data/doc/classes/Ranker/Point.src/M000016.html +18 -0
  27. data/doc/classes/Ranker/Point.src/M000017.html +24 -0
  28. data/doc/classes/Ranker/Point.src/M000018.html +18 -0
  29. data/doc/classes/Ranker/Point.src/M000019.html +18 -0
  30. data/doc/classes/Ranker/Point.src/M000020.html +18 -0
  31. data/doc/classes/Ranker/Point.src/M000021.html +26 -0
  32. data/doc/classes/Ranker/Point.src/M000022.html +18 -0
  33. data/doc/created.rid +1 -0
  34. data/doc/files/lib/fastout/ranker_rb.html +121 -0
  35. data/doc/files/lib/fastout/version_rb.html +101 -0
  36. data/doc/files/lib/fastout_rb.html +108 -0
  37. data/doc/files/spec/fastout/ranker_spec_rb.html +109 -0
  38. data/doc/files/spec/spec_helper_rb.html +110 -0
  39. data/doc/fr_class_index.html +29 -0
  40. data/doc/fr_file_index.html +28 -0
  41. data/doc/fr_method_index.html +48 -0
  42. data/doc/index.html +24 -0
  43. data/doc/rdoc-style.css +208 -0
  44. data/fastout.gemspec +29 -0
  45. data/lib/fastout.rb +1 -0
  46. data/lib/fastout/ranker.rb +243 -0
  47. data/lib/fastout/version.rb +3 -0
  48. data/spec/fastout/ranker_spec.rb +252 -0
  49. data/spec/parkinsons.csv +1 -0
  50. data/spec/spec_helper.rb +9 -0
  51. metadata +217 -0
data/.gitignore ADDED
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+ pkg/*
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+ *.gem
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+ .bundle
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+ *.swp
data/.rspec ADDED
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+ --color
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+ --format nested
data/Gemfile ADDED
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+ source "http://rubygems.org"
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+
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+ # Specify your gem's dependencies in fastout.gemspec
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+ gemspec
data/Gemfile.lock ADDED
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+ PATH
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+ remote: .
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+ specs:
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+ fastout (0.0.1)
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+
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+ GEM
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+ remote: http://rubygems.org/
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+ specs:
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+ autotest (4.4.5)
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+ autotest-fsevent (0.2.3)
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+ sys-uname
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+ autotest-growl (0.2.6)
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+ diff-lcs (1.1.2)
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+ fastercsv (1.5.3)
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+ redgreen (1.2.2)
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+ rr (1.0.2)
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+ rspec (2.1.0)
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+ rspec-core (~> 2.1.0)
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+ rspec-expectations (~> 2.1.0)
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+ rspec-mocks (~> 2.1.0)
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+ rspec-core (2.1.0)
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+ rspec-expectations (2.1.0)
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+ diff-lcs (~> 1.1.2)
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+ rspec-mocks (2.1.0)
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+ sys-uname (0.8.4)
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+
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+ PLATFORMS
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+ ruby
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+
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+ DEPENDENCIES
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+ autotest
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+ autotest-fsevent
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+ autotest-growl
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+ fastercsv
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+ fastout!
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+ redgreen
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+ rr
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+ rspec (~> 2.0)
data/MIT-LICENSE ADDED
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+ Copyright (c) 2004-2010 David Heinemeier Hansson
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
data/README.md ADDED
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+ FastOut
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+ =======
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+
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+ Outlier detection using the FASTOUT algorithm by Foss et al. [FZ10] in Ruby!
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+
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+ References
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+ ==========
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+ [FZ10] Andrew Foss and Osmar R. Zaıäne. Class separation through variance: a new application of outlier detection. Knowledge and Information Systems, 2010.
data/Rakefile ADDED
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+ require 'bundler'
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+ Bundler::GemHelper.install_tasks
data/doc/classes/Fastout.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Module: Fastout</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">Fastout</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../files/spec/fastout/ranker_spec_rb.html">
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+ spec/fastout/ranker_spec.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/doc/classes/Ranker.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Class: Ranker</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+
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+ elemStyle = elem.style;
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+
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ } else {
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+ elemStyle.display = "none"
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+ }
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+
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Class</strong></td>
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+ <td class="class-name-in-header">Ranker</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../files/lib/fastout/ranker_rb.html">
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+ lib/fastout/ranker.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ <tr class="top-aligned-row">
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+ <td><strong>Parent:</strong></td>
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+ <td>
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+ Object
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+ </td>
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+ </tr>
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+
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+
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+ <div id="contextContent">
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+
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+ <div id="description">
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+ <p>
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+ Takes a data set and determines the outliers using the FASTOUT algorithm
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+ from Foss et al., &quot;Class Separation through Variance: a <a
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+ href="Ranker.html#M000002">new</a> application of outlier detection&quot;,
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+ Knowledge and Information Systems, 2010.
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+ </p>
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+ <table>
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+ <tr><td valign="top">Author:</td><td>Jason Dew (<a href="mailto:jason.dew@gmail.com">jason.dew@gmail.com</a>)
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+
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+ </td></tr>
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+ <tr><td valign="top">Copyright:</td><td>Copyright (c) 2010 Jason Dew
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+
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+ </td></tr>
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+ <tr><td valign="top">License:</td><td>MIT
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+
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+ </td></tr>
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+ </table>
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+
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+ </div>
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+
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000011">assign_points_to_bins!</a>&nbsp;&nbsp;
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+ <a href="#M000012">bin_index</a>&nbsp;&nbsp;
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+ <a href="#M000004">calculate_theta</a>&nbsp;&nbsp;
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+ <a href="#M000008">cluster_neighbors</a>&nbsp;&nbsp;
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+ <a href="#M000015">compute_bin_count</a>&nbsp;&nbsp;
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+ <a href="#M000014">compute_bin_widths</a>&nbsp;&nbsp;
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+ <a href="#M000013">compute_minimums_and_maximums</a>&nbsp;&nbsp;
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+ <a href="#M000002">new</a>&nbsp;&nbsp;
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+ <a href="#M000003">optimized_ranking</a>&nbsp;&nbsp;
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+ <a href="#M000001">pointify</a>&nbsp;&nbsp;
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+ <a href="#M000007">random_attribute_indexes</a>&nbsp;&nbsp;
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+ <a href="#M000005">ranked_outliers</a>&nbsp;&nbsp;
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+ <a href="#M000009">recursively_cluster_neighbors</a>&nbsp;&nbsp;
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+ <a href="#M000006">score_points_from_a_random_set_of_attributes!</a>&nbsp;&nbsp;
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+ <a href="#M000010">unclustered_points</a>&nbsp;&nbsp;
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+ <div id="class-list">
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+ <h3 class="section-bar">Classes and Modules</h3>
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+
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+ Class <a href="Ranker/Point.html" class="link">Ranker::Point</a><br />
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+
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+ </div>
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+
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+
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+
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+
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+ <div id="attribute-list">
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+ <h3 class="section-bar">Attributes</h3>
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+
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+ <div class="name-list">
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+ <table>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">data</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">maximums</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">minimums</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">points</td>
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+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
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+ <td class="context-item-desc"></td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Class methods</h3>
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+
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+ <div id="method-M000002" class="method-detail">
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+ <a name="M000002"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000002.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000002.html');return false;">
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+ <span class="method-name">new</span><span class="method-args">(data)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ takes a 2-d array, <tt>data</tt>, where the rows are data points and the
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+ columns are the attributes, values should all be numerical
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+ </p>
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+ <ul>
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+ <li><tt>data</tt> should not be empty or nil will be returned
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+
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+ </li>
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+ <li>also generates minimum and maximum values for each attribute for later use
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+
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+ </li>
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+ </ul>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000001" class="method-detail">
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+ <a name="M000001"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000001.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000001.html');return false;">
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+ <span class="method-name">pointify</span><span class="method-args">(data)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000011" class="method-detail">
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+ <a name="M000011"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000011.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000011.html');return false;">
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+ <span class="method-name">assign_points_to_bins!</span><span class="method-args">(bin_widths, bin_count)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ assign each of the data points to a bin based on the given
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+ <tt>bin_widths</tt>, returns a 2-d array in attribute-major order
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000012" class="method-detail">
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+ <a name="M000012"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000012.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000012.html');return false;">
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+ <span class="method-name">bin_index</span><span class="method-args">(point, attribute_index, bin_width)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ <div id="method-M000004" class="method-detail">
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+ <a name="M000004"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000004.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000004.html');return false;">
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+ <span class="method-name">calculate_theta</span><span class="method-args">(sample, k, n, q)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ find and rank the points by their outlier score and determine theta (the
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+ number of points with an outlier score of <tt>n</tt>)
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000008" class="method-detail">
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+ <a name="M000008"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000008.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000008.html');return false;">
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+ <span class="method-name">cluster_neighbors</span><span class="method-args">(point, cluster, attribute_indexes, bin_widths)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ find all unclustered points that are neighbors of <tt>point</tt> on
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+ <b>all</b> selected attributes or neighbors in the neighborhood of
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+ <tt>point</tt>; find recursively until no additions can be made
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000015" class="method-detail">
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+ <a name="M000015"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000015.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000015.html');return false;">
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+ <span class="method-name">compute_bin_count</span><span class="method-args">(q)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ compute the number of bins for a given <tt>q</tt>
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000014" class="method-detail">
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+ <a name="M000014"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000014.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000014.html');return false;">
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+ <span class="method-name">compute_bin_widths</span><span class="method-args">(q, bin_count)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ determine the widths of the bins based on <tt>q</tt>
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000013" class="method-detail">
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+ <a name="M000013"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000013.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000013.html');return false;">
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+ <span class="method-name">compute_minimums_and_maximums</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ </div>
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+ </div>
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+
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+ <div id="method-M000003" class="method-detail">
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+ <a name="M000003"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000003.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000003.html');return false;">
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+ <span class="method-name">optimized_ranking</span><span class="method-args">(sample, n, theta_target=1)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ searches the parameter space to find the optimized values of <tt>k</tt> and
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+ <tt>q</tt>
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+ </p>
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+ <ul>
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+ <li><tt>theta_target</tt> is the maximum acceptable value of theta, default is
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+ 1
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+
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+ </li>
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+ <li><tt>sample</tt> is the number of iterations to perform in estimating the
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+ parameters
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+
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+ </li>
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+ <li><tt>n</tt> is the number of points to rank
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+
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+ </li>
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+ </ul>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000007" class="method-detail">
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+ <a name="M000007"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000007.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000007.html');return false;">
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+ <span class="method-name">random_attribute_indexes</span><span class="method-args">(number)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ randomly choose <tt>number</tt> of attribute indexes
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000005" class="method-detail">
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+ <a name="M000005"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000005.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000005.html');return false;">
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+ <span class="method-name">ranked_outliers</span><span class="method-args">(sample_size, k, q)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ chooses <tt>k</tt> random attributes with an average of <tt>q</tt> data
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+ points in each bin <tt>sample</tt> times to determine outliers
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000009" class="method-detail">
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+ <a name="M000009"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000009.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000009.html');return false;">
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+ <span class="method-name">recursively_cluster_neighbors</span><span class="method-args">(point, cluster, attribute_indexes, bin_widths, neighbors)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ recursive step of <a href="Ranker.html#M000008">cluster_neighbors</a>
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000006" class="method-detail">
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+ <a name="M000006"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000006.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000006.html');return false;">
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+ <span class="method-name">score_points_from_a_random_set_of_attributes!</span><span class="method-args">(number_of_attributes_to_choose, all_bin_widths)</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
433
+ pick a random set of attributes and compute the outlier score for each of
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+ the points
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+ </p>
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+ </div>
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+ </div>
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+
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+ <div id="method-M000010" class="method-detail">
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+ <a name="M000010"></a>
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+
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+ <div class="method-heading">
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+ <a href="Ranker.src/M000010.html" target="Code" class="method-signature"
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+ onclick="popupCode('Ranker.src/M000010.html');return false;">
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+ <span class="method-name">unclustered_points</span><span class="method-args">()</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
451
+ find all of the points that don&#8216;t already belong to a cluster
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+ </p>
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+ </div>
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>