ai4r 1.4 → 1.5

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Files changed (62) hide show
  1. data/README.rdoc +24 -3
  2. data/examples/decision_trees/id3_example.rb +1 -1
  3. data/examples/genetic_algorithm/genetic_algorithm_example.rb +1 -1
  4. data/lib/ai4r.rb +11 -0
  5. data/lib/ai4r/classifiers/classifier.rb +2 -0
  6. data/lib/ai4r/classifiers/id3.rb +3 -2
  7. data/lib/ai4r/classifiers/multilayer_perceptron.rb +135 -0
  8. data/lib/ai4r/classifiers/one_r.rb +2 -1
  9. data/lib/ai4r/classifiers/prism.rb +2 -1
  10. data/lib/ai4r/classifiers/zero_r.rb +2 -1
  11. data/lib/ai4r/clusterers/average_linkage.rb +60 -0
  12. data/lib/ai4r/clusterers/bisecting_k_means.rb +17 -39
  13. data/lib/ai4r/clusterers/clusterer.rb +25 -0
  14. data/lib/ai4r/clusterers/complete_linkage.rb +62 -0
  15. data/lib/ai4r/clusterers/k_means.rb +18 -25
  16. data/lib/ai4r/clusterers/single_linkage.rb +179 -0
  17. data/lib/ai4r/data/data_set.rb +33 -41
  18. data/lib/ai4r/data/proximity.rb +82 -0
  19. data/lib/ai4r/data/statistics.rb +77 -0
  20. data/lib/ai4r/experiment/classifier_evaluator.rb +95 -0
  21. data/lib/ai4r/genetic_algorithm/genetic_algorithm.rb +2 -4
  22. data/site/build/site/en/build/tmp/build-info.xml +5 -0
  23. data/site/build/site/en/build/tmp/plugins-1.xml +212 -0
  24. data/site/build/site/en/build/tmp/plugins-2.xml +252 -0
  25. data/site/build/site/en/build/tmp/projfilters.properties +41 -0
  26. data/site/build/site/en/downloads.html +1 -1
  27. data/site/build/site/en/geneticAlgorithms.html +1 -1
  28. data/site/build/site/en/index.html +44 -7
  29. data/site/build/site/en/index.pdf +278 -155
  30. data/site/build/site/en/linkmap.html +2 -2
  31. data/site/build/site/en/linkmap.pdf +12 -12
  32. data/site/build/site/en/machineLearning.html +1 -1
  33. data/site/build/site/en/neuralNetworks.html +1 -1
  34. data/site/build/site/en/sourceCode.html +244 -0
  35. data/site/build/site/en/sourceCode.pdf +278 -0
  36. data/site/build/site/en/svn.html +34 -42
  37. data/site/build/site/en/svn.pdf +86 -114
  38. data/site/build/tmp/cocoon-work/cache-dir/cocoon-ehcache-1.data +0 -0
  39. data/site/build/tmp/cocoon-work/cache-dir/cocoon-ehcache-1.index +0 -0
  40. data/site/build/tmp/projfilters.properties +1 -1
  41. data/site/build/webapp/WEB-INF/logs/core.log +628 -629
  42. data/site/build/webapp/WEB-INF/logs/error.log +213 -213
  43. data/site/src/documentation/content/xdocs/index.xml +20 -1
  44. data/site/src/documentation/content/xdocs/site.xml +1 -1
  45. data/site/src/documentation/content/xdocs/sourceCode.xml +43 -0
  46. data/site/src/documentation/resources/images/sigmoid.png +0 -0
  47. data/test/classifiers/id3_test.rb +0 -1
  48. data/test/classifiers/multilayer_perceptron_test.rb +79 -0
  49. data/test/classifiers/one_r_test.rb +0 -2
  50. data/test/classifiers/prism_test.rb +0 -2
  51. data/test/classifiers/zero_r_test.rb +0 -2
  52. data/test/clusterers/average_linkage_test.rb +45 -0
  53. data/test/clusterers/bisecting_k_means_test.rb +0 -2
  54. data/test/clusterers/complete_linkage_test.rb +45 -0
  55. data/test/clusterers/k_means_test.rb +0 -2
  56. data/test/clusterers/single_linkage_test.rb +113 -0
  57. data/test/data/data_set_test.rb +3 -15
  58. data/test/data/proximity_test.rb +71 -0
  59. data/test/data/statistics_test.rb +65 -0
  60. data/test/experiment/classifier_evaluator_test.rb +76 -0
  61. metadata +27 -6
  62. data/site/src/documentation/content/xdocs/svn.xml +0 -41
data/lib/ai4r/data/statistics.rb ADDED
@@ -0,0 +1,77 @@
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+ # Author:: Sergio Fierens
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+ # License:: MPL 1.1
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+ # Project:: ai4r
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+ # Url:: http://ai4r.rubyforge.org/
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+ #
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+ # You can redistribute it and/or modify it under the terms of
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+ # the Mozilla Public License version 1.1 as published by the
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+ # Mozilla Foundation at http://www.mozilla.org/MPL/MPL-1.1.txt
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+
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+ require File.dirname(__FILE__) + '/data_set'
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+
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+ module Ai4r
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+ module Data
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+
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+ # This module provides some basic statistics functions to operate on
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+ # data set attributes.
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+ module Statistics
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+
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+ # Get the sample mean
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+ def self.mean(data_set, attribute)
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+ index = data_set.get_index(attribute)
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+ sum = 0.0
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+ data_set.data_items.each { |item| sum += item[index] }
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+ return sum / data_set.data_items.length
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+ end
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+
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+ # Get the variance.
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+ # You can provide the mean if you have it already, to speed up things.
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+ def self.variance(data_set, attribute, mean = nil)
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+ index = data_set.get_index(attribute)
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+ mean = mean(data_set, attribute)
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+ sum = 0.0
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+ data_set.data_items.each { |item| sum += (item[index]-mean)**2 }
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+ return sum / (data_set.data_items.length-1)
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+ end
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+
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+ # Get the standard deviation.
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+ # You can provide the variance if you have it already, to speed up things.
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+ def self.standard_deviation(data_set, attribute, variance = nil)
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+ variance ||= variance(data_set, attribute)
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+ Math.sqrt(variance)
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+ end
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+
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+ # Get the sample mode.
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+ def self.mode(data_set, attribute)
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+ index = data_set.get_index(attribute)
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+ count = Hash.new {0}
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+ max_count = 0
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+ mode = nil
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+ data_set.data_items.each do |data_item|
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+ attr_value = data_item[index]
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+ attr_count = (count[attr_value] += 1)
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+ if attr_count > max_count
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+ mode = attr_value
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+ max_count = attr_count
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+ end
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+ end
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+ return mode
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+ end
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+
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+ # Get the maximum value of an attribute in the data set
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+ def self.max(data_set, attribute)
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+ index = data_set.get_index(attribute)
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+ item = data_set.data_items.max {|x,y| x[index] <=> y[index]}
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+ return (item) ? item[index] : (-1.0/0)
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+ end
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+
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+ # Get the minimum value of an attribute in the data set
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+ def self.min(data_set, attribute)
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+ index = data_set.get_index(attribute)
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+ item = data_set.data_items.min {|x,y| x[index] <=> y[index]}
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+ return (item) ? item[index] : (1.0/0)
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+ end
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+
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+ end
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+ end
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+ end
data/lib/ai4r/experiment/classifier_evaluator.rb ADDED
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+ require 'benchmark'
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+ require File.dirname(__FILE__) + '/../data/data_set'
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+
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+
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+ module Ai4r
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+
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+ module Experiment
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+
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+ # The ClassifierEvaluator is useful to compare different classifiers
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+ # algorithms. The evaluator builds the Classifiers using the same data
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+ # examples, and provides methods to evalute their performance in parallel.
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+ # It is a nice tool to compare and evaluate the performance of different
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+ # algorithms, the same algorithm with different parameters, or your own new
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+ # algorithm against the classic classifiers.
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+ class ClassifierEvaluator
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+
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+ attr_reader :build_times, :eval_times, :classifiers
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+
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+ def initialize
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+ @classifiers = []
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+ end
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+
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+ # Add a classifier instance to the test batch
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+ def add_classifier(classifier)
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+ @classifiers << classifier
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+ return self
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+ end
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+
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+ alias :<< :add_classifier
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+
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+ # Build all classifiers, using data examples found in data_set.
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+ # The last attribute of each item is considered as the
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+ # item class.
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+ # Building times are measured by separate, and can be accessed
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+ # through build_times attribute reader.
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+ def build(data_set)
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+ @build_times = []
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+ @classifiers.each do |classifier|
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+ @build_times << Benchmark.measure { classifier.build data_set }
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+ end
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+ return self
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+ end
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+
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+ # You can evaluate new data, predicting its class.
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+ # e.g.
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+ # classifier.eval(['New York', '<30', 'F'])
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+ # => ['Y', 'Y', 'Y', 'N', 'Y', 'Y', 'N']
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+ # Evaluation times are measured by separate, and can be accessed
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+ # through eval_times attribute reader.
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+ def eval(data)
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+ @eval_times = []
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+ results = []
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+ @classifiers.each do |classifier|
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+ @eval_times << Benchmark.measure { results << classifier.eval(data) }
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+ end
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+ return results
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+ end
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+
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+ # Test classifiers using a data set. The last attribute of each item
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+ # is considered as the expected class. Data items are evaluated
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+ # using all classifiers: evalution times, sucess rate, and quantity of
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+ # classification errors are returned in a data set.
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+ # The return data set has a row for every classifier tested, and the
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+ # following attributes:
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+ # ["Classifier", "Testing Time", "Errors", "Success rate"]
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+ def test(data_set)
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+ result_data_items = []
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+ @classifiers.each do |classifier|
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+ result_data_items << test_classifier(classifier, data_set)
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+ end
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+ return Ai4r::Data::DataSet.new(:data_items => result_data_items,
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+ :data_labels => ["Classifier","Testing Time","Errors","Success rate"])
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+ end
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+
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+ private
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+ def test_classifier(classifier, data_set)
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+ data_set_size = data_set.data_items.length
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+ errors = 0
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+ testing_times = Benchmark.measure do
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+ data_set.data_items.each do |data_item|
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+ data = data_item[0...-1]
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+ expected_result = data_item.last
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+ result = classifier.eval data
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+ errors += 1 if result != expected_result
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+ end
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+ end
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+ return [classifier, testing_times.real, errors,
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+ ((data_set_size-errors*1.0)/data_set_size)]
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+ end
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+
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+ end
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+
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+ end
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+
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+ end
data/lib/ai4r/genetic_algorithm/genetic_algorithm.rb CHANGED
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- #
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  # Author:: Sergio Fierens
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  # License:: MPL 1.1
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  # Project:: ai4r
@@ -7,7 +6,6 @@
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  # You can redistribute it and/or modify it under the terms of
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  # the Mozilla Public License version 1.1 as published by the
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  # Mozilla Foundation at http://www.mozilla.org/MPL/MPL-1.1.txt
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-
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  module Ai4r
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  # The GeneticAlgorithm module implements the GeneticSearch and Chromosome
@@ -15,10 +13,10 @@ module Ai4r
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  # any kind of problems. The GeneticSearch class performs a stochastic search
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  # of the solution of a given problem.
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  #
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- # The Chromosome is "problem specific". Ai4r built-in Chromosomeclass was
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+ # The Chromosome is "problem specific". Ai4r built-in Chromosome class was
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  # designed to model the Travelling salesman problem. If you want to solve other
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  # type of problem, you will have to modify the Chromosome class, by overwriting
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- # its fitness, reproduce, and mutate functions, to model you specific problem.
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+ # its fitness, reproduce, and mutate functions, to model your specific problem.
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  module GeneticAlgorithm
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  # This class is used to automatically:
data/site/build/site/en/build/tmp/build-info.xml ADDED
@@ -0,0 +1,5 @@
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+ <project-skin>pelt</project-skin>
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+ </info>
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+ Licensed to the Apache Software Foundation (ASF) under one or more
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+ contributor license agreements. See the NOTICE file distributed with
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+ this work for additional information regarding copyright ownership.
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+ The ASF licenses this file to You under the Apache License, Version 2.0
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+ (the "License"); you may not use this file except in compliance with
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+ the License. You may obtain a copy of the License at
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+
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+ http://www.apache.org/licenses/LICENSE-2.0
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+
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+ Unless required by applicable law or agreed to in writing, software
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+ distributed under the License is distributed on an "AS IS" BASIS,
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+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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+ See the License for the specific language governing permissions and
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+ limitations under the License.
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+ contributor license agreements. See the NOTICE file distributed with
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+ The ASF licenses this file to You under the Apache License, Version 2.0
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+ the License. You may obtain a copy of the License at
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+
10
+ http://www.apache.org/licenses/LICENSE-2.0
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+
12
+ Unless required by applicable law or agreed to in writing, software
13
+ distributed under the License is distributed on an "AS IS" BASIS,
14
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
15
+ See the License for the specific language governing permissions and
16
+ limitations under the License.
17
+ -->
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+ <!DOCTYPE plugins [
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+ <!ENTITY % links.att 'name CDATA #REQUIRED'>
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+ <!ENTITY % link.att 'name CDATA #REQUIRED href CDATA #REQUIRED'>
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+ <!ELEMENT plugins (plugin*)>
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+ <!ATTLIST plugins type CDATA #REQUIRED>
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+ <!ELEMENT plugin (description, forrestVersion)>
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+ <!ATTLIST plugin name CDATA #REQUIRED
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+ type (input|output|internal) #REQUIRED
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+ url CDATA #REQUIRED
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+ author CDATA #REQUIRED
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+ website CDATA #IMPLIED
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+ version CDATA #IMPLIED>
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+ <!ELEMENT description (#PCDATA)>
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+ <!ELEMENT forrestVersion (#PCDATA)>
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+ ]>
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+ <plugins type="whiteboard">
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+ <!-- ================================================================== -->
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+ <!-- Input Plugins -->
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+ <!-- ================================================================== -->
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+ <plugin name="org.apache.forrest.plugin.input.citations"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.citations/"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ List of citations.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.Daisy"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.Daisy/"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Allow content to be included from a Daisy CMS repository.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.doap"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.doap/"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Embed DOAP files in forrest content objects.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.glossary"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.glossary/"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Enable glossary: a list of technical terms and definitions.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.logs"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_70/org.apache.forrest.plugin.input.logs"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Embed log file output in Forrest sites. If Forrest is running in a dynamic
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+ environment, then pages can be updated to show recent changes in the log
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+ whenever required.
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+ </description>
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+ <forrestVersion>0.7</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.odt"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.odt"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Use OpenDocument Writer files (*.odt) as input sources.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.Resume"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.Resume"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Basic support for Resumes, renders a single resume, or alloes sorting of a
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+ number of resumes on skill.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.serverStatus"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.serverStatus"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Provides a list of the Cocoon cache and other server status information.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <!-- ================================================================== -->
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+ <!-- Output Plugins -->
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+ <!-- ================================================================== -->
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+ <plugin name="org.apache.forrest.plugin.output.Anakia"
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+ type="output"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.output.Anakia/"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Produce output in Anakia "xdoc" format.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.output.Chart"
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+ type="output"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_70/org.apache.forrest.plugin.output.Chart"
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+ url="http://forrest.apache.org/plugins/"
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+ version="0.1">
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+ <description>
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+ Charting plugin that utilises JChart.
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+ </description>
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+ <forrestVersion>0.7</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.input.ecs"
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+ type="input"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.input.ecs/"
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+ url="http://forrest.apache.org/plugins"
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+ version="0.1">
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+ <description>
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+ Process responses from Amaozons E-Commerce System web services.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.output.htmlArea"
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+ type="output"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_70/org.apache.forrest.plugin.output.htmlArea"
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+ url="http://forrest.apache.org/plugins/"
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+ version="0.1">
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+ <description>
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+ WYSIWYG editing of HTML documents (requires Forrest to be running
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+ dynamically).
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+ </description>
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+ <forrestVersion>0.7</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.output.voice"
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+ type="output"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.output.voice"
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+ url="http://forrest.apache.org/plugins/"
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+ version="0.1">
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+ <description>
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+ Add voiceXML content to a Forrest page. This allows the page to be read by
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+ a voice synthesiser and navigated with voice commands.
185
+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.plugin.output.solr"
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+ type="output"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.output.solr"
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+ url="http://forrest.apache.org/plugins/"
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+ version="0.1">
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+ <description>
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+ Generates solr documents from xdos. Further when run with the dispatcher
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+ it provides a GUI to manage your project in solr and a search interface to
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+ search your solr server.
198
+ </description>
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+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
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+ <plugin name="org.apache.forrest.themes.core"
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+ type="output"
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+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.themes.core"
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+ url="http://forrest.apache.org/plugins/"
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+ version="0.1">
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+ <description>
208
+ The core theme package for the dispatcher.
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+ </description>
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+ <forrestVersion>0.8</forrestVersion>
211
+ </plugin>
212
+ <!-- ================================================================== -->
213
+ <!-- Internal Plugins -->
214
+ <!-- ================================================================== -->
215
+ <plugin name="org.apache.forrest.plugin.internal.IMSManifest"
216
+ type="internal"
217
+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_70/org.apache.forrest.plugin.internal.IMSManifest"
219
+ url="http://forrest.apache.org/plugins/"
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+ version="0.1">
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+ <description>
222
+ Use an IMS Manifest file to manage site structure. Generates site.xml and
223
+ tabs.xml from an imsmanifest.xml file when one is available. Also enables
224
+ content in one Content Package to be embedded in another.
225
+ </description>
226
+ <forrestVersion>0.7</forrestVersion>
227
+ </plugin>
228
+ <plugin name="org.apache.forrest.plugin.internal.NoteTaking"
229
+ type="internal"
230
+ author="Apache Forrest Project"
231
+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.NoteTaking"
232
+ url="http://forrest.apache.org/plugins/"
233
+ version="0.1">
234
+ <description>
235
+ Provides facilities for adding notes to pages when Forrest is run in
236
+ dynamic mode.
237
+ </description>
238
+ <forrestVersion>0.8</forrestVersion>
239
+ </plugin>
240
+ <plugin name="org.apache.forrest.plugin.internal.dispatcher"
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+ type="internal"
242
+ author="Apache Forrest Project"
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+ website="http://forrest.apache.org/pluginDocs/plugins_0_80/org.apache.forrest.plugin.internal.dispatcher"
244
+ url="http://forrest.apache.org/plugins/"
245
+ version="0.1">
246
+ <description>
247
+ Enable Forrest to use page-specific views and contracts. Next generation
248
+ skinning.
249
+ </description>
250
+ <forrestVersion>0.8</forrestVersion>
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+ </plugin>
252
+ </plugins>