nimbus 1.0.1 → 2.0.0

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Files changed (29) hide show
  1. data/README.md +149 -0
  2. data/lib/nimbus.rb +15 -11
  3. data/lib/nimbus/application.rb +20 -23
  4. data/lib/nimbus/classification_tree.rb +111 -0
  5. data/lib/nimbus/configuration.rb +52 -37
  6. data/lib/nimbus/forest.rb +56 -20
  7. data/lib/nimbus/individual.rb +7 -7
  8. data/lib/nimbus/loss_functions.rb +44 -10
  9. data/lib/nimbus/regression_tree.rb +103 -0
  10. data/lib/nimbus/training_set.rb +4 -4
  11. data/lib/nimbus/tree.rb +20 -83
  12. data/lib/nimbus/version.rb +3 -0
  13. data/spec/classification_tree_spec.rb +132 -0
  14. data/spec/configuration_spec.rb +46 -19
  15. data/spec/fixtures/classification_config.yml +13 -0
  16. data/spec/fixtures/classification_random_forest.yml +922 -0
  17. data/spec/fixtures/classification_testing.data +500 -0
  18. data/spec/fixtures/classification_training.data +1000 -0
  19. data/spec/forest_spec.rb +109 -50
  20. data/spec/individual_spec.rb +2 -2
  21. data/spec/loss_functions_spec.rb +71 -0
  22. data/spec/nimbus_spec.rb +4 -4
  23. data/spec/regression_tree_spec.rb +129 -0
  24. data/spec/training_set_spec.rb +5 -5
  25. data/spec/tree_spec.rb +4 -115
  26. metadata +53 -45
  27. data/spec/fixtures/regression_snp_importances.txt +0 -200
  28. data/spec/fixtures/regression_testing_file_predictions.txt +0 -200
  29. data/spec/fixtures/regression_training_file_predictions.txt +0 -758
metadata CHANGED
@@ -1,105 +1,113 @@
1
- --- !ruby/object:Gem::Specification
1
+ --- !ruby/object:Gem::Specification
2
2
  name: nimbus
3
- version: !ruby/object:Gem::Version
3
+ version: !ruby/object:Gem::Version
4
+ version: 2.0.0
4
5
  prerelease:
5
- version: 1.0.1
6
6
  platform: ruby
7
- authors:
8
- - "Juanjo Baz\xC3\xA1n"
9
- - "Oscar Gonz\xC3\xA1lez Recio"
7
+ authors:
8
+ - Juanjo Bazán
9
+ - Oscar González Recio
10
10
  autorequire:
11
11
  bindir: bin
12
12
  cert_chain: []
13
-
14
- date: 2011-08-25 00:00:00 Z
15
- dependencies:
16
- - !ruby/object:Gem::Dependency
13
+ date: 2012-07-26 00:00:00.000000000 Z
14
+ dependencies:
15
+ - !ruby/object:Gem::Dependency
17
16
  name: rspec
18
- prerelease: false
19
- requirement: &id001 !ruby/object:Gem::Requirement
17
+ requirement: &2156549180 !ruby/object:Gem::Requirement
20
18
  none: false
21
- requirements:
22
- - - ">="
23
- - !ruby/object:Gem::Version
24
- version: 2.5.0
19
+ requirements:
20
+ - - ! '>='
21
+ - !ruby/object:Gem::Version
22
+ version: 2.11.0
25
23
  type: :development
26
- version_requirements: *id001
27
- description: Nimbus is a Ruby gem to implement Random Forest in a genomic selection context.
28
- email:
24
+ prerelease: false
25
+ version_requirements: *2156549180
26
+ description: Nimbus is a Ruby gem to implement Random Forest in a genomic selection
27
+ context.
28
+ email:
29
29
  - jjbazan@gmail.com
30
- executables:
30
+ executables:
31
31
  - nimbus
32
32
  extensions: []
33
-
34
33
  extra_rdoc_files: []
35
-
36
- files:
34
+ files:
37
35
  - MIT-LICENSE.txt
36
+ - README.md
38
37
  - lib/nimbus/application.rb
38
+ - lib/nimbus/classification_tree.rb
39
39
  - lib/nimbus/configuration.rb
40
40
  - lib/nimbus/exceptions.rb
41
41
  - lib/nimbus/forest.rb
42
42
  - lib/nimbus/individual.rb
43
43
  - lib/nimbus/loss_functions.rb
44
+ - lib/nimbus/regression_tree.rb
44
45
  - lib/nimbus/training_set.rb
45
46
  - lib/nimbus/tree.rb
47
+ - lib/nimbus/version.rb
46
48
  - lib/nimbus.rb
49
+ - spec/classification_tree_spec.rb
47
50
  - spec/configuration_spec.rb
51
+ - spec/fixtures/classification_config.yml
52
+ - spec/fixtures/classification_random_forest.yml
53
+ - spec/fixtures/classification_testing.data
54
+ - spec/fixtures/classification_training.data
48
55
  - spec/fixtures/regression_config.yml
49
56
  - spec/fixtures/regression_random_forest.yml
50
- - spec/fixtures/regression_snp_importances.txt
51
57
  - spec/fixtures/regression_testing.data
52
- - spec/fixtures/regression_testing_file_predictions.txt
53
58
  - spec/fixtures/regression_training.data
54
- - spec/fixtures/regression_training_file_predictions.txt
55
59
  - spec/forest_spec.rb
56
60
  - spec/individual_spec.rb
61
+ - spec/loss_functions_spec.rb
57
62
  - spec/nimbus_spec.rb
63
+ - spec/regression_tree_spec.rb
58
64
  - spec/spec_helper.rb
59
65
  - spec/training_set_spec.rb
60
66
  - spec/tree_spec.rb
61
67
  - bin/nimbus
62
68
  homepage: http://nimbusgem.org
63
69
  licenses: []
64
-
65
70
  post_install_message:
66
- rdoc_options:
71
+ rdoc_options:
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72
  - --main
68
73
  - README.rdoc
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74
  - --charset=UTF-8
70
- require_paths:
75
+ require_paths:
71
76
  - lib
72
- required_ruby_version: !ruby/object:Gem::Requirement
77
+ required_ruby_version: !ruby/object:Gem::Requirement
73
78
  none: false
74
- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: "0"
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- required_rubygems_version: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  requirements: []
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-
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90
  rubyforge_project:
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- rubygems_version: 1.8.6
91
+ rubygems_version: 1.8.15
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92
  signing_key:
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  specification_version: 3
90
94
  summary: Random Forest algorithm for Genomics
91
- test_files:
95
+ test_files:
96
+ - spec/classification_tree_spec.rb
92
97
  - spec/configuration_spec.rb
98
+ - spec/fixtures/classification_config.yml
99
+ - spec/fixtures/classification_random_forest.yml
100
+ - spec/fixtures/classification_testing.data
101
+ - spec/fixtures/classification_training.data
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102
  - spec/fixtures/regression_config.yml
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103
  - spec/fixtures/regression_random_forest.yml
95
- - spec/fixtures/regression_snp_importances.txt
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104
  - spec/fixtures/regression_testing.data
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- - spec/fixtures/regression_testing_file_predictions.txt
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  - spec/fixtures/regression_training.data
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- - spec/fixtures/regression_training_file_predictions.txt
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  - spec/forest_spec.rb
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  - spec/individual_spec.rb
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+ - spec/loss_functions_spec.rb
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  - spec/nimbus_spec.rb
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+ - spec/regression_tree_spec.rb
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111
  - spec/spec_helper.rb
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112
  - spec/training_set_spec.rb
105
113
  - spec/tree_spec.rb
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