nimbus 1.0.1 → 2.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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:
67
72
  - --main
68
73
  - README.rdoc
69
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:
75
- - - ">="
76
- - !ruby/object:Gem::Version
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- version: "0"
78
- 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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89
  requirements: []
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-
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  rubyforge_project:
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- rubygems_version: 1.8.6
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+ 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
93
102
  - spec/fixtures/regression_config.yml
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103
  - spec/fixtures/regression_random_forest.yml
95
- - spec/fixtures/regression_snp_importances.txt
96
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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106
  - 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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109
  - 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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