nimbus 1.0.1 → 2.0.0
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- data/README.md +149 -0
- data/lib/nimbus.rb +15 -11
- data/lib/nimbus/application.rb +20 -23
- data/lib/nimbus/classification_tree.rb +111 -0
- data/lib/nimbus/configuration.rb +52 -37
- data/lib/nimbus/forest.rb +56 -20
- data/lib/nimbus/individual.rb +7 -7
- data/lib/nimbus/loss_functions.rb +44 -10
- data/lib/nimbus/regression_tree.rb +103 -0
- data/lib/nimbus/training_set.rb +4 -4
- data/lib/nimbus/tree.rb +20 -83
- data/lib/nimbus/version.rb +3 -0
- data/spec/classification_tree_spec.rb +132 -0
- data/spec/configuration_spec.rb +46 -19
- data/spec/fixtures/classification_config.yml +13 -0
- data/spec/fixtures/classification_random_forest.yml +922 -0
- data/spec/fixtures/classification_testing.data +500 -0
- data/spec/fixtures/classification_training.data +1000 -0
- data/spec/forest_spec.rb +109 -50
- data/spec/individual_spec.rb +2 -2
- data/spec/loss_functions_spec.rb +71 -0
- data/spec/nimbus_spec.rb +4 -4
- data/spec/regression_tree_spec.rb +129 -0
- data/spec/training_set_spec.rb +5 -5
- data/spec/tree_spec.rb +4 -115
- metadata +53 -45
- data/spec/fixtures/regression_snp_importances.txt +0 -200
- data/spec/fixtures/regression_testing_file_predictions.txt +0 -200
- data/spec/fixtures/regression_training_file_predictions.txt +0 -758
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#Input files
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input:
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training: classification_training.data
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testing: classification_testing.data
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forest: classification_random_forest.yml
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classes: [0,1]
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#Forest parameters
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forest:
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forest_size: 3 #how many trees
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SNP_sample_size_mtry: 33 #mtry
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SNP_total_count: 100
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node_min_size: 5
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- 4:
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|
748
|
+
- '0'
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749
|
+
- '0'
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|
750
|
+
- '1'
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751
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+
- '0'
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752
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- '1'
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753
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- '1'
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754
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- 1:
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755
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- '1'
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756
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- '0'
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757
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- '1'
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758
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- 97:
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759
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- 36:
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760
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- 75:
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761
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- '1'
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762
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- '0'
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763
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- '1'
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764
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- 48:
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765
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- 20:
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766
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- '0'
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767
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- '1'
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768
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- '0'
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769
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- '1'
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770
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- 47:
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771
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- '0'
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772
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- '1'
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773
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- '0'
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774
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- '1'
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775
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- 46:
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776
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- 21:
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777
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- '0'
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778
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- '1'
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779
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+
- '1'
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780
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- 45:
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|
781
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- '1'
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782
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- '1'
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783
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+
- '0'
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784
|
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- 31:
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|
785
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- '0'
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786
|
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- '1'
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787
|
+
- '0'
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788
|
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- 93:
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|
789
|
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- 5:
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790
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- '0'
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791
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- '1'
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792
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- '0'
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793
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- 4:
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|
794
|
+
- '0'
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795
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- '1'
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796
|
+
- '0'
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797
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- 5:
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|
798
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- '1'
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- '1'
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800
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- '1'
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801
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- 71:
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|
802
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- 21:
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803
|
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- 20:
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804
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- '1'
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805
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- '0'
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806
|
+
- '1'
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807
|
+
- '1'
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808
|
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- 92:
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|
809
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- '0'
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810
|
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- '0'
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811
|
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- '1'
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812
|
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- 78:
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|
813
|
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- 56:
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814
|
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- '1'
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815
|
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- 16:
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|
816
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- '1'
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817
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818
|
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- '1'
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819
|
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- '0'
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|
820
|
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- 30:
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|
821
|
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- '0'
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822
|
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- '0'
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|
823
|
+
- '1'
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|
824
|
+
- 40:
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|
825
|
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- '1'
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|
826
|
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- 6:
|
|
827
|
+
- '0'
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|
828
|
+
- '0'
|
|
829
|
+
- '1'
|
|
830
|
+
- '0'
|
|
831
|
+
- 60:
|
|
832
|
+
- '0'
|
|
833
|
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- 65:
|
|
834
|
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- '0'
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835
|
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- '1'
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|
836
|
+
- '1'
|
|
837
|
+
- 3:
|
|
838
|
+
- '0'
|
|
839
|
+
- '0'
|
|
840
|
+
- '1'
|
|
841
|
+
- 98:
|
|
842
|
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- 9:
|
|
843
|
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- '1'
|
|
844
|
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- 99:
|
|
845
|
+
- '1'
|
|
846
|
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- 25:
|
|
847
|
+
- '1'
|
|
848
|
+
- '0'
|
|
849
|
+
- '1'
|
|
850
|
+
- 17:
|
|
851
|
+
- '0'
|
|
852
|
+
- '0'
|
|
853
|
+
- '1'
|
|
854
|
+
- 61:
|
|
855
|
+
- 18:
|
|
856
|
+
- '0'
|
|
857
|
+
- '1'
|
|
858
|
+
- '1'
|
|
859
|
+
- '1'
|
|
860
|
+
- 21:
|
|
861
|
+
- '1'
|
|
862
|
+
- '1'
|
|
863
|
+
- '1'
|
|
864
|
+
- 3:
|
|
865
|
+
- 1:
|
|
866
|
+
- '1'
|
|
867
|
+
- '1'
|
|
868
|
+
- '1'
|
|
869
|
+
- 52:
|
|
870
|
+
- '1'
|
|
871
|
+
- 7:
|
|
872
|
+
- '0'
|
|
873
|
+
- '1'
|
|
874
|
+
- '0'
|
|
875
|
+
- 21:
|
|
876
|
+
- 13:
|
|
877
|
+
- '0'
|
|
878
|
+
- '1'
|
|
879
|
+
- '0'
|
|
880
|
+
- '1'
|
|
881
|
+
- '0'
|
|
882
|
+
- 71:
|
|
883
|
+
- '1'
|
|
884
|
+
- 17:
|
|
885
|
+
- '0'
|
|
886
|
+
- '0'
|
|
887
|
+
- '1'
|
|
888
|
+
- 27:
|
|
889
|
+
- '1'
|
|
890
|
+
- '0'
|
|
891
|
+
- '1'
|
|
892
|
+
- 31:
|
|
893
|
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- 35:
|
|
894
|
+
- 6:
|
|
895
|
+
- '1'
|
|
896
|
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- '0'
|
|
897
|
+
- '1'
|
|
898
|
+
- 14:
|
|
899
|
+
- '1'
|
|
900
|
+
- '0'
|
|
901
|
+
- 100:
|
|
902
|
+
- '0'
|
|
903
|
+
- '1'
|
|
904
|
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- '0'
|
|
905
|
+
- '0'
|
|
906
|
+
- 39:
|
|
907
|
+
- 32:
|
|
908
|
+
- '0'
|
|
909
|
+
- '1'
|
|
910
|
+
- '0'
|
|
911
|
+
- 37:
|
|
912
|
+
- '0'
|
|
913
|
+
- '0'
|
|
914
|
+
- '1'
|
|
915
|
+
- '1'
|
|
916
|
+
- 18:
|
|
917
|
+
- '0'
|
|
918
|
+
- '1'
|
|
919
|
+
- 4:
|
|
920
|
+
- '1'
|
|
921
|
+
- '0'
|
|
922
|
+
- '1'
|