lazar 0.9.3 → 1.0.0

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Files changed (88) hide show
  1. checksums.yaml +4 -4
  2. data/.gitignore +1 -4
  3. data/README.md +5 -15
  4. data/VERSION +1 -1
  5. data/ext/lazar/extconf.rb +1 -1
  6. data/ext/lazar/rinstall.R +9 -7
  7. data/java/CdkDescriptorInfo.class +0 -0
  8. data/java/CdkDescriptorInfo.java +3 -2
  9. data/java/CdkDescriptors.class +0 -0
  10. data/java/CdkDescriptors.java +28 -28
  11. data/java/Rakefile +3 -3
  12. data/java/{cdk-1.4.19.jar → cdk-2.0-SNAPSHOT.jar} +0 -0
  13. data/lazar.gemspec +6 -7
  14. data/lib/algorithm.rb +2 -11
  15. data/lib/caret.rb +96 -0
  16. data/lib/classification.rb +14 -22
  17. data/lib/compound.rb +21 -87
  18. data/lib/crossvalidation.rb +80 -279
  19. data/lib/dataset.rb +105 -174
  20. data/lib/feature.rb +11 -18
  21. data/lib/feature_selection.rb +42 -0
  22. data/lib/import.rb +122 -0
  23. data/lib/lazar.rb +14 -4
  24. data/lib/leave-one-out-validation.rb +46 -192
  25. data/lib/model.rb +319 -128
  26. data/lib/nanoparticle.rb +98 -0
  27. data/lib/opentox.rb +7 -4
  28. data/lib/overwrite.rb +24 -3
  29. data/lib/physchem.rb +11 -10
  30. data/lib/regression.rb +7 -137
  31. data/lib/rest-client-wrapper.rb +0 -6
  32. data/lib/similarity.rb +65 -0
  33. data/lib/substance.rb +8 -0
  34. data/lib/train-test-validation.rb +69 -0
  35. data/lib/validation-statistics.rb +223 -0
  36. data/lib/validation.rb +17 -100
  37. data/scripts/mg2mmol.rb +17 -0
  38. data/scripts/mirror-enm2test.rb +4 -0
  39. data/scripts/mmol2-log10.rb +32 -0
  40. data/test/compound.rb +4 -94
  41. data/test/data/EPAFHM.medi_log10.csv +92 -0
  42. data/test/data/EPAFHM.mini_log10.csv +16 -0
  43. data/test/data/EPAFHM_log10.csv +581 -0
  44. data/test/data/loael_log10.csv +568 -0
  45. data/test/dataset.rb +195 -133
  46. data/test/descriptor.rb +27 -18
  47. data/test/error.rb +2 -2
  48. data/test/experiment.rb +4 -4
  49. data/test/feature.rb +2 -3
  50. data/test/gridfs.rb +10 -0
  51. data/test/model-classification.rb +106 -0
  52. data/test/model-nanoparticle.rb +128 -0
  53. data/test/model-regression.rb +171 -0
  54. data/test/model-validation.rb +19 -0
  55. data/test/nanomaterial-model-validation.rb +55 -0
  56. data/test/setup.rb +8 -4
  57. data/test/validation-classification.rb +67 -0
  58. data/test/validation-nanoparticle.rb +133 -0
  59. data/test/validation-regression.rb +92 -0
  60. metadata +50 -121
  61. data/test/classification.rb +0 -41
  62. data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +0 -13553
  63. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +0 -436
  64. data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +0 -568
  65. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +0 -87
  66. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +0 -978
  67. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +0 -1120
  68. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +0 -1113
  69. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +0 -850
  70. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +0 -829
  71. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +0 -1198
  72. data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +0 -1505
  73. data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +0 -581
  74. data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +0 -1217
  75. data/test/data/LOAEL_log_mg_corrected_smiles.csv +0 -568
  76. data/test/data/LOAEL_log_mmol_corrected_smiles.csv +0 -568
  77. data/test/data/boiling_points.ext.sdf +0 -11460
  78. data/test/data/cpdb_100.csv +0 -101
  79. data/test/data/hamster_carcinogenicity.ntriples +0 -618
  80. data/test/data/hamster_carcinogenicity.sdf +0 -2805
  81. data/test/data/hamster_carcinogenicity.xls +0 -0
  82. data/test/data/hamster_carcinogenicity.yaml +0 -352
  83. data/test/dataset-long.rb +0 -114
  84. data/test/lazar-long.rb +0 -92
  85. data/test/lazar-physchem-short.rb +0 -31
  86. data/test/prediction_models.rb +0 -20
  87. data/test/regression.rb +0 -43
  88. data/test/validation.rb +0 -108

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