RubyGems - lazar - Versions diffs - 0.9.3 → 1.0.0 - Mend

lazar 0.9.3 → 1.0.0

Files changed (88) hide show

checksums.yaml +4 -4
data/.gitignore +1 -4
data/README.md +5 -15
data/VERSION +1 -1
data/ext/lazar/extconf.rb +1 -1
data/ext/lazar/rinstall.R +9 -7
data/java/CdkDescriptorInfo.class +0 -0
data/java/CdkDescriptorInfo.java +3 -2
data/java/CdkDescriptors.class +0 -0
data/java/CdkDescriptors.java +28 -28
data/java/Rakefile +3 -3
data/java/{cdk-1.4.19.jar → cdk-2.0-SNAPSHOT.jar} +0 -0
data/lazar.gemspec +6 -7
data/lib/algorithm.rb +2 -11
data/lib/caret.rb +96 -0
data/lib/classification.rb +14 -22
data/lib/compound.rb +21 -87
data/lib/crossvalidation.rb +80 -279
data/lib/dataset.rb +105 -174
data/lib/feature.rb +11 -18
data/lib/feature_selection.rb +42 -0
data/lib/import.rb +122 -0
data/lib/lazar.rb +14 -4
data/lib/leave-one-out-validation.rb +46 -192
data/lib/model.rb +319 -128
data/lib/nanoparticle.rb +98 -0
data/lib/opentox.rb +7 -4
data/lib/overwrite.rb +24 -3
data/lib/physchem.rb +11 -10
data/lib/regression.rb +7 -137
data/lib/rest-client-wrapper.rb +0 -6
data/lib/similarity.rb +65 -0
data/lib/substance.rb +8 -0
data/lib/train-test-validation.rb +69 -0
data/lib/validation-statistics.rb +223 -0
data/lib/validation.rb +17 -100
data/scripts/mg2mmol.rb +17 -0
data/scripts/mirror-enm2test.rb +4 -0
data/scripts/mmol2-log10.rb +32 -0
data/test/compound.rb +4 -94
data/test/data/EPAFHM.medi_log10.csv +92 -0
data/test/data/EPAFHM.mini_log10.csv +16 -0
data/test/data/EPAFHM_log10.csv +581 -0
data/test/data/loael_log10.csv +568 -0
data/test/dataset.rb +195 -133
data/test/descriptor.rb +27 -18
data/test/error.rb +2 -2
data/test/experiment.rb +4 -4
data/test/feature.rb +2 -3
data/test/gridfs.rb +10 -0
data/test/model-classification.rb +106 -0
data/test/model-nanoparticle.rb +128 -0
data/test/model-regression.rb +171 -0
data/test/model-validation.rb +19 -0
data/test/nanomaterial-model-validation.rb +55 -0
data/test/setup.rb +8 -4
data/test/validation-classification.rb +67 -0
data/test/validation-nanoparticle.rb +133 -0
data/test/validation-regression.rb +92 -0
metadata +50 -121
data/test/classification.rb +0 -41
data/test/data/CPDBAS_v5c_1547_29Apr2008part.sdf +0 -13553
data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv +0 -436
data/test/data/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_rat_TD50.csv +0 -568
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Hamster.csv +0 -87
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mouse.csv +0 -978
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall.csv +0 -1120
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_MultiCellCall_no_duplicates.csv +0 -1113
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity.csv +0 -850
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Mutagenicity_no_duplicates.csv +0 -829
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_Rat.csv +0 -1198
data/test/data/CPDBAS_v5d_cleaned/DSSTox_Carcinogenic_Potency_DBS_SingleCellCall.csv +0 -1505
data/test/data/EPA_v4b_Fathead_Minnow_Acute_Toxicity_LC50_mmol.csv +0 -581
data/test/data/FDA_v3b_Maximum_Recommended_Daily_Dose_mmol.csv +0 -1217
data/test/data/LOAEL_log_mg_corrected_smiles.csv +0 -568
data/test/data/LOAEL_log_mmol_corrected_smiles.csv +0 -568
data/test/data/boiling_points.ext.sdf +0 -11460
data/test/data/cpdb_100.csv +0 -101
data/test/data/hamster_carcinogenicity.ntriples +0 -618
data/test/data/hamster_carcinogenicity.sdf +0 -2805
data/test/data/hamster_carcinogenicity.xls +0 -0
data/test/data/hamster_carcinogenicity.yaml +0 -352
data/test/dataset-long.rb +0 -114
data/test/lazar-long.rb +0 -92
data/test/lazar-physchem-short.rb +0 -31
data/test/prediction_models.rb +0 -20
data/test/regression.rb +0 -43
data/test/validation.rb +0 -108

data/test/data/loael_log10.csv ADDED Viewed

@@ -0,0 +1,568 @@
+SMILES,-log10(LOAEL)
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+CO[C@H]1C[C@H](O[C@H]2[C@@H](C)C=CC=C3CO[C@H]4[C@]3(O)[C@@H](C=C([C@H]4O)C)C(=O)O[C@H]3C[C@@H](CC=C2C)O[C@]2(C3)C=C[C@@H]([C@H](O2)[C@H](CC)C)C)O[C@H]([C@@H]1O[C@H]1C[C@H](OC)[C@H]([C@@H](O1)C)O)C,2.6400224921305777
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+Clc1nc(nc(n1)Cl)Nc1ccccc1Cl,2.3794581267004147
+Clc1cccc(n1)C(Cl)(Cl)Cl,2.363436572226187
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