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

lazar 0.9.3 → 1.0.0

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 (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/CPDBAS_v5d_cleaned/CPDBAS_v5d_20Nov2008_mouse_TD50.csv DELETED Viewed

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