├── .github └── workflows │ └── tests.yml ├── .gitignore ├── .readthedocs.yaml ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── conf.py ├── image │ ├── abic_lingam1.svg │ ├── bootstrap_dag.svg │ ├── bootstrap_hist.png │ ├── bootstrap_with_imputation.png │ ├── bootstrap_with_imputation.svg │ ├── bottom_up_parce.svg │ ├── bottom_up_parce2.svg │ ├── bottom_up_parce_hist.png │ ├── camuvexmpl.png │ ├── dag.png │ ├── datageneration_CAMUV.png │ ├── draw_graph1.svg │ ├── draw_graph10.svg │ ├── draw_graph11.svg │ ├── draw_graph12.svg │ ├── draw_graph13.svg │ ├── draw_graph14.svg │ ├── draw_graph2.svg │ ├── draw_graph3.svg │ ├── draw_graph4.svg │ ├── draw_graph5.svg │ ├── draw_graph6.svg │ ├── draw_graph7.svg │ ├── draw_graph8.svg │ ├── draw_graph9.svg │ ├── extract_ancestors.svg │ ├── f_correlation1.png │ ├── f_correlation2.png │ ├── f_correlation3.png │ ├── f_correlation4.png │ ├── group_direct_lingam.svg │ ├── group_direct_lingam2.svg │ ├── group_direct_lingam3.png │ ├── group_lingam.svg │ ├── group_lingam2.svg │ ├── group_lingam3.svg │ ├── group_lingam4.png │ ├── high_dim.svg │ ├── high_dim2.svg │ ├── lingam1.svg │ ├── lingam2.svg │ ├── longitudinal_dag1.svg │ ├── longitudinal_dag2.svg │ ├── longitudinal_dag3.svg │ ├── longitudinal_hist.png │ ├── longitudinal_scatter1.png │ ├── longitudinal_scatter2.png │ ├── multi_camuv1.svg │ ├── multi_camuv2.svg │ ├── multi_camuv3.svg │ ├── multi_rcd_dag1.svg │ ├── multi_rcd_dag2.svg │ ├── multi_rcd_dag3.svg │ ├── multi_rcd_dag4.svg │ ├── multi_rcd_dag5.svg │ ├── multi_resit1.svg │ ├── multiple_dataset_dag1.svg │ ├── multiple_dataset_dag2.svg │ ├── multiple_dataset_dag3.svg │ ├── multiple_dataset_dag4.svg │ ├── multiple_dataset_dag5.svg │ ├── multiple_dataset_hist.png │ ├── nan_reason.png │ ├── pk_directlingam1.svg │ ├── pk_directlingam2.svg │ ├── pk_directlingam3.svg │ ├── pk_directlingam4.svg │ ├── pk_parcelingam1.svg │ ├── pk_parcelingam2.svg │ ├── pk_parcelingam3.svg │ ├── pk_parcelingam4.svg │ ├── pk_resit1.svg │ ├── pk_resit2.svg │ ├── pk_resit3.svg │ ├── pk_resit4.svg │ ├── rcd_dag1.svg │ ├── rcd_dag2.svg │ ├── rcd_hist.png │ ├── resit_dag1.svg │ ├── resit_dag2.svg │ ├── var_dag.svg │ ├── var_hist.png │ ├── varma_dag.svg │ ├── varma_hist.png │ ├── visualize_nonlinear_causal_effect1.svg │ └── visualize_nonlinear_causal_effect2.svg ├── index.rst ├── installation.rst ├── make.bat ├── reference │ ├── abic_lingam.rst │ ├── bootstrap.rst │ ├── bottom_up_parce_lingam.rst │ ├── camuv.rst │ ├── causal_effect.rst │ ├── direct_lingam.rst │ ├── group_direct_lingam.rst │ ├── group_lingam.rst │ ├── high_dim_direct_lingam.rst │ ├── ica_lingam.rst │ ├── index.rst │ ├── lim.rst │ ├── lina.rst │ ├── longitudinal_bootstrap.rst │ ├── longitudinal_lingam.rst │ ├── missingness_lingam.rst │ ├── multi_group_camuv.rst │ ├── multi_group_direct_lingam.rst │ ├── multi_group_rcd.rst │ ├── multi_group_resit.rst │ ├── rcd.rst │ ├── resit.rst │ ├── tools.rst │ ├── utils.rst │ ├── var_bootstrap.rst │ ├── var_lingam.rst │ ├── varma_bootstrap.rst │ └── varma_lingam.rst ├── requirements-doc.txt └── tutorial │ ├── abic_lingam.rst │ ├── bootstrap.rst │ ├── bootstrap_with_imputation.rst │ ├── bottom_up_parce.rst │ ├── camuv.rst │ ├── causal_effect.rst │ ├── draw_graph.rst │ ├── evaluate_model_fit.rst │ ├── extract_ancestors.rst │ ├── f_correlation.rst │ ├── group_direct_lingam.rst │ ├── group_lingam.rst │ ├── high_dim_direct_lingam.rst │ ├── index.rst │ ├── lim.rst │ ├── lina.rst │ ├── lingam.rst │ ├── longitudinal.rst │ ├── missingness_lingam.rst │ ├── multi_group_camuv.rst │ ├── multi_group_rcd.rst │ ├── multi_group_resit.rst │ ├── multiple_dataset.rst │ ├── pk_bottom_up_parce.rst │ ├── pk_direct.rst │ ├── pk_resit.rst │ ├── rcd.rst │ ├── resit.rst │ ├── total_effect.rst │ ├── var.rst │ ├── varma.rst │ └── visualize_nonlinear_causal_effect.rst ├── examples ├── ABIC-LiNGAM.ipynb ├── Bootstrap.ipynb ├── BootstrapWithImputation.ipynb ├── BottomUpParceLiNGAM.ipynb ├── BottomUpParceLiNGAM_f-correlation.ipynb ├── CAMUV.ipynb ├── CAMUV_f-correlation.ipynb ├── CausalBasedSimulator_estimating_functional_relationships.ipynb ├── CausalBasedSimulator_generating_simulated_data.ipynb ├── CausalBasedSimulator_introduction.ipynb ├── CausalDataGenerator_discrete.ipynb ├── CausalDataGenerator_introduction.ipynb ├── CausalEffect(LassoCV).ipynb ├── CausalEffect(LightGBM).ipynb ├── CausalEffect(LogisticRegression).ipynb ├── CausalEffect.ipynb ├── CommonEdgeAnalysis.ipynb ├── CommonEdgeAnalysisWithMultiGroupModel.ipynb ├── CommonEdgeAnalysisWithVAR-LiNGAM.ipynb ├── DirectLiNGAM(Kernel).ipynb ├── DirectLiNGAM.ipynb ├── DirectLiNGAM_fast.py ├── DrawGraph.ipynb ├── EvaluateModelFit.ipynb ├── Example_to_analyze_clinical_data.ipynb ├── Example_to_handle_groups_of_variables_with_known_causal_orders_btw_the_groups.ipynb ├── Example_to_handle_groups_of_varibles_with_known_causal_orders_btw_the_groups_for_multiple_datasets.ipynb ├── Example_to_perform_RESIT_on_data_with_discrete_variables.ipynb ├── Example_to_perform_causal_discovery_on_data_with_discrete_variables.ipynb ├── Example_to_perform_causal_discovery_using_CAMUV_with_bootstrap_and_imputation_on_data_with_discrete_variables.ipynb ├── Example_to_perform_causal_discovery_using_RCD_with_bootstrap_and_imputation_on_data_with_discrete_variables.ipynb ├── Example_to_perform_causal_discovery_using_RESIT_with_bootstrap_and_imputation_on_data_with_discrete_variables.ipynb ├── Example_to_perform_causal_discovery_using_bootstrap_with_imputation_on_data_with_discrete_variables.ipynb ├── GroupDirectLiNGAM.ipynb ├── GroupLiNGAM.ipynb ├── HighDimDirectLiNGAM.ipynb ├── LongitudinalLiNGAM.ipynb ├── MissingnessLiNGAM.ipynb ├── MultGroupCAMUV.ipynb ├── MultiGroupDirectLiNGAM.ipynb ├── MultiGroupRCD.ipynb ├── MultiGroupRCD_f-correlation.ipynb ├── MultiGroupRESIT.ipynb ├── OutOfSampleCausalTuning.ipynb ├── RCD.ipynb ├── RCD_f-correlation.ipynb ├── RESIT.ipynb ├── TotalEffect.ipynb ├── Use_prior_knowledge_in_BottomUpParceLiNGAM.ipynb ├── Use_prior_knowledge_in_DirectLiNGAM.ipynb ├── Use_prior_knowledge_in_GroupDirectLiNGAM.ipynb ├── Use_prior_knowledge_in_RESIT.ipynb ├── UsingSampleData.ipynb ├── VARLiNGAM.ipynb ├── VARMALiNGAM.ipynb ├── VisualizeNonlinearCausalEffect.ipynb ├── data │ ├── 5vars_longitudinal_t0.csv │ ├── 5vars_longitudinal_t1.csv │ ├── 5vars_longitudinal_t2.csv │ ├── 5vars_var.csv │ ├── 5vars_varma.csv │ ├── 6vars.csv │ ├── 6vars_mid_latent.csv │ ├── 6vars_top_latent.csv │ ├── GenerateDatasets.ipynb │ ├── create_5vars_longitudinal.py │ ├── create_5vars_var.py │ ├── create_5vars_varma.py │ ├── create_6vars.py │ ├── create_6vars_mid_latent.py │ ├── create_6vars_top_latent.py │ ├── nonlinear_data.csv │ ├── sample_data_var_lingam.csv │ └── sample_data_varma_lingam.csv ├── datageneration_CAMUV.png ├── images │ ├── example_to_analyze_data_with_discrete_variables.png │ ├── example_to_analyze_data_with_discrete_variables2.png │ ├── example_to_analyze_data_with_discrete_variables3.png │ ├── example_to_analyze_data_with_discrete_variables4.png │ ├── example_to_analyze_data_with_discrete_variables5.png │ └── example_to_analyze_data_with_discrete_variables6.png └── utils.ipynb ├── lingam ├── __init__.py ├── abic_lingam.py ├── base.py ├── bootstrap.py ├── bottom_up_parce_lingam.py ├── camuv.py ├── causal_based_simulator.py ├── causal_effect.py ├── direct_lingam.py ├── experimental │ ├── __init__.py │ ├── cdg.py │ └── oct.py ├── group_direct_lingam.py ├── group_lingam.py ├── high_dim_direct_lingam.py ├── hsic.py ├── ica_lingam.py ├── lim.py ├── lina.py ├── longitudinal_lingam.py ├── missingness_lingam.py ├── multi_group_camuv.py ├── multi_group_direct_lingam.py ├── multi_group_rcd.py ├── multi_group_resit.py ├── rcd.py ├── resit.py ├── tools │ └── __init__.py ├── utils │ ├── __init__.py │ ├── _common_edge.py │ ├── _f_correlation.py │ ├── _mggd.py │ ├── _rcd.py │ └── _visualize_nonlinear_causal_effect.py ├── var_lingam.py └── varma_lingam.py ├── requirements.txt ├── setup.py └── tests ├── __init__.py ├── test_abic_lingam.py ├── test_bootstrap.py ├── test_bottom_up_parce_lingam.py ├── test_camuv.py ├── test_causal_based_simulator.py ├── test_causal_based_simulator ├── test_run-simulated_data.csv ├── test_run2-simulated_data.csv ├── test_run3-simulated_data.csv ├── test_run4-simulated_data.csv ├── test_run5-simulated_data.csv ├── test_run6-simulated_data.csv ├── test_train2_params.json ├── test_train2_resid.json ├── test_train3_params.json ├── test_train3_resid.json ├── test_train4_params.json ├── test_train4_resid.json ├── test_train_params.json └── test_train_resid.json ├── test_causal_data_generator.py ├── test_causal_effect.py ├── test_direct_lingam.py ├── test_group_direct_lingam.py ├── test_group_lingam.py ├── test_high_dim_direct_lingam.py ├── test_ica_lingam.py ├── test_lim.py ├── test_lim_data.csv ├── test_lina_MIT.py ├── test_lina_data.csv ├── test_longitudinal_lingam.py ├── 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