├── .gitignore ├── AssortativityBias ├── README.md ├── simulation.py ├── stochblock.dat ├── stochblock_groups.dat └── utils.py ├── BridgeComparisonIntro ├── Python │ ├── Chimera │ │ ├── chimera │ │ │ ├── __init__.py │ │ │ ├── fusion_estimator.py │ │ │ ├── utilities.py │ │ │ └── version.py │ │ └── setup.py │ ├── README.md │ ├── actg_analysis.py │ ├── actg_diagnostic.py │ ├── sim_utils.py │ ├── simulations.py │ └── versions.py ├── R │ ├── Chimera.R │ ├── actg_analysis.R │ └── actg_diagnostic.R ├── README.md ├── SAS │ ├── Chimera.sas │ ├── actg_analysis.sas │ ├── actg_diagnostic.sas │ └── permute_tools.sas └── data │ ├── actg_data.csv │ └── actg_data_formatted.csv ├── CausalRNG ├── README.md ├── dgm.py ├── estimator.py ├── generate_data.py ├── nuisance_estimators.py ├── run_iterations.sbatch ├── single_scftmle.py ├── stack_iterations.py ├── summarize.py └── truth.py ├── ConfRegions ├── Case-Studies-Appendix.ipynb ├── Case-Studies.R ├── Case-Studies.ipynb ├── Case-Studies.sas ├── README.md └── data │ ├── actg.csv │ ├── actg_predict_g1000.csv │ └── actg_predict_g50.csv ├── DoubleCrossFit ├── Python │ ├── dgm.py │ ├── estimators.py │ ├── sim_aipw.py │ ├── sim_dcaipw.py │ ├── sim_dctmle.py │ ├── sim_gform.py │ ├── sim_iptw.py │ ├── sim_single_example.py │ ├── sim_tmle.py │ └── super_learner.py ├── R │ ├── desktop.ini │ ├── estimators.R │ └── example.R └── README.md ├── FusedCohortStudies ├── README.md ├── fusion_examples.py └── fusion_examples.sas ├── GCompMSM ├── README.md ├── actg.csv ├── application.R ├── application.py └── application.sas ├── GCompSelection ├── README.md ├── data │ ├── example1.csv │ └── example2.csv ├── examples.Rmd ├── examples.ipynb └── simulations │ ├── dgm.py │ ├── estfun.py │ ├── postprocess.py │ ├── sim_case-study1.py │ └── sim_case-study2.py ├── ImprovedPooledLogit ├── README.md ├── lau.csv ├── pooled_logit.R ├── pooled_logit.py └── pooled_logit.sas ├── M-estimator_ICE ├── README.md ├── applications │ ├── data_example.R │ ├── data_example.py │ ├── data_timed.py │ ├── efuncs.py │ ├── funcs.py │ ├── process_simulation.py │ └── simulation.py └── data │ ├── data_clean.py │ └── data_describe.py ├── MissingDataEpi ├── README.md ├── ipop_missing.R ├── ipop_missing.py └── ipop_missing.sas ├── NeuralNetworkPrimer ├── README.md ├── activations.py ├── application.R ├── application.py └── nhanes.csv ├── PerProtocolBounds ├── README.md ├── data │ ├── actg320.dat │ └── ipop.dat ├── example1.R ├── example1.do ├── example1.py ├── example1.sas ├── example2.R ├── example2.do ├── example2.py └── example2.sas ├── PooledLogitEE ├── Collett.ipynb ├── Lau.ipynb ├── README.md ├── appendix.py ├── data │ ├── collett.dat │ └── lau.csv ├── efuncs.py ├── plots │ ├── collett.py │ ├── lau.py │ └── plotting.py ├── sims │ ├── dgm.py │ ├── estimators.py │ ├── simulation.py │ └── truth.py └── time-trials │ ├── collett.py │ ├── lau.py │ └── standard.py ├── PooledLogitMultinom ├── R │ ├── 01_comparing_approaches.R │ ├── 01a_naive_AJ.R │ ├── 01b_multiple_pooled_logit.R │ ├── 01c_pooled_multinomial_logit.R │ ├── 01d_merge_results.R │ └── 02_applied_example.R ├── README.md └── SAS │ ├── 00_multinomial_exposure_macro.sas │ ├── 01_comparing_approaches.sas │ ├── 01a_naive_AJ.sas │ ├── 01b_multiple_pooled_logit.sas │ ├── 01c_pooled_multinomial_logit.sas │ ├── 01d_merge_results.sas │ └── 02_applied_example.sas ├── PooledTestingSARS2 ├── README.md ├── results.py └── test_efficiency.py ├── ProximalCI ├── README.md ├── proximal_sims_python.py ├── proximal_sims_r.R └── proximal_sims_sas.sas ├── README.md ├── ReBalancingIntercept ├── README.md ├── balance_intercept.R └── balance_intercept.py ├── ReBespokeIV ├── README.md ├── estfunc.py ├── example.R ├── example.py ├── example.sas ├── process_data.py └── simulation.py ├── RobinsSensitivityAnalysis ├── README.md ├── lau_wihs.dat ├── sensitivity_analysis.ipynb └── sensitivity_analysis.sas ├── SynthesisContinuous ├── README.md ├── application.py ├── dgm.py ├── efuncs.py ├── helper.py ├── process_data.py ├── run_simulations.py ├── statistical.py └── synthesis.py ├── SynthesisMNTE ├── Python │ ├── analysis.py │ ├── appendix2.py │ ├── appendix3.py │ ├── bounds.py │ ├── diagnostic.py │ ├── figure.py │ └── mathmodel.py ├── R │ ├── analysis.R │ ├── appendix2.R │ ├── appendix3.R │ ├── bounds.R │ └── diagnostic.R ├── README.md └── data │ ├── height_params.csv │ ├── nhanes.csv │ └── sbp_params.csv ├── TransportNoPositivity ├── README.md ├── continuous.py ├── dgm.py ├── efuncs.py ├── helper.py ├── process_results.py ├── process_wilson.py ├── run_estimators.py ├── solution_1.py ├── solution_2.py ├── solution_3_gcomp.py ├── solution_3_ipw.py └── truth.py ├── TwisterPlots ├── README.md ├── data_twister.csv ├── extract_data.py ├── twister.R ├── twister.py └── twister.sas └── networkTMLE ├── AmonHen ├── amonhen │ ├── __init__.py │ ├── sr_estimators.py │ ├── tmle_network.py │ ├── tmle_stochastic.py │ ├── utils.py │ └── version.py ├── setup.py └── tests │ ├── cross-comparison │ ├── comparison_w_tmlenet.py │ ├── comparison_with_tmlenet.R │ ├── tmlenet_r_data.csv │ └── tmlenet_r_processed.csv │ ├── test_net-tmle.py │ ├── test_tmle.py │ ├── test_utils.py │ └── tmlenet_r_data.csv ├── Beowulf ├── beowulf │ ├── __init__.py │ ├── data_files │ │ ├── dgm-diet-cpl-1k.csv │ │ ├── dgm-diet-cpl-2k.csv │ │ ├── dgm-diet-cpl.csv │ │ ├── dgm-diet-uniform-1k.csv │ │ ├── dgm-diet-uniform-2k.csv │ │ ├── dgm-diet-uniform.csv │ │ ├── dgm-naloxone-cpl-1k.csv │ │ ├── dgm-naloxone-cpl-2k.csv │ │ ├── dgm-naloxone-cpl.csv │ │ ├── dgm-naloxone-uniform-1k.csv │ │ ├── dgm-naloxone-uniform-2k.csv │ │ ├── dgm-naloxone-uniform.csv │ │ ├── dgm-statin-cpl-1k.csv │ │ ├── dgm-statin-cpl-2k.csv │ │ ├── dgm-statin-cpl.csv │ │ ├── dgm-statin-uniform-1k.csv │ │ ├── dgm-statin-uniform-2k.csv │ │ ├── dgm-statin-uniform.csv │ │ ├── dgm-vaccine-cpl-1k.csv │ │ ├── dgm-vaccine-cpl-2k.csv │ │ ├── dgm-vaccine-cpl.csv │ │ ├── dgm-vaccine-uniform-1k.csv │ │ ├── dgm-vaccine-uniform-2k.csv │ │ ├── dgm-vaccine-uniform.csv │ │ ├── network-random-1k.csv │ │ ├── network-random-2k.csv │ │ ├── network-random.csv │ │ ├── network-uniform-1k.csv │ │ ├── network-uniform-2k.csv │ │ └── network-uniform.csv │ ├── dgm │ │ ├── __init__.py │ │ ├── diet.py │ │ ├── naloxone.py │ │ ├── sofrygin.py │ │ ├── statin.py │ │ ├── utils.py │ │ └── vaccine.py │ ├── load_networks.py │ ├── network_generators │ │ ├── README.md │ │ ├── network-random-1k.py │ │ ├── network-random-2k.py │ │ ├── network-random.py │ │ ├── network-uniform-1k.py │ │ ├── network-uniform-2k.py │ │ └── network-uniform.py │ ├── truth.py │ ├── version.py │ └── w_dist_generators │ │ ├── README.md │ │ ├── dgm-2k.py │ │ ├── dgm-diet.py │ │ ├── dgm-naloxone.py │ │ ├── dgm-statin.py │ │ └── dgm-vaccine.py └── setup.py ├── README.md ├── example_usage.py └── sims ├── README.md ├── generalized_diet.py ├── generalized_naloxone.py ├── generalized_statin.py ├── generalized_vaccine.py ├── run_generalized.sh ├── truth_sims ├── README.md ├── 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