├── .gitignore ├── LICENSE.md ├── README.md ├── gene_tf ├── README.md ├── dat │ └── rawdat │ │ └── hapmap │ │ ├── README.md │ │ ├── clean_csv │ │ ├── Fs.csv │ │ ├── genes.csv │ │ ├── hapmap_mimno_genes_clean.csv │ │ ├── hapmap_mimno_genes_clean_Fs.csv │ │ ├── hapmap_mimno_genes_clean_ps.csv │ │ └── ps.csv │ │ ├── clean_hapmap.py │ │ ├── hapmap_url.md │ │ ├── mimno_hapmap3 │ │ ├── hapmap3.bed │ │ ├── hapmap3.bim │ │ ├── hapmap3.fam │ │ └── hapmap3.pops │ │ ├── raw_csv │ │ ├── hapmap_mimno_genes.csv │ │ └── hapmap_mimno_pops.csv │ │ └── read_hapmap.py ├── envr.txt ├── res │ ├── BN_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── BN_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── BN_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── BN_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha100_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha100_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha100_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha100_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha10_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha10_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha10_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha10_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha1_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha1_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha1_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha1_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha50_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha50_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── PSDalpha50_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── PSDalpha50_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha100_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha100_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha100_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha100_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha10_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha10_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha10_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha10_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha25_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha25_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha25_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha25_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha50_units5000_causes100000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha50_units5000_causes100000_cv0_snipsig40_confint40_cp10_avg.csv │ ├── SPalpha50_units5000_causes5000_cv0_snipsig10_confint20_cp10_avg.csv │ ├── SPalpha50_units5000_causes5000_cv0_snipsig40_confint40_cp10_avg.csv │ └── output.md └── src │ ├── agg_dfs.py │ ├── causalest.py │ ├── fitfactor.py │ ├── run_script_causalest.sh │ ├── run_script_causalest_base_emayhem.sh │ ├── run_script_fitfactor.sh │ ├── run_script_fitfactor_base_emayhem.sh │ ├── run_script_simdat.sh │ ├── run_script_simdat_base_emayhem.sh │ ├── simdat.py │ └── utils.py ├── movie_py ├── README.md ├── dat │ ├── tmdb_proc │ │ ├── casts_df_clean.csv │ │ ├── genres_df_clean.csv │ │ ├── production_companies_clean.csv │ │ ├── production_countries_clean.csv │ │ ├── spoken_languages_clean.csv │ │ ├── tmdb_clean.csv │ │ ├── train.csv │ │ ├── train_full.csv │ │ ├── unique_sid.txt │ │ ├── unique_uid.txt │ │ └── validation.csv │ └── tmdb_raw │ │ └── tmdb-5000-movie-dataset │ │ ├── tmdb_5000_credits.csv │ │ └── tmdb_5000_movies.csv ├── res │ └── factorfit │ │ ├── cause_def_k_U.csv │ │ ├── cause_def_k_Xpost.csv │ │ ├── cause_pca_k50_U.csv │ │ ├── cause_pca_k50_V.csv │ │ ├── cause_pmf_k50_U.csv │ │ └── cause_pmf_k50_V.csv └── src │ ├── fit_def.py │ ├── movie-actor-py2-causalest.ipynb │ ├── movie-actor-py2-subconf.ipynb │ ├── pmf.py │ └── tmdb_movie_preprocess.ipynb └── smoking_R ├── README.md ├── dat └── nmes_data.csv ├── envr.txt ├── res ├── dep_linear_1_Actrl_20235400_20133224_20144133_avg.csv ├── dep_linear_1_Zctrl_20235400_20133224_20144133_avg.csv ├── dep_linear_1_nctrl_22145515_20133224_20144133_avg.csv ├── dep_linear_1_oracle_21195346_20133224_20144133_avg.csv ├── dep_quadratic_1_Actrl_21155118_20133224_20144133_avg.csv ├── dep_quadratic_1_Zctrl_22195956_20133224_20144133_avg.csv ├── indep_linear_1_Actrl_431966185_1549139415_771254748_avg.csv ├── indep_linear_1_Zctrl_431966185_1549139415_36127605_avg.csv ├── indep_linear_1_nctrl_431966185_1549139415_36127605_avg.csv ├── indep_linear_1_oracle_431966185_1549139415_36127605_avg.csv ├── indep_quadratic_1_Acovctrl_594924916_1549139415_771254748_avg.csv ├── indep_quadratic_1_Actrl_431966185_1549139415_1549139415_avg.csv ├── indep_quadratic_1_Zcovctrl_594924916_1549139415_771254748_avg.csv ├── indep_quadratic_1_Zctrl_431966185_1549139415_771254748_avg.csv ├── indep_quadratic_2_Actrl_431966185_1549139415_179267981_avg.csv ├── indep_quadratic_2_Zctrl_431966185_1549139415_659677507_avg.csv ├── indep_quadratic_3_Actrl_431966185_1549139415_659677507_avg.csv ├── indep_quadratic_3_Zctrl_431966185_1549139415_179267981_avg.csv └── output.md └── src ├── agg_dfs.py ├── causalest.R ├── fitfactor.R ├── linearfactor_knownvar.stan ├── quadraticfactor_knownvar.stan ├── run_script_causalest.sh ├── run_script_causalest_base.sh ├── run_script_fitfactor.sh ├── run_script_fitfactor_base.sh ├── 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