LICENSE
MANIFEST.in
README.md
pyproject.toml
BayesForge/__init__.py
BayesForge.egg-info/PKG-INFO
BayesForge.egg-info/SOURCES.txt
BayesForge.egg-info/dependency_links.txt
BayesForge.egg-info/requires.txt
BayesForge.egg-info/top_level.txt
BayesForge/BNN/__init__.py
BayesForge/BNN/activations.py
BayesForge/BNN/bnn.py
BayesForge/Build/Build_NP_light.py
BayesForge/Build/Build_R_documentation.py
BayesForge/Build/Build_TFP_light.py
BayesForge/Build/Build_test_file.py
BayesForge/Data/manip.py
BayesForge/Diagnostic/Diag.py
BayesForge/Diagnostic/Diag2.py
BayesForge/Diagnostic/__init__.py
BayesForge/Diagnostic/jax_diagnostics.py
BayesForge/Diagnostic/jax_summary.py
BayesForge/Diagnostic/patch_diag.py
BayesForge/Diagnostic/ppc.py
BayesForge/Diagnostic/regression_plot.py
BayesForge/Diagnostic/sensitivity.py
BayesForge/Distributions/__init__.py
BayesForge/Distributions/np_dists.py
BayesForge/Distributions/np_dists_old.py
BayesForge/Distributions/tfp_dists.py
BayesForge/ML/KMeans.py
BayesForge/ML/__init__.py
BayesForge/ML/ml.py
BayesForge/Main/__init__.py
BayesForge/Main/main.py
BayesForge/Models/BNNC.py
BayesForge/Models/DPMM.py
BayesForge/Models/GMM.py
BayesForge/Models/PCA.py
BayesForge/Models/SRM.py
BayesForge/Models/__init__.py
BayesForge/Models/models.py
BayesForge/Models/surv.py
BayesForge/NBDA/NBDA.py
BayesForge/NBDA/__init__.py
BayesForge/Network/Net.py
BayesForge/Network/__init__.py
BayesForge/Network/metrics.py
BayesForge/Network/model_effects.py
BayesForge/Network/util.py
BayesForge/PostModel/__init__.py
BayesForge/PostModel/to_latex.py
BayesForge/R/BF doc.py
BayesForge/Resources/__init__.py
BayesForge/Resources/datasets.py
BayesForge/Samplers/Model_handler.py
BayesForge/Samplers/__init__.py
BayesForge/Samplers/mcmc_numpyro.py
BayesForge/Samplers/mcmc_tfp.py
BayesForge/Samplers/SVI/__init__.py
BayesForge/Samplers/SVI/svi_numpyro.py
BayesForge/SetDevice/__init__.py
BayesForge/SetDevice/set.py
BayesForge/Utils/Effects.py
BayesForge/Utils/Gaussian.py
BayesForge/Utils/ImportManager.py
BayesForge/Utils/SampledData.py
BayesForge/Utils/__init__.py
BayesForge/Utils/link.py
Documentation/__init__.py
Documentation/_setup.py
Test/Models.py
Test/test_BF_simple.py
Test/test_save_load.py
Test/Capture-Recapture (WIP)/check_parity.py
Test/Capture-Recapture (WIP)/compare_cjs_ms.py
Test/Capture-Recapture (WIP)/model_BF.py
Test/Capture-Recapture (WIP)/plot_comparison.py
Test/Capture-Recapture (WIP)/prepare_data.py
Test/Capture-Recapture (WIP)/run_phase3_scalability.py
Test/Capture-Recapture (WIP)/run_stan_benchmark.py
Test/Capture-Recapture (WIP)/verify_data.py
Test/Copula (WIP)/gaussian_copula_approaches.py
Test/Copula (WIP)/test_icdf_patch.py
Test/Copula (WIP)/test_inference.py
Test/Copula (WIP)/test_mock.py
Test/DP-VAE (WIP)/perfect_dp_mixture.py
Test/Diagnostic/diagnose sampling/__init__.py
Test/Diagnostic/diagnose sampling/diagnose.py
Test/Diagnostic/personality_traits/traits.py
Test/Diagnostic/ppc/test_ppc.py
Test/Diagnostic/regression/test_regression.py
Test/Diagnostic/sensitivity/test_sensitivity.py
Test/Diagnostic/summary/diag test.py
Test/Diagnostic/summary/jax_diagnostics.py
Test/Diagnostic/summary/patch_diag.py
Test/Distributions/distribution_numpyro.py
Test/Distributions/distribution_tfp.py
Test/EWA/run_comparison.py
Test/EWA/BI_backend/model.py
Test/GMM (WIP)/compare.py
Test/GMM (WIP)/ggmm_BF.py
Test/HGAM (WIP)/benchmark_hgam_BF.py
Test/HGAM (WIP)/gam_utils.py
Test/HGAM (WIP)/plot_hgam_comparison.py
Test/HGAM (WIP)/test_native_gam.py
Test/MGM and DPMM/7.MGM_DPM_Similarity_Test.py
Test/MGM and DPMM/Similarity_Test.py
Test/Modeling Evolutionary Heterogeneity (WIP)/compare_3way_beast.py
Test/Modeling Evolutionary Heterogeneity (WIP)/compare_beast_BF.py
Test/Modeling Evolutionary Heterogeneity (WIP)/compare_bl_beast_equivalence.py
Test/Modeling Evolutionary Heterogeneity (WIP)/compare_estimations.py
Test/Modeling Evolutionary Heterogeneity (WIP)/compare_posteriors.py
Test/Modeling Evolutionary Heterogeneity (WIP)/compare_posteriors_blmarg.py
Test/Modeling Evolutionary Heterogeneity (WIP)/create_xmls.py
Test/Modeling Evolutionary Heterogeneity (WIP)/tree_data.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_1_Spatial_Heterogeneity/fit_BF_gamma.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_1_Spatial_Heterogeneity/fit_BF_gamma_fixed.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_1_Spatial_Heterogeneity/fit_BF_gamma_fixed2.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_1_Spatial_Heterogeneity/fit_BF_gamma_fixed3.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_1_Spatial_Heterogeneity/fit_BF_gamma_vec.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_1_Spatial_Heterogeneity/parse_trees.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_2_Temporal_Heterogeneity/fit_BF_ucln.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_2_Temporal_Heterogeneity/fit_BF_ucln_vec.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_3_Spatial_BLMarg/fit_BF_gamma_blmarg.py
Test/Modeling Evolutionary Heterogeneity (WIP)/Model_4_Temporal_BLMarg/fit_BF_ucln_blmarg.py
Test/Modeling Evolutionary Heterogeneity (WIP)/scripts/check_vectorization_logic.py
Test/Modeling Evolutionary Heterogeneity (WIP)/scripts/generate_xtx_log.py
Test/Modeling Evolutionary Heterogeneity (WIP)/scripts/load_data.py
Test/Modeling Evolutionary Heterogeneity (WIP)/scripts/tree_6.py
Test/Modeling Evolutionary Heterogeneity (WIP)/scripts/tree_data.py
Test/Nested effect/builtin_function.py
Test/Network/Multiplex (WIP)/SIM.py
Test/Network/Network metrics/network_metrics.py
Test/Network/SRM/SIM.py
Test/Network/SRM/benchmark_stan2.py
Test/Network/SRM/fit_comparison.py
Test/Network/SRM/benchmark_suite/benchmark_stan2.py
Test/PCA/PCA.py
Test/Phylogenic analysis/Model_1_Simple/fit_BF_simple.py
Test/Phylogenic analysis/Model_2_Poisson/fit_BF_pois.py
Test/Phylogenic analysis/Model_3_Repeated/fit_BF_repeat.py
Test/Phylogenic analysis/Model_4_Meta/fit_BF_meta.py
Test/Phylogenic analysis/Model_5_Slopes/fit_BF_slopes.py
Test/Repertoire/BF_only.py
Test/Repertoire/benchmark.py
Test/Repertoire/check_stan.py
Test/Repertoire/compare_moments_p.py
Test/Repertoire/compare_summary.py
Test/Repertoire/save_stan_samples.py
Test/Rethinking/Numpyro backend/1.Continuous variable.py
Test/Rethinking/Numpyro backend/10.Zero inflated.py
Test/Rethinking/Numpyro backend/11.Varying intercepts.py
Test/Rethinking/Numpyro backend/12.Varying effects.py
Test/Rethinking/Numpyro backend/13.Gaussian processes.py
Test/Rethinking/Numpyro backend/2.Categorical variable.py
Test/Rethinking/Numpyro backend/3.Continuous interactions.py
Test/Rethinking/Numpyro backend/4.Binomial.py
Test/Rethinking/Numpyro backend/5.Binomial with indices.py
Test/Rethinking/Numpyro backend/6.Poisson.py
Test/Rethinking/Numpyro backend/7.Negative binomial.py
Test/Rethinking/Numpyro backend/8.Multinomial.py
Test/Rethinking/Numpyro backend/9.Beta binomial.py
Test/Rethinking/Numpyro backend/Utils.py
Test/Rethinking/Numpyro backend/run_all.py
Test/Rethinking/TFP backend/1.Continuous variable.py
Test/Rethinking/TFP backend/10.Zero inflated.py
Test/Rethinking/TFP backend/11.Varying intercepts.py
Test/Rethinking/TFP backend/12.Varying effects.py
Test/Rethinking/TFP backend/13.Gaussian processes.py
Test/Rethinking/TFP backend/2.Categorical variable.py
Test/Rethinking/TFP backend/3.Continuous interactions.py
Test/Rethinking/TFP backend/4.Binomial.py
Test/Rethinking/TFP backend/5.Binomial with indices.py
Test/Rethinking/TFP backend/6.Poisson.py
Test/Rethinking/TFP backend/7.Negative binomial.py
Test/Rethinking/TFP backend/8.Multinomial.py
Test/Rethinking/TFP backend/9.Beta binomial.py
Test/Rethinking/TFP backend/Utils.py
Test/Rethinking/TFP backend/run_all.py
Test/Rethinking/TFP backend/scratch/check_summary.py
Test/Rethinking/TFP backend/scratch/test_df.py
Test/Survival analysis/Survival analysis.py
Test/Survival analysis/Survival_analysis_verify.py
Test/VINE (WIP)/__init__.py
Test/VINE (WIP)/data_parser.py
Test/VINE (WIP)/decoder.py
Test/VINE (WIP)/embeddings.py
Test/VINE (WIP)/likelihood.py
Test/VINE (WIP)/optimizer.py
Test/VINE (WIP)/validation.py
Test/Workflow/workflow.py