Files in hyunjimoon/SBC
Simulation Based Calibration for rstan/cmdstanr models

.Rbuildignore
.Rprofile
.gitignore
CITATION.cff
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/SBC-deprecated.R R/backend-brms.R R/backend-cmdstanr.R R/backend-mock.R R/backend-rjags.R R/backend-rstan.R R/backend-stan-shared.R R/backends.R R/brms-helpers.R R/calculate.R R/datasets.R R/derived-quantities.R R/example.R R/generator-brms.R R/metric.R R/onLoad.R R/plot.R R/results.R R/util.R README.md
SBC.Rproj
_pkgdown.yml
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/SBC.html
docs/articles/SBC_files/figure-html/ecdf-1.png
docs/articles/SBC_files/figure-html/ecdf_diff-1.png
docs/articles/SBC_files/figure-html/rank_hist-1.png
docs/articles/bad_parametrization.html
docs/articles/bad_parametrization_files/figure-html/results1_ecdf_diff-1.png
docs/articles/bad_parametrization_files/figure-html/results1_other-1.png
docs/articles/bad_parametrization_files/figure-html/results1_other-2.png
docs/articles/bad_parametrization_files/figure-html/results2_plots-1.png
docs/articles/bad_parametrization_files/figure-html/results2_plots-2.png
docs/articles/bad_parametrization_files/figure-html/results2_plots-3.png
docs/articles/brms.html
docs/articles/brms_files/figure-html/results_func2_plots-1.png
docs/articles/brms_files/figure-html/results_func2_plots-2.png
docs/articles/brms_files/figure-html/results_func_plots-1.png
docs/articles/brms_files/figure-html/results_func_plots-2.png
docs/articles/brms_files/figure-html/results_plots-1.png
docs/articles/brms_files/figure-html/results_plots-2.png
docs/articles/computational_algorithm1.html
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson-1.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson-2.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson_100-1.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson_100-2.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson_optimizing-1.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson_optimizing-2.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson_optimizing_100-1.png
docs/articles/computational_algorithm1_files/figure-html/ecdf_rank_poisson_optimizing_100-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_2_coverage-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_2_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_2_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_coverage-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_fullrank_coverage-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_fullrank_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_fullrank_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_lowtol_coverage-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_lowtol_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_lowtol_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_optimizing_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_optimizing_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ordered_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ordered_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ordered_fullrank_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ordered_fullrank_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ordered_optimizing_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_ordered_optimizing_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_sample_ecdf_ranks-1.png
docs/articles/computational_algorithm1_files/figure-html/hmm_sample_ecdf_ranks-2.png
docs/articles/computational_algorithm1_files/figure-html/hmm_time-1.png
docs/articles/discrete_vars.html
docs/articles/discrete_vars_files/figure-html/ranks_jags-1.png
docs/articles/discrete_vars_files/figure-html/ranks_jags-2.png
docs/articles/discrete_vars_files/figure-html/ranks_jags_marginalized-1.png
docs/articles/discrete_vars_files/figure-html/ranks_jags_marginalized-2.png
docs/articles/discrete_vars_files/figure-html/results1_plots-1.png
docs/articles/discrete_vars_files/figure-html/results1_plots-2.png
docs/articles/discrete_vars_files/figure-html/results_2_all_plots-1.png
docs/articles/discrete_vars_files/figure-html/results_2_all_plots-2.png
docs/articles/discrete_vars_files/figure-html/results_2_plots-1.png
docs/articles/discrete_vars_files/figure-html/results_2_plots-2.png
docs/articles/implementing_backends.html
docs/articles/implementing_backends_files/figure-html/indo_complex_narrow_ranks-1.png
docs/articles/implementing_backends_files/figure-html/indo_complex_narrow_ranks-2.png
docs/articles/implementing_backends_files/figure-html/indo_complex_ranks-1.png
docs/articles/implementing_backends_files/figure-html/indo_complex_ranks-2.png
docs/articles/implementing_backends_files/figure-html/indo_sim_coverage-1.png
docs/articles/implementing_backends_files/figure-html/indo_simple_narrow_ranks-1.png
docs/articles/implementing_backends_files/figure-html/indo_simple_narrow_ranks-2.png
docs/articles/implementing_backends_files/figure-html/indo_simple_ranks-1.png
docs/articles/implementing_backends_files/figure-html/indo_simple_ranks-2.png
docs/articles/implementing_backends_files/figure-html/indo_simple_sim_est-1.png
docs/articles/implementing_backends_files/figure-html/indo_simple_sim_est_ugly-1.png
docs/articles/implementing_backends_files/figure-html/poisson_ranks-1.png
docs/articles/implementing_backends_files/figure-html/poisson_ranks-2.png
docs/articles/implementing_backends_files/figure-html/poisson_sim_estimated-1.png
docs/articles/index.html
docs/articles/indexing.html
docs/articles/indexing_files/figure-html/plots_regression1-1.png
docs/articles/indexing_files/figure-html/plots_regression1-2.png
docs/articles/indexing_files/figure-html/plots_regression2-1.png
docs/articles/indexing_files/figure-html/plots_regression2-2.png
docs/articles/indexing_files/figure-html/plots_regression3-1.png
docs/articles/indexing_files/figure-html/plots_regression3-2.png
docs/articles/limits_of_SBC.html
docs/articles/limits_of_SBC_files/figure-html/dens_compare-1.png
docs/articles/limits_of_SBC_files/figure-html/log_dens_compare-1.png
docs/articles/limits_of_SBC_files/figure-html/results_corr-1.png
docs/articles/limits_of_SBC_files/figure-html/results_corr-2.png
docs/articles/limits_of_SBC_files/figure-html/results_corr_dq-1.png
docs/articles/limits_of_SBC_files/figure-html/results_corr_dq-2.png
docs/articles/limits_of_SBC_files/figure-html/results_corr_gq-1.png
docs/articles/limits_of_SBC_files/figure-html/results_corr_gq-2.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_100_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_100_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_10_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_10_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_200_coverage-1.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_200_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_200_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_minor_200_sim_estimated-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_2_contraction-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_2_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_2_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_2_sim_estimated-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_contraction-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_dq_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_dq_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_gq_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_gq_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_plots-1.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_plots-2.png
docs/articles/limits_of_SBC_files/figure-html/results_missing_sim_estimated-1.png
docs/articles/overview_wide.png
docs/articles/rank_visualizations.html
docs/articles/rank_visualizations_files/figure-html/coverage_50-1.png
docs/articles/rank_visualizations_files/figure-html/coverage_diff_50-1.png
docs/articles/rank_visualizations_files/figure-html/densities-1.png
docs/articles/rank_visualizations_files/figure-html/ecdf_1000-1.png
docs/articles/rank_visualizations_files/figure-html/ecdf_50-1.png
docs/articles/rank_visualizations_files/figure-html/ecdf_diff_1000-1.png
docs/articles/rank_visualizations_files/figure-html/ecdf_diff_50-1.png
docs/articles/rank_visualizations_files/figure-html/rank_hist_1000-1.png
docs/articles/rank_visualizations_files/figure-html/rank_hist_50_100-1.png
docs/articles/rank_visualizations_files/figure-html/rank_hist_50_17-1.png
docs/articles/rank_visualizations_files/figure-html/rank_hist_50_default-1.png
docs/articles/rank_visualizations_files/figure-html/side_by_side_1000_exact_match-1.png
docs/articles/rank_visualizations_files/figure-html/side_by_side_50_exact_match-1.png
docs/articles/rank_visualizations_files/figure-html/side_by_side_50_overest-1.png
docs/articles/rank_visualizations_files/figure-html/side_by_side_50_too_certain-1.png
docs/articles/rank_visualizations_files/figure-html/side_by_side_50_too_uncertain-1.png
docs/articles/rank_visualizations_files/figure-html/side_by_side_50_underest-1.png
docs/articles/rejection_sampling.html
docs/articles/rejection_sampling_files/figure-html/reject_unobserved_plots-1.png
docs/articles/rejection_sampling_files/figure-html/reject_unobserved_plots-2.png
docs/articles/rejection_sampling_files/figure-html/reject_y_plot-1.png
docs/articles/rejection_sampling_files/figure-html/reject_y_plot-2.png
docs/articles/rejection_sampling_files/figure-html/results1_plots-1.png
docs/articles/rejection_sampling_files/figure-html/results1_plots-2.png
docs/articles/small_model_workflow.html
docs/articles/small_model_workflow_files/figure-html/beta_first_10_pairs-1.png
docs/articles/small_model_workflow_files/figure-html/beta_first_10_pairs_subset-1.png
docs/articles/small_model_workflow_files/figure-html/beta_first_10_pairs_subset-2.png
docs/articles/small_model_workflow_files/figure-html/beta_first_10_pairs_subset-3.png
docs/articles/small_model_workflow_files/figure-html/beta_first_10_pairs_subset-4.png
docs/articles/small_model_workflow_files/figure-html/beta_first_10_pairs_subset-5.png
docs/articles/small_model_workflow_files/figure-html/beta_first_results-1.png
docs/articles/small_model_workflow_files/figure-html/beta_first_results-2.png
docs/articles/small_model_workflow_files/figure-html/combined_fanos-1.png
docs/articles/small_model_workflow_files/figure-html/combined_reject_coverage-1.png
docs/articles/small_model_workflow_files/figure-html/combined_reject_plots-1.png
docs/articles/small_model_workflow_files/figure-html/combined_reject_plots-2.png
docs/articles/small_model_workflow_files/figure-html/fanos_divergent-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_first_convergence-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_fixed_log_mix_pairs-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_fixed_log_mix_rhat-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_fixed_ordered_pairs-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_fixed_ordered_subset_coverage-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_fixed_ordered_subset_results-1.png
docs/articles/small_model_workflow_files/figure-html/mixture_fixed_ordered_subset_results-2.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_100_plots-1.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_100_plots-2.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_10_plots-1.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_10_plots-2.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_fixed_prior_200_coverage-1.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_fixed_prior_200_plots-1.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_fixed_prior_200_plots-2.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_fixed_prior_plots-1.png
docs/articles/small_model_workflow_files/figure-html/results_beta_precision_fixed_prior_plots-2.png
docs/articles/small_model_workflow_files/figure-html/results_combined_plots-1.png
docs/articles/small_model_workflow_files/figure-html/results_combined_plots-2.png
docs/articles/small_model_workflow_files/figure-html/results_combined_reject_more_coverage-1.png
docs/articles/small_model_workflow_files/figure-html/results_combined_reject_more_plots-1.png
docs/articles/small_model_workflow_files/figure-html/results_combined_reject_more_plots-2.png
docs/articles/small_model_workflow_files/figure-html/results_fixed_ordered_combined_results-1.png
docs/articles/small_model_workflow_files/figure-html/results_fixed_ordered_combined_results-2.png
docs/articles/small_model_workflow_files/figure-html/results_fixed_ordered_combined_results_coverage-1.png
docs/articles/small_model_workflow_files/figure-html/sim_estimated_final-1.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/ECDF-plots.html
docs/reference/Rplot001.png
docs/reference/SBC-deprecated.html
docs/reference/SBC_backend_brms.html
docs/reference/SBC_backend_brms_from_generator.html
docs/reference/SBC_backend_cmdstan_sample.html
docs/reference/SBC_backend_cmdstan_variational.html
docs/reference/SBC_backend_default_thin_ranks.html
docs/reference/SBC_backend_hash_for_cache.html
docs/reference/SBC_backend_iid_draws.html
docs/reference/SBC_backend_mock.html
docs/reference/SBC_backend_rjags.html
docs/reference/SBC_backend_rstan_optimizing.html
docs/reference/SBC_backend_rstan_sample.html
docs/reference/SBC_datasets.html
docs/reference/SBC_example_backend.html
docs/reference/SBC_example_generator.html
docs/reference/SBC_example_results.html
docs/reference/SBC_fit.html
docs/reference/SBC_fit_to_diagnostics.html
docs/reference/SBC_fit_to_draws_matrix.html
docs/reference/SBC_generator_brms.html
docs/reference/SBC_generator_custom.html
docs/reference/SBC_generator_function.html
docs/reference/SBC_print_example_model.html
docs/reference/SBC_results.html
docs/reference/SBC_statistics_from_single_fit.html
docs/reference/bind_datasets.html
docs/reference/bind_derived_quantities.html
docs/reference/bind_generated_quantities-deprecated.html
docs/reference/bind_globals.html
docs/reference/bind_results.html
docs/reference/brms_full_ppred.html
docs/reference/brms_response_sequence.html
docs/reference/calculate_prior_sd.html
docs/reference/calculate_ranks_draws_matrix.html
docs/reference/check_all_SBC_diagnostics.html
docs/reference/cjs_dist.html
docs/reference/combine-functions.html
docs/reference/combine_args.html
docs/reference/compute_SBC.html
docs/reference/compute_dquants.html
docs/reference/compute_gen_quants-deprecated.html
docs/reference/compute_results-deprecated.html
docs/reference/data_for_ecdf_plots.html
docs/reference/default_chunk_size.html
docs/reference/default_cores_per_fit.html
docs/reference/derived_quantities.html
docs/reference/empirical_coverage.html
docs/reference/generate_datasets.html
docs/reference/generated_quantities-deprecated.html
docs/reference/generated_quantities.html
docs/reference/get_diagnostic_messages.html
docs/reference/guess_rank_hist_bins.html
docs/reference/index.html
docs/reference/max_diff.html
docs/reference/plot_contraction.html
docs/reference/plot_coverage.html
docs/reference/plot_rank_hist.html
docs/reference/plot_sim_estimated.html
docs/reference/rank2unif.html
docs/reference/rdunif.html
docs/reference/recompute_SBC_statistics.html
docs/reference/recompute_statistics-deprecated.html
docs/reference/set2set.html
docs/reference/sub-.SBC_datasets.html
docs/reference/sub-.SBC_results.html
docs/reference/validate_derived_quantities.html
docs/reference/wasserstein.html
docs/sitemap.xml
inst/CITATION
inst/normal_bad.jags
inst/normal_bad.stan
inst/normal_sd.jags
inst/normal_sd.stan
man/ECDF-plots.Rd man/SBC-deprecated.Rd man/SBC_backend_brms.Rd man/SBC_backend_brms_from_generator.Rd man/SBC_backend_cmdstan_sample.Rd man/SBC_backend_cmdstan_variational.Rd man/SBC_backend_default_thin_ranks.Rd man/SBC_backend_hash_for_cache.Rd man/SBC_backend_iid_draws.Rd man/SBC_backend_mock.Rd man/SBC_backend_rjags.Rd man/SBC_backend_rstan_optimizing.Rd man/SBC_backend_rstan_sample.Rd man/SBC_datasets.Rd man/SBC_example_backend.Rd man/SBC_example_generator.Rd man/SBC_example_results.Rd man/SBC_fit.Rd man/SBC_fit_to_diagnostics.Rd man/SBC_fit_to_draws_matrix.Rd man/SBC_generator_brms.Rd man/SBC_generator_custom.Rd man/SBC_generator_function.Rd man/SBC_print_example_model.Rd man/SBC_results.Rd man/SBC_statistics_from_single_fit.Rd man/bind_datasets.Rd man/bind_derived_quantities.Rd man/bind_generated_quantities-deprecated.Rd man/bind_globals.Rd man/bind_results.Rd man/brms_full_ppred.Rd man/brms_response_sequence.Rd man/calculate_prior_sd.Rd man/calculate_ranks_draws_matrix.Rd man/check_all_SBC_diagnostics.Rd man/cjs_dist.Rd man/combine-functions.Rd man/combine_args.Rd man/compute_SBC.Rd man/compute_dquants.Rd man/compute_gen_quants-deprecated.Rd man/compute_results-deprecated.Rd man/data_for_ecdf_plots.Rd man/default_chunk_size.Rd man/default_cores_per_fit.Rd man/derived_quantities.Rd man/empirical_coverage.Rd man/generate_datasets.Rd man/generated_quantities-deprecated.Rd man/get_diagnostic_messages.Rd man/guess_rank_hist_bins.Rd man/max_diff.Rd man/plot_contraction.Rd man/plot_coverage.Rd man/plot_rank_hist.Rd man/plot_sim_estimated.Rd man/rank2unif.Rd man/rdunif.Rd man/recompute_SBC_statistics.Rd man/recompute_statistics-deprecated.Rd man/set2set.Rd man/sub-.SBC_datasets.Rd man/sub-.SBC_results.Rd man/validate_derived_quantities.Rd man/wasserstein.Rd
pkgdown/templates/in-header.html
tests/testthat/test-backends.R tests/testthat/test-brms.R tests/testthat/test-datasets.R tests/testthat/test-empirical-coverage.R tests/testthat/test-integration.R tests/testthat/test-plot-helpers.R tests/testthat/test-results.R tests/testthat/test-utils.R vignettes/SBC.Rmd vignettes/bad_parametrization.Rmd vignettes/brms.Rmd vignettes/computational_algorithm1.Rmd vignettes/discrete_vars.Rmd vignettes/implementing_backends.Rmd vignettes/indexing.Rmd vignettes/limits_of_SBC.Rmd
vignettes/other_models/changepoint.jags
vignettes/other_models/changepoint_marginalized.jags
vignettes/overview.graphml
vignettes/overview.png
vignettes/overview_wide.graphml
vignettes/overview_wide.png
vignettes/rank_visualizations.Rmd vignettes/rejection_sampling.Rmd vignettes/small_model_workflow.Rmd
vignettes/small_model_workflow/beta_first.stan
vignettes/small_model_workflow/beta_precision.stan
vignettes/small_model_workflow/beta_precision_fixed_prior.stan
vignettes/small_model_workflow/combined_first.stan
vignettes/small_model_workflow/mixture_first.stan
vignettes/small_model_workflow/mixture_fixed_log_mix.stan
vignettes/small_model_workflow/mixture_fixed_ordered.stan
vignettes/stan/bad_parametrization1.stan
vignettes/stan/bad_parametrization2.stan
vignettes/stan/discrete_vars1.stan
vignettes/stan/hmm_poisson.stan
vignettes/stan/hmm_poisson_ordered.stan
vignettes/stan/minor_discrepancy.stan
vignettes/stan/missing_likelihood.stan
vignettes/stan/partially_missing_likelihood.stan
vignettes/stan/poisson.stan
vignettes/stan/regression1.stan
vignettes/stan/regression2.stan
vignettes/stan/regression3.stan
vignettes/stan/rejection_sampling.stan
hyunjimoon/SBC documentation built on March 15, 2024, 3:18 a.m.