Merge pull request #114 from hyunjimoon/rewrite-diagnostics

Rewrite diagnostics

Author: martinmodrak

DESCRIPTION

@@ -1,8 +1,14 @@
 Package: SBC
 Title: Simulation Based Calibration for Bayesian models
-Version: 0.4.0.9000
+Version: 0.5.0.9000
 Authors@R: 
-    c(person(given = "Shinyoung",
+    c(
+    person(given = "Martin",
+           family = "Modrák",
+           role = c("aut"),
+           email = "martin.modrak@biomed.cas.cz",
+           comment = c(ORCID= "0000-0002-8886-7797")),
+    person(given = "Shinyoung",
            family = "Kim",
            role = c("aut"),
            email = "tttllshin@gmail.com",
@@ -12,11 +18,6 @@ Authors@R:
            role = c("aut", "cre"),
            email = "amoon@mit.edu",
            comment = c()),
-    person(given = "Martin",
-           family = "Modrák",
-           role = c("aut"),
-           email = "martin.modrak@biomed.cas.cz",
-           comment = c(ORCID= "0000-0002-8886-7797")),
     person(given = "Teemu",
            family = "Säilynoja",
            role = "aut"),

NAMESPACE

@@ -63,29 +63,30 @@ S3method(SBC_fit_to_draws_matrix,default)
 S3method(SBC_posterior_cdf,SBC_fit_bridgesampling)
 S3method(SBC_posterior_cdf,SBC_fit_extractBF_comparison)
 S3method(SBC_posterior_cdf,default)
+S3method(base::rbind,SBC_bridgesampling_diagnostics)
 S3method(brms_response_sequence,bform)
 S3method(brms_response_sequence,brmsfit)
 S3method(brms_response_sequence,brmsterms)
 S3method(brms_response_sequence,btl)
 S3method(brms_response_sequence,mvbrmsterms)
-S3method(check_all_SBC_diagnostics,SBC_results)
-S3method(check_all_SBC_diagnostics,default)
 S3method(data_for_ecdf_plots,SBC_results)
 S3method(data_for_ecdf_plots,data.frame)
 S3method(data_for_ecdf_plots,matrix)
+S3method(diagnostic_types,SBC_ADVI_diagnostics)
+S3method(diagnostic_types,SBC_RStanOptimizing_diagnostics)
+S3method(diagnostic_types,SBC_bridgesampling_diagnostics)
+S3method(diagnostic_types,SBC_nuts_diagnostics)
+S3method(diagnostic_types,default)
+S3method(dplyr::select,SBC_bridgesampling_diagnostics)
 S3method(generate_datasets,SBC_generator_brms)
 S3method(generate_datasets,SBC_generator_custom)
 S3method(generate_datasets,SBC_generator_function)
-S3method(get_diagnostic_messages,SBC_ADVI_diagnostics)
-S3method(get_diagnostic_messages,SBC_ADVI_diagnostics_summary)
-S3method(get_diagnostic_messages,SBC_RStanOptimizing_diagnostics)
-S3method(get_diagnostic_messages,SBC_RStanOptimizing_diagnostics_summary)
-S3method(get_diagnostic_messages,SBC_bridgesampling_diagnostics)
-S3method(get_diagnostic_messages,SBC_bridgesampling_diagnostics_summary)
-S3method(get_diagnostic_messages,SBC_nuts_diagnostics_summary)
-S3method(get_diagnostic_messages,SBC_results)
-S3method(get_diagnostic_messages,SBC_results_summary)
-S3method(get_diagnostic_messages,default)
+S3method(get_diagnostic_messages_single,SBC_count_diagnostic)
+S3method(get_diagnostic_messages_single,SBC_default_diagnostic)
+S3method(get_diagnostic_messages_single,SBC_logical_diagnostic)
+S3method(get_diagnostic_messages_single,SBC_numeric_diagnostic)
+S3method(get_diagnostic_messages_single,SBC_skip_diagnostic)
+S3method(get_diagnostic_messages_single,SBC_submodel_diagnostic)
 S3method(length,SBC_datasets)
 S3method(length,SBC_results)
 S3method(plot_binary_calibration,SBC_results)
@@ -102,14 +103,8 @@ S3method(plot_rank_hist,SBC_results)
 S3method(plot_rank_hist,data.frame)
 S3method(plot_sim_estimated,SBC_results)
 S3method(plot_sim_estimated,data.frame)
-S3method(print,SBC_diagnostic_messages)
-S3method(print,SBC_nuts_diagnostics_summary)
 S3method(print,SBC_results)
 S3method(print,SBC_results_summary)
-S3method(summary,SBC_ADVI_diagnostics)
-S3method(summary,SBC_RStanOptimizing_diagnostics)
-S3method(summary,SBC_bridgesampling_diagnostics)
-S3method(summary,SBC_nuts_diagnostics)
 S3method(summary,SBC_results)
 export(SBC_backend_bridgesampling)
 export(SBC_backend_brms)
@@ -132,7 +127,6 @@ export(SBC_backend_rstan_optimizing)
 export(SBC_backend_rstan_sample)
 export(SBC_datasets)
 export(SBC_datasets_for_bf)
-export(SBC_diagnostic_messages)
 export(SBC_example_backend)
 export(SBC_example_generator)
 export(SBC_example_results)
@@ -147,6 +141,8 @@ export(SBC_generator_function)
 export(SBC_posterior_cdf)
 export(SBC_print_example_model)
 export(SBC_results)
+export(SBC_results_diagnostic_messages)
+export(SBC_results_diagnostics)
 export(SBC_statistics_from_single_fit)
 export(attribute_present)
 export(attribute_present_stats)
@@ -172,10 +168,14 @@ export(compute_SBC)
 export(compute_dquants)
 export(compute_gen_quants)
 export(compute_results)
+export(count_diagnostic)
 export(data_for_ecdf_plots)
 export(default_chunk_size)
 export(default_cores_per_fit)
+export(default_diagnostic)
+export(default_diagnostics_types)
 export(derived_quantities)
+export(diagnostic_types)
 export(draws_rvars_to_standata)
 export(draws_rvars_to_standata_single)
 export(empirical_coverage)
@@ -184,13 +184,16 @@ export(gaffke_p)
 export(gaffke_test)
 export(generate_datasets)
 export(generated_quantities)
-export(get_diagnostic_messages)
+export(get_all_diagnostic_messages)
+export(get_diagnostic_messages_single)
 export(get_stats_for_submodel)
 export(hidden_var_attribute)
 export(inf_valid_var_attribute)
+export(logical_diagnostic)
 export(miscalibration_resampling_p)
 export(miscalibration_resampling_test)
 export(na_valid_var_attribute)
+export(numeric_diagnostic)
 export(plot_binary_calibration)
 export(plot_binary_calibration_diff)
 export(plot_contraction)
@@ -204,7 +207,9 @@ export(possibly_constant_var_attribute)
 export(recompute_SBC_statistics)
 export(recompute_statistics)
 export(remove_attribute_from_stats)
+export(skip_diagnostic)
 export(split_SBC_results_for_bf)
+export(submodel_diagnostic)
 export(submodel_var_attribute)
 export(validate_SBC_datasets)
 export(validate_SBC_results)