{
  "_id": "69b06ca49182b4497fddfc7f",
  "Package": "SBC",
  "Title": "Simulation Based Calibration for Bayesian models",
  "Version": "0.5.0.0",
  "Authors@R": "c(\nperson(given = \"Martin\",\nfamily = \"Modrák\",\nrole = c(\"aut\"),\nemail = \"martin.modrak@biomed.cas.cz\",\ncomment = c(ORCID= \"0000-0002-8886-7797\")),\nperson(given = \"Shinyoung\",\nfamily = \"Kim\",\nrole = c(\"aut\"),\nemail = \"tttllshin@gmail.com\",\ncomment = c()),\nperson(given = \"Angie.H\",\nfamily = \"Moon\",\nrole = c(\"aut\", \"cre\"),\nemail = \"amoon@mit.edu\",\ncomment = c()),\nperson(given = \"Teemu\",\nfamily = \"Säilynoja\",\nrole = \"aut\"),\nperson(given = \"Luna\",\nfamily = \"Fazio\",\nrole = \"ctb\"),\nperson(given = \"Timo\",\nfamily = \"Stenz\",\nrole = \"ctb\")\n)",
  "Description": "SBC helps perform Simulation Based Calibration on Bayesian\nmodels. SBC lets you check for bugs in your model code and/or\nalgorithm that fits the model. SBC focuses on models built with\n'Stan' <https://mc-stan.org>, but can support other modelling\nlanguages as well.",
  "License": "MIT + file LICENSE",
  "URL": "https://hyunjimoon.github.io/SBC/,\nhttps://github.com/hyunjimoon/SBC/",
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  "Author": "Martin Modrák [aut] (ORCID: <https://orcid.org/0000-0002-8886-7797>),\nShinyoung Kim [aut],\nAngie.H Moon [aut, cre],\nTeemu Säilynoja [aut],\nLuna Fazio [ctb],\nTimo Stenz [ctb]",
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  "_exports": [
    "attribute_present",
    "attribute_present_stats",
    "binary_calibration_from_bp",
    "binary_miscalibration",
    "binary_probabilities_from_stats",
    "binary_var_attribute",
    "bind_datasets",
    "bind_derived_quantities",
    "bind_generated_quantities",
    "bind_results",
    "brier_resampling_p",
    "brier_resampling_test",
    "cached_fit_filename",
    "calculate_prior_sd",
    "calculate_ranks_draws_matrix",
    "calculate_sds_draws_matrix",
    "check_all_SBC_diagnostics",
    "combine_all_variables",
    "combine_array_elements",
    "combine_var_attributes",
    "compute_dquants",
    "compute_gen_quants",
    "compute_results",
    "compute_SBC",
    "count_diagnostic",
    "data_for_ecdf_plots",
    "default_chunk_size",
    "default_cores_per_fit",
    "default_diagnostic",
    "default_diagnostics_types",
    "derived_quantities",
    "diagnostic_types",
    "dquants_var_attributes",
    "draws_rvars_to_standata",
    "draws_rvars_to_standata_single",
    "empirical_coverage",
    "extract_attribute_arguments_stats",
    "gaffke_ci",
    "gaffke_p",
    "gaffke_test",
    "generate_datasets",
    "generated_quantities",
    "get_all_diagnostic_messages",
    "get_diagnostic_messages_single",
    "get_stats_for_submodel",
    "hidden_var_attribute",
    "inf_valid_var_attribute",
    "logical_diagnostic",
    "miscalibration_resampling_p",
    "miscalibration_resampling_test",
    "na_valid_var_attribute",
    "numeric_diagnostic",
    "plot_binary_calibration",
    "plot_binary_calibration_diff",
    "plot_contraction",
    "plot_coverage",
    "plot_coverage_diff",
    "plot_ecdf",
    "plot_ecdf_diff",
    "plot_rank_hist",
    "plot_sim_estimated",
    "possibly_constant_var_attribute",
    "posterior_cdf_from_model_probs",
    "recompute_SBC_statistics",
    "recompute_statistics",
    "remove_attribute_from_stats",
    "SBC_backend_bridgesampling",
    "SBC_backend_brms",
    "SBC_backend_brms_from_generator",
    "SBC_backend_cached",
    "SBC_backend_cmdstan_sample",
    "SBC_backend_cmdstan_variational",
    "SBC_backend_default_thin_ranks",
    "SBC_backend_extractBF_comparison",
    "SBC_backend_function",
    "SBC_backend_hash_for_cache",
    "SBC_backend_iid_draws",
    "SBC_backend_lmBF",
    "SBC_backend_mock",
    "SBC_backend_mock_rng",
    "SBC_backend_postprocess_cached_fit",
    "SBC_backend_preprocess_fit_for_cache",
    "SBC_backend_rjags",
    "SBC_backend_rstan_optimizing",
    "SBC_backend_rstan_sample",
    "SBC_datasets",
    "SBC_datasets_for_bf",
    "SBC_example_backend",
    "SBC_example_generator",
    "SBC_example_results",
    "SBC_fit",
    "SBC_fit_specific_dquants",
    "SBC_fit_to_BFBayesFactor",
    "SBC_fit_to_bridge_sampler",
    "SBC_fit_to_diagnostics",
    "SBC_fit_to_draws_matrix",
    "SBC_generator_brms",
    "SBC_generator_custom",
    "SBC_generator_function",
    "SBC_posterior_cdf",
    "SBC_print_example_model",
    "SBC_results",
    "SBC_results_diagnostic_messages",
    "SBC_results_diagnostics",
    "SBC_statistics_from_single_fit",
    "skip_diagnostic",
    "split_SBC_results_for_bf",
    "submodel_diagnostic",
    "submodel_var_attribute",
    "top_model_dquants",
    "validate_derived_quantities",
    "validate_generated_quantities",
    "validate_SBC_datasets",
    "validate_SBC_results",
    "validate_var_attributes",
    "var_attributes"
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  "_help": [
    {
      "page": "sub-.SBC_datasets",
      "title": "Subset an 'SBC_datasets' object.",
      "topics": [
        "[.SBC_datasets"
      ]
    },
    {
      "page": "sub-.SBC_results",
      "title": "Subset the results.",
      "topics": [
        "[.SBC_results"
      ]
    },
    {
      "page": "attribute_present",
      "title": "Get attribute presence for a vector of variable names.",
      "topics": [
        "attribute_present"
      ]
    },
    {
      "page": "attribute_present_stats",
      "title": "Check an attribute in the $stats element of the results for presence of an attribute.",
      "topics": [
        "attribute_present_stats"
      ]
    },
    {
      "page": "binary_calibration",
      "title": "Binary prediction calibration computation and visualisation.",
      "topics": [
        "binary_calibration_from_bp",
        "plot_binary_calibration",
        "plot_binary_calibration.data.frame",
        "plot_binary_calibration.SBC_results",
        "plot_binary_calibration_diff",
        "plot_binary_calibration_diff.data.frame",
        "plot_binary_calibration_diff.SBC_results"
      ]
    },
    {
      "page": "binary_probabilities_from_stats",
      "title": "Extract binary probabilities from SBC stats.",
      "topics": [
        "binary_probabilities_from_stats"
      ]
    },
    {
      "page": "bind_datasets",
      "title": "Combine multiple datasets together.",
      "topics": [
        "bind_datasets"
      ]
    },
    {
      "page": "bind_derived_quantities",
      "title": "Combine two lists of derived quantities",
      "topics": [
        "bind_derived_quantities"
      ]
    },
    {
      "page": "bind_globals",
      "title": "Combine two sets globals for use in derived quantities or backend",
      "topics": [
        "bind_globals"
      ]
    },
    {
      "page": "bind_results",
      "title": "Combine multiple SBC results together.",
      "topics": [
        "bind_results"
      ]
    },
    {
      "page": "binary-calibration-tests",
      "title": "Binary calibration tests",
      "topics": [
        "binary_miscalibration",
        "brier_resampling_p",
        "brier_resampling_test",
        "miscalibration_resampling_p",
        "miscalibration_resampling_test"
      ]
    },
    {
      "page": "cached_fit_filename",
      "title": "Provide a file where a cached result of a fit will be/was stored.",
      "topics": [
        "cached_fit_filename"
      ]
    },
    {
      "page": "calculate_prior_sd",
      "title": "Calculate prior standard deviation of a dataset",
      "topics": [
        "calculate_prior_sd"
      ]
    },
    {
      "page": "calculate_ranks_draws_matrix",
      "title": "Calculate ranks given variable values within a posterior distribution.",
      "topics": [
        "calculate_ranks_draws_matrix"
      ]
    },
    {
      "page": "check_all_SBC_diagnostics",
      "title": "Check diagnostics for an SBC results object.",
      "topics": [
        "check_all_SBC_diagnostics"
      ]
    },
    {
      "page": "combine-functions",
      "title": "Helper functions to be passed to ECDF-plots to combine variables in a single panel.",
      "topics": [
        "combine_all_variables",
        "combine_array_elements"
      ]
    },
    {
      "page": "combine_args",
      "title": "Combine two named lists and overwrite elements with the same name using the value from args2",
      "topics": [
        "combine_args"
      ]
    },
    {
      "page": "combine_var_attributes",
      "title": "Combine multiple sets of variable attributes.",
      "topics": [
        "combine_var_attributes"
      ]
    },
    {
      "page": "compute_dquants",
      "title": "Compute derived quantities based on given data and posterior draws.",
      "topics": [
        "compute_dquants"
      ]
    },
    {
      "page": "compute_SBC",
      "title": "Fit datasets and evaluate diagnostics and SBC metrics.",
      "topics": [
        "compute_SBC"
      ]
    },
    {
      "page": "data_for_ecdf_plots",
      "title": "Maybe not export in the end? Useful for debugging",
      "topics": [
        "data_for_ecdf_plots"
      ]
    },
    {
      "page": "default_chunk_size",
      "title": "Determines the default chunk size.",
      "topics": [
        "default_chunk_size"
      ]
    },
    {
      "page": "default_cores_per_fit",
      "title": "Determines the default cores per single fit.",
      "topics": [
        "default_cores_per_fit"
      ]
    },
    {
      "page": "derived_quantities",
      "title": "Create a definition of derived quantities evaluated in R.",
      "topics": [
        "derived_quantities"
      ]
    },
    {
      "page": "dquants_var_attributes",
      "title": "Get the 'var_attributes()' object associated with the derived quantities",
      "topics": [
        "dquants_var_attributes"
      ]
    },
    {
      "page": "empirical_coverage",
      "title": "Compute observed coverage of posterior credible intervals.",
      "topics": [
        "empirical_coverage"
      ]
    },
    {
      "page": "extract_attribute_arguments_stats",
      "title": "Extract arguments of a given attribute from the $stats element of the results",
      "topics": [
        "extract_attribute_arguments_stats"
      ]
    },
    {
      "page": "gaffke_test",
      "title": "Non-parametric test for the mean of a bounded variable.",
      "topics": [
        "gaffke_ci",
        "gaffke_p",
        "gaffke_test"
      ]
    },
    {
      "page": "generate_datasets",
      "title": "Generate datasets.",
      "topics": [
        "generate_datasets"
      ]
    },
    {
      "page": "get_stats_for_submodel",
      "title": "Extract stats for a submodel from a Bayes factor results",
      "topics": [
        "get_stats_for_submodel"
      ]
    },
    {
      "page": "guess_rank_hist_bins",
      "title": "Guess the number of bins for 'plot_rank_hist()'.",
      "topics": [
        "guess_rank_hist_bins"
      ]
    },
    {
      "page": "plot_contraction",
      "title": "Prior/posterior contraction plot.",
      "topics": [
        "plot_contraction",
        "plot_contraction.data.frame"
      ]
    },
    {
      "page": "plot_coverage",
      "title": "Plot the observed coverage and its uncertainty.",
      "topics": [
        "plot_coverage",
        "plot_coverage_diff"
      ]
    },
    {
      "page": "ECDF-plots",
      "title": "Plot the ECDF-based plots.",
      "topics": [
        "plot_ecdf",
        "plot_ecdf_diff"
      ]
    },
    {
      "page": "plot_rank_hist",
      "title": "Plot rank histogram of an SBC results.",
      "topics": [
        "plot_rank_hist",
        "plot_rank_hist.data.frame"
      ]
    },
    {
      "page": "plot_sim_estimated",
      "title": "Plot the simulated \"true\" values versus posterior estimates",
      "topics": [
        "plot_sim_estimated",
        "plot_sim_estimated.data.frame"
      ]
    },
    {
      "page": "rbind.SBC_bridgesampling_diagnostics",
      "title": "Custom rbind implementation maintainig information about submodels",
      "topics": [
        "rbind.SBC_bridgesampling_diagnostics"
      ]
    },
    {
      "page": "recompute_SBC_statistics",
      "title": "Recompute SBC statistics without refitting models.",
      "topics": [
        "recompute_SBC_statistics"
      ]
    },
    {
      "page": "remove_attribute_from_stats",
      "title": "Remove an attribute from a 'data.frame' column with attributes.",
      "topics": [
        "remove_attribute_from_stats"
      ]
    },
    {
      "page": "SBC_backend_bridgesampling",
      "title": "Backend using bridgesampling to do Bayes factor calculation (and Bayesian Model Averaging) over two candidate models.",
      "topics": [
        "SBC_backend_bridgesampling"
      ]
    },
    {
      "page": "SBC_backend_brms",
      "title": "Build a backend based on the 'brms' package.",
      "topics": [
        "SBC_backend_brms"
      ]
    },
    {
      "page": "SBC_backend_brms_from_generator",
      "title": "Build a brms backend, reusing the compiled model from a previously created 'SBC_generator_brms' object.",
      "topics": [
        "SBC_backend_brms_from_generator"
      ]
    },
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