# Contract-First Bayesian Workflows for Hierarchical Behavioural Data

## Documentation for package ‘gp3bayes’ version 0.5.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M P R S T V W

## -- A --

advanced_pupil_trajectory_table | Summarise an advanced pupil trajectory
analysis_bundle_table | Analysis-Bundle Status Table
analysis_manifest_table | Summarise Manifest Components
apply_transformation_recipe | Apply a Recorded Transformation Recipe
as.data.frame.gp3bayes_pupil_contract | Convert a pupil contract to a transparent table
as.data.frame.gp3bayes_pupil_estimand | Convert a pupil estimand to a data frame
assess_binary_prior_sensitivity | Assess Binary Prior Sensitivity
assess_duration_prior_sensitivity | Assess Duration Prior Sensitivity
assess_powerscaled_sensitivity | Assess Power-Scaled Prior and Likelihood Sensitivity
as_pupil_prediction_draws | Create a lightweight pupil prediction object from frozen draws
audit_advanced_pupil_identifiability | Audit empirical support for an advanced pupil model specification
audit_backend_parity | Audit Posterior Parity Across rstan and cmdstanr
audit_binocular_pupil_readiness | Audit binocular pupil availability and agreement descriptively
audit_design_support | Audit Overall Design Support
audit_duration_boundaries | Audit Duration Range and Censoring Boundaries
audit_duration_unit_invariance | Audit Duration-Unit Invariance
audit_estimand_invariance | Audit Estimand Invariance Against a Declared Tolerance
audit_fixed_effect_design | Audit the Fixed-Effects Design Matrix
audit_missingness_structure | Audit Missingness Structure Before Model Fitting
audit_model_readiness | Audit Data Readiness for an Approved Model Contract
audit_model_readiness_strict | Run a Strict Model-Readiness Audit
audit_prediction_support | Audit Prediction Support
audit_pupil_computational_budget | Audit computational complexity before fitting an advanced pupil model
audit_pupil_measurement_context | Audit pupil measurement and confound context
audit_pupil_measurement_model | Audit a declared measurement model against data
audit_pupil_missingness | Audit missingness in an advanced pupil specification
audit_pupil_predictive_calibration | Audit posterior predictive calibration on explicit evaluation data
audit_pupil_readiness | Audit pupil-timecourse readiness
audit_pupil_temporal_dependence | Audit empirical temporal dependence before model fitting
audit_random_effects_support | Audit Random-Effects Support

## -- B --

backend_capabilities | Report Bayesian Backend Capabilities
backend_environment_table | Backend-Environment Table
backend_parity_table | Backend-Parity Table
bayesian_backend_capabilities | Report Optional Bayesian Backend Capabilities
binary_calibration_error | Binary Calibration Error
binary_calibration_table | Binary Calibration Table
binary_calibration_uncertainty | Binary Calibration Uncertainty
binary_calibration_uncertainty_table | Binary Calibration-Uncertainty Table
binary_confusion_table | Binary Confusion Table
binary_group_calibration | Grouped Binary Calibration
binary_precision_recall_curve | Binary Precision-Recall Curve
binary_prediction_scores | Binary Prediction Scores
binary_roc_curve | Binary ROC Curve
binary_threshold_metrics | Binary Threshold-Metric Curve
build_model_formula | Build an Approved Model Formula

## -- C --

capture_gp3bayes_schema | Capture the Structural Schema of a gp3bayes Object
check_advanced_pupil_prior_predictive | Check advanced pupil priors through prior-only simulation
check_binary_posterior_predictive | Check Binary Posterior Predictive Behaviour
check_binary_ppc_details | Run Detailed Binary Posterior Predictive Checks
check_binary_prior_predictive | Check Binary Prior Predictive Behaviour
check_cmdstan_backend | Check the CmdStanR Backend
check_duration_posterior_predictive | Check Duration Posterior Predictive Behaviour
check_duration_ppc_details | Run Detailed Duration Posterior Predictive Checks
check_duration_prior_predictive | Check Duration Prior Predictive Behaviour
check_model_ppc | Check Posterior Predictive Behaviour
check_pupil_posterior_predictive | Run pupil-specific posterior predictive checks
check_pupil_prior_predictive | Check the approved pupil priors predictively
collect_model_evidence | Collect Model Evidence Without Declaring Model Adequacy
compare_analysis_manifests | Compare Analysis Manifests
compare_estimand_sensitivity | Compare Estimand Sensitivity Across Alternative Fits
compare_gp3bayes_schemas | Compare gp3bayes Object Schemas
compare_psis_loo | Compare Models with PSIS-LOO
compare_pupil_autocorrelation | Compare residual autocorrelation across fitted advanced models
compare_pupil_lfo | Compare executed leave-future-out validations
compare_pupil_models | Compare fitted pupil models predictively
compare_pupil_sensitivity_estimands | Compare declared pupil sensitivity estimands
compute_kfold_cv | Compute Governed Exact K-Fold Cross-Validation
compute_loo_model_weights | Compute LOO Model-Averaging Weights
compute_psis_loo | Compute PSIS-LOO for a gp3bayes Fit
compute_psis_loo_from_log_lik | Compute PSIS-LOO from a Log-Likelihood Matrix
create_advanced_pupil_prior_specification | Create an advanced pupil prior specification
create_analysis_bundle | Create a Structured Post-Fit Analysis Bundle
create_analysis_figure_set | Create Publication Figures from an Analysis Bundle
create_analysis_manifest | Create an Analysis Manifest
create_binary_model_report | Create a Structured Binary Model Report
create_brms_sbc_plan | Create a brms-Based Simulation-Based Calibration Plan
create_complete_evidence_inventory | Create a Complete Evidence Inventory
create_contrast_coding_sensitivity_specification | Create a Contrast-Coding Sensitivity Specification
create_custom_sbc_plan | Create an Expert Custom SBC Plan
create_diagnostic_dashboard | Create a Diagnostic Dashboard Object
create_diagnostic_dashboard_figures | Create Diagnostic Dashboard Figures
create_duration_model_report | Create a Structured Duration Model Report
create_duration_unit_sensitivity_specification | Create a Duration-Unit Sensitivity Specification
create_figure_set | Create a Named Figure Set
create_group_deletion_sensitivity_plan | Create a Group-Deletion Sensitivity Plan
create_loo_influence_atlas | Create a LOO Influence Atlas
create_model_card | Create a gp3bayes Model Card
create_model_contract | Create an Approved Bayesian Model Contract
create_model_evidence_report | Create a Model Evidence Report
create_model_specification | Create a Complete Model Specification
create_prediction_contrast_profile | Create a Prediction Contrast Profile
create_prediction_grid | Create a Governed Prediction Grid
create_prediction_profile | Create a Numeric Prediction Profile
create_prediction_surface | Create a Two-Dimensional Prediction Surface
create_predictive_distribution_atlas | Create a Posterior-Predictive Distribution Atlas
create_predictor_scaling_sensitivity_specification | Create a Predictor-Scaling Sensitivity Specification
create_prior_specification | Create a Backend-Independent Prior Specification
create_publication_registry | Create a Publication Registry
create_publication_table_set | Extract Publication Tables from an Analysis Bundle
create_pupil_advanced_sensitivity_suite | Create a pre-fit advanced pupillometry sensitivity suite
create_pupil_arma_spec | Create an explicit bounded ARMA configuration
create_pupil_contract | Create a governed pupil-timecourse contract
create_pupil_gp_spec | Create a Gaussian-process configuration for pupil trajectories
create_pupil_lfo_plan | Create an explicit leave-future-out validation plan
create_pupil_measurement_model | Create a governed measurement-uncertainty specification
create_pupil_missingness_spec | Create a governed missingness specification
create_pupil_model_set | Create a named set of fitted pupil models
create_pupil_sensitivity_suite | Create a governed pupil sensitivity suite
create_pupil_validation_plan | Create an explicit pupil predictive-validation plan
create_random_slope_sensitivity_plan | Create a Random-Slope Sensitivity Plan
create_reporting_checklist | Create a Reporting Checklist
create_sensitivity_suite_plan | Create a Sensitivity Suite Plan
create_transformation_recipe | Create a Reusable Transformation Recipe

## -- D --

design_support_table | Design-Support Table
detect_binary_separation | Detect Separation in the Binary Fixed-Effects Screen
diagnose_advanced_pupil_fit | Diagnose an advanced pupil fit
diagnose_binary_fit | Diagnose a Fitted Binary Model
diagnose_duration_fit | Diagnose a Fitted Duration Model
diagnose_model_fit | Diagnose an Approved gp3bayes Fit
diagnose_pupil_fit | Diagnose temporal and sampling behaviour of a pupil fit
diagnostic_dashboard_table | Diagnostic Dashboard Table
duration_pit_table | Duration Probability-Integral-Transform Table
duration_prediction_scores | Duration Prediction Scores
duration_qq_table | Duration Predictive Q-Q Table
duration_quantile_calibration | Duration Quantile Calibration
duration_tail_check | Duration Tail Check

## -- E --

estimand_sensitivity_table | Estimand Sensitivity Table
estimate_binocular_pupil_trajectory | Estimate joint binocular posterior trajectories
estimate_model_estimands | Estimate the Approved Primary Estimands
estimate_pupil_auc | Estimate area under a declared pupil-response window
estimate_pupil_dynamic_contrast | Estimate a dynamic posterior contrast between two pupil conditions
estimate_pupil_peak | Estimate posterior peak pupil response inside a declared window
estimate_pupil_peak_latency | Estimate posterior peak latency inside a declared window
estimate_pupil_residual_scale | Estimate the residual-scale trajectory from a distributional model
estimate_pupil_response_parameters | Estimate nonlinear response-shape parameters
estimate_pupil_threshold_duration | Estimate posterior duration above a prespecified dynamic threshold
estimate_pupil_trajectory | Estimate posterior pupil trajectories
estimate_pupil_trajectory_derivative | Estimate posterior temporal derivatives of a pupil trajectory
estimate_pupil_window | Estimate a declared-window mean pupil response
estimate_standardized_duration_estimands | Estimate Design-Standardised Duration Estimands
estimate_standardized_probability_contrast | Estimate a Design-Standardised Binary Probability Contrast
evaluate_pathological_simulation | Evaluate a Pathological Simulation Against the Contract Gate
evidence_inventory_table | Evidence Inventory Table
extract_expected_predictions | Extract Expected Posterior Predictions
extract_linear_predictions | Extract Linear-Predictor Draws
extract_log_likelihood | Extract Pointwise Log-Likelihood Draws
extract_posterior_draws | Extract Posterior Draws from a gp3bayes Fit
extract_posterior_predictions | Extract Posterior Predictive Draws
extract_sampler_diagnostics | Extract NUTS Sampler Diagnostics

## -- F --

fit_advanced_pupil_model | Fit an advanced pupil model using rstan
fit_advanced_pupil_model_backend | Fit an advanced pupil model through an approved brms backend
fit_advanced_pupil_model_cmdstanr | Fit an advanced pupil model using cmdstanr
fit_binary_model | Fit an Approved Hierarchical Binary Model
fit_binary_model_backend | Fit a Binary Model with a Selected Full-MCMC Backend
fit_binary_model_cmdstanr | Fit a Binary Model with a Selected Full-MCMC Backend
fit_binocular_pupil_model | Fit a joint binocular pupil model
fit_duration_model | Fit an Approved Hierarchical Lognormal Duration Model
fit_duration_model_backend | Fit a Duration Model with a Selected Full-MCMC Backend
fit_duration_model_cmdstanr | Fit a Duration Model with a Selected Full-MCMC Backend
fit_pupil_model | Fit a pupil model through the fixed rstan route
fit_pupil_model_backend | Fit the restricted pupil time-course model with an approved backend
fit_pupil_model_cmdstanr | Fit a pupil model through the fixed cmdstanr route
fit_pupil_response_shape_model | Fit the experimental nonlinear response-shape model
freeze_analysis_manifest | Freeze an Analysis Manifest
freeze_gp3bayes_schema | Freeze a gp3bayes Object Schema

## -- G --

gazepoint_pupil_mapping_table | Return the Gazepoint pupil mapping audit table
gp3bayes_specification_traceability | Specification-Closure Traceability Matrix
grouped_prediction_check | Grouped Posterior Predictive Check
group_deletion_sensitivity_table | Group-Deletion Sensitivity Table
group_effect_draws_table | Group-Level Posterior Draw Table
group_effect_rank_probability_table | Group-Level Rank-Probability Table
group_effect_table | Group-Level Effect Table
group_prediction_summary | Group Prediction Summary

## -- I --

identify_identifier_like_predictors | Identify Identifier-Like Numeric Predictors
identify_loo_influential_observations | Identify Influential PSIS-LOO Observations
identify_mcmc_issues | Identify MCMC Diagnostic Flags
inspect_gazepoint_pupil_schema | Inspect verified Gazepoint pupil and gaze fields
interaction_prior_summary | Summarise Separate Interaction Prior Metadata
invert_transformation_recipe | Invert a Recorded Transformation Recipe

## -- L --

loo_diagnostic_table | LOO Diagnostic Table
loo_flagged_data | Flagged LOO Observation Data
loo_group_influence_table | Aggregate LOO Influence by a Declared Group
loo_influence_atlas_table | LOO Influence Atlas Table
loo_influence_summary | LOO Influence Summary
loo_pointwise_table | Pointwise LOO Table
loo_summary_table | LOO Summary Table

## -- M --

manifest_comparison_table | Manifest-Comparison Table
materialize_pupil_advanced_sensitivity_scenario | Materialize one advanced sensitivity scenario
materialize_pupil_sensitivity_scenario | Materialize one declared pupil sensitivity scenario
mcmc_diagnostic_table | Modern MCMC Diagnostic Table
missingness_audit_table | Missingness-Audit Table
model_card_table | Model-Card Evidence Table
model_comparison_table | LOO Model-Comparison Table
model_evidence_table | Model-Evidence Table
model_weights_table | LOO Model-Weight Table
model_workflow_status | Summarise Workflow Stage Completion

## -- P --

plot.gp3bayes_kfold_cv | Plot Governed Exact K-Fold Results
plot.gp3bayes_strict_readiness_audit | Plot a Strict Readiness Audit
plot_advanced_pupil_simulation | Plot simulated advanced pupil trajectories
plot_advanced_pupil_trajectory | Plot an advanced posterior pupil trajectory
plot_autocorrelation | Autocorrelation Diagnostic Plot
plot_backend_environment_gg | Plot Backend Environment Checks with ggplot2
plot_backend_parity_gg | Plot Backend Parity with ggplot2
plot_binary_calibration | Binary Calibration Plot
plot_binary_calibration_uncertainty | Plot Binary Calibration Uncertainty
plot_binary_group_calibration | Grouped Binary Calibration Plot
plot_binary_precision_recall | Binary Precision-Recall Plot
plot_binary_roc | Binary ROC Plot
plot_binary_threshold_metrics | Binary Threshold-Metric Plot
plot_binocular_pupil_trajectory | Plot binocular posterior trajectories
plot_design_support_gg | Plot Design-Support Components with ggplot2
plot_diagnostic_dashboard | Plot Diagnostic Dashboard Availability
plot_duration_pit | Duration PIT Plot
plot_duration_qq | Duration Predictive Q-Q Plot
plot_duration_quantile_calibration | Duration Quantile-Calibration Plot
plot_duration_tail | Duration Tail-Check Plot
plot_estimand_intervals | Estimand Interval Plot
plot_estimand_sensitivity_gg | Plot Estimand Sensitivity with ggplot2
plot_exceedance_probability | Prediction Exceedance-Probability Plot
plot_grouped_prediction_check | Grouped Posterior Predictive Plot
plot_group_deletion_sensitivity | Plot Group-Deletion Sensitivity
plot_group_effects | Group-Effect Plot
plot_group_effect_distribution | Plot Group-Effect Posterior Distributions
plot_group_effect_rank_probability | Plot Group-Effect Rank Probabilities
plot_group_predictions | Group Prediction Plot
plot_loo_group_elpd | Plot Grouped Pointwise ELPD Contribution
plot_loo_group_influence | Plot Grouped LOO Influence
plot_loo_influence | LOO Influence Plot
plot_loo_influence_rank | Plot Ranked LOO Influence
plot_loo_pareto_vs_elpd | Plot Pareto-k versus Pointwise ELPD
plot_loo_pointwise_elpd | Plot Pointwise LOO ELPD
plot_manifest_comparison_gg | Plot Manifest Differences with ggplot2
plot_mcmc_quality | MCMC Review-Flag Plot
plot_missingness_gg | Plot Missingness Fractions with ggplot2
plot_model_comparison | LOO Model-Comparison Plot
plot_model_evidence_gg | Plot Model-Evidence Availability with ggplot2
plot_model_weights | LOO Model-Weight Plot
plot_posterior_areas | Posterior Area Plot
plot_posterior_correlations | Posterior Correlation Plot
plot_posterior_density | Posterior Density Plot
plot_posterior_intervals | Posterior Interval Plot
plot_posterior_pairs | Posterior Pairs Plot
plot_powerscale_sensitivity_gg | Plot Power-Scale Sensitivity with ggplot2
plot_ppc_statistic | Posterior Predictive Statistic Plot
plot_prediction_contrast_profile | Plot a Prediction Contrast Profile
plot_prediction_draws | Prediction-Draw Distribution Plot
plot_prediction_gradient | Plot Prediction-Profile Gradients
plot_prediction_intervals | Prediction-Interval Plot
plot_prediction_interval_width | Prediction Interval-Width Plot
plot_prediction_profile | Plot a Prediction Profile
plot_prediction_rank_probabilities | Prediction Rank-Probability Plot
plot_prediction_score_uncertainty | Plot Prediction Score Uncertainty
plot_prediction_support | Prediction-Support Plot
plot_prediction_surface | Plot a Prediction Surface
plot_prediction_surface_uncertainty | Plot Prediction-Surface Uncertainty
plot_predictive_atlas_statistics | Plot Predictive Atlas Statistics
plot_predictive_coverage | Predictive-Coverage Plot
plot_predictive_quantile_envelope | Plot Posterior-Predictive Quantile Envelope
plot_predictive_residuals | Predictive-Residual Plot
plot_prior_posterior_contraction | Plot Prior-to-Posterior Contraction
plot_prior_posterior_density | Plot Declared Prior and Posterior Densities
plot_prior_posterior_intervals | Plot Prior and Posterior Intervals
plot_prior_posterior_shift | Plot Prior-to-Posterior Location Shift
plot_prior_sensitivity | Plot Prior-Scale Sensitivity
plot_prior_sensitivity_scenarios | Plot Prior-Sensitivity Scenario Maxima
plot_pupil_autocorrelation_comparison | Plot residual autocorrelation comparison
plot_pupil_dynamic_contrast | Plot a dynamic pupil condition contrast
plot_pupil_estimand | Plot declared-window pupil estimands
plot_pupil_gp_hyperparameters | Plot Gaussian-process hyperparameters
plot_pupil_identifiability_audit | Plot advanced identifiability/design-support audit
plot_pupil_lfo | Plot leave-future-out scores
plot_pupil_measurement_audit | Plot gaze/PFE and luminance measurement-context evidence
plot_pupil_measurement_uncertainty | Plot measurement-uncertainty audit
plot_pupil_missingness | Plot missing-response fraction over time
plot_pupil_model_comparison | Plot predictive model comparison
plot_pupil_model_complexity | Plot advanced model computational complexity
plot_pupil_observed_trajectory | Plot observed pupil trajectories
plot_pupil_posterior_trajectory | Plot posterior pupil trajectories or condition differences
plot_pupil_ppc | Plot pupil posterior-predictive evidence
plot_pupil_predictive_calibration | Plot posterior predictive calibration
plot_pupil_readiness | Plot pupil readiness evidence
plot_pupil_residual_acf | Plot pupil residual autocorrelation
plot_pupil_residual_scale | Plot posterior residual scale over time
plot_pupil_residual_spectrum | Plot residual spectrum
plot_pupil_response_parameters | Plot experimental nonlinear response parameters
plot_pupil_sensitivity | Plot pupil sensitivity scenarios or result comparisons
plot_pupil_temporal_dependence | Plot empirical temporal-dependence audit
plot_pupil_trajectory_derivative | Plot posterior pupil trajectory derivative
plot_pupil_validation | Plot pupil validation evidence
plot_random_intercept_variance_partition | Plot Random-Intercept Variance Partition
plot_random_slope_sensitivity | Plot Random-Slope Sensitivity
plot_rank_diagnostics | Rank-Diagnostic Plot
plot_recovery_bias | Plot Recovery Standardized Bias
plot_recovery_coverage | Plot Recovery Coverage
plot_recovery_estimates | Plot Repetition-Level Recovery Estimates
plot_recovery_fit_status | Plot Recovery Fit Status
plot_recovery_rmse | Plot Recovery RMSE
plot_reporting_checklist | Plot a Reporting Checklist
plot_sampler_diagnostics | Sampler-Diagnostic Plot
plot_sampling_diagnostics | Plot Sampling Diagnostics
plot_sbc_coverage_gg | SBC Coverage Plot
plot_sbc_ecdf_gg | SBC ECDF-Difference Plot
plot_sbc_rank_gg | SBC Rank-Histogram Plot
plot_sbc_simulated_vs_estimated_gg | SBC Simulated-versus-Estimated Plot
plot_schema_comparison_gg | Plot Schema Differences with ggplot2
plot_sensitivity_suite_gg | Plot a Sensitivity Suite with ggplot2
plot_uncertainty_decomposition | Prediction-Uncertainty Plot
plot_variance_components | Variance-Component Plot
posterior_correlation_table | Posterior Correlation Table
posterior_interval_table | Posterior Interval Table
posterior_predictive_statistic | Posterior Predictive Statistic Check
posterior_predictive_summary_table | Posterior Predictive Summary Table
posterior_probability_table | Posterior Direction and ROPE Probability Table
powerscale_sensitivity_table | Power-Scale Sensitivity Table
powerscale_sequence_for_fit | Create a Power-Scaling Sequence
ppc_statistic_table | Posterior Predictive Statistic Table
prediction_contrast | Posterior Prediction Contrast
prediction_contrast_profile_table | Prediction Contrast Profile Table
prediction_draws_long | Convert Prediction Draws to Long Form
prediction_exceedance_probability | Posterior Exceedance Probabilities
prediction_gradient_table | Prediction-Profile Gradient Table
prediction_interval_width | Prediction Interval Width Table
prediction_pairwise_contrasts | Pairwise Prediction Contrasts
prediction_profile_table | Prediction Profile Table
prediction_rank_probabilities | Posterior Ranking Probabilities for Prediction Rows
prediction_score_uncertainty | Posterior Uncertainty in Prediction Scores
prediction_score_uncertainty_table | Prediction Score-Uncertainty Table
prediction_support_table | Prediction-Support Table
prediction_surface_table | Prediction Surface Table
prediction_table | Prediction Summary Table
prediction_uncertainty_decomposition | Decompose Prediction Uncertainty Descriptively
predictive_coverage_table | Posterior Predictive Coverage Table
predictive_distribution_atlas_table | Predictive Distribution Atlas Table
predictive_quantile_envelope | Posterior-Predictive Quantile Envelope
predictive_residuals | Posterior Predictive Residuals
predict_advanced_pupil_trajectory | Predict an advanced pupil trajectory
predict_binary_probability | Binary Event-Probability Predictions
predict_duration | Duration Predictions
predict_model | Posterior Prediction for Approved gp3bayes Models
predict_pupil_trajectory | Predict governed pupil trajectories
preflight_model_specification | Preflight an Approved Model Specification
prepare_binocular_pupil_timecourse | Prepare binocular pupil data without averaging eyes
prepare_hierarchical_binary_data | Prepare Hierarchical Binary Data
prepare_hierarchical_duration_data | Prepare Hierarchical Duration Data
prepare_pupil_timecourse | Prepare a pupil time course under explicit transformations
prior_posterior_bridge | Create a Declared-Prior versus Posterior Bridge
prior_posterior_distance_table | Prior-versus-Posterior Distance Table
prior_posterior_draws_long | Long Prior and Posterior Draw Table
prior_posterior_summary_table | Prior-versus-Posterior Summary Table
prior_sensitivity_scenario_table | Prior Sensitivity Scenario Table
prior_sensitivity_table | Prior Sensitivity Table
prior_specification_table | Prior-Specification Table
publication_registry_table | Publication Registry Table
pupil_advanced_capabilities | Report the gp3bayes 0.5 advanced-pupillometry capability boundary
pupil_advanced_compatibility_table | Report governed compatibility rules for 0.5 advanced models
pupil_advanced_mapping_table | Inspect the resolved 0.5 pupil column mapping
pupil_advanced_specification_table | Tabulate an advanced pupil model specification
pupil_autocorrelation_table | Tabulate a temporal-dependence audit
pupil_binocular_agreement_table | Summarise binocular posterior agreement
pupil_binocular_correlation | Extract posterior residual binocular correlation
pupil_binocular_difference | Estimate posterior right-minus-left binocular differences
pupil_condition_contrast | Estimate a posterior condition-difference trajectory
pupil_distribution_table | Tabulate a pupil distribution declaration or advanced specification
pupil_dynamic_contrast_table | Tabulate a dynamic pupil contrast
pupil_gp_hyperparameters | Extract Gaussian-process hyperparameters
pupil_gp_table | Tabulate GP hyperparameters
pupil_identifiability_table | Tabulate advanced pupil identifiability/design-support audit
pupil_measurement_audit_table | Extract a pupil measurement-context table
pupil_measurement_uncertainty_table | Summarise measurement uncertainty declared in a model
pupil_missingness_table | Tabulate missingness audit results
pupil_model_card | Build an auditable advanced pupil model card
pupil_model_card_table | Tabulate a pupil model card
pupil_model_comparison_table | Tabulate model comparison
pupil_model_weights | Compute explicit predictive model weights
pupil_ppc_table | Extract pupil PPC evidence tables
pupil_readiness_table | Extract pupil readiness tables
pupil_residual_acf | Summarise residual autocorrelation for a pupil fit
pupil_residual_scale_table | Tabulate posterior residual scale
pupil_residual_spectrum | Compute a descriptive residual spectrum
pupil_response_parameter_table | Tabulate nonlinear response parameters
pupil_sensitivity_table | Extract pupil sensitivity scenarios or comparison results
pupil_specification_table | Convert a pupil specification to a publication-ready table
pupil_trajectory_derivative_table | Tabulate posterior pupil trajectory derivatives
pupil_trajectory_table | Convert a pupil trajectory to a table
pupil_validation_table | Extract a pupil validation table

## -- R --

random_intercept_variance_partition | Random-Intercept Latent Variance Partition
random_intercept_variance_partition_table | Random-Intercept Variance-Partition Table
random_slope_sensitivity_table | Random-Slope Sensitivity Table
read_analysis_manifest | Read a Frozen Analysis Manifest
read_gp3bayes_schema | Read a Frozen gp3bayes Object Schema
recovery_estimate_table | Recovery Estimate Table
recovery_fit_status_table | Recovery Fit-Status Table
recovery_parameter_table | Recovery Parameter Summary Table
register_publication_figure | Register a Publication Figure
register_publication_table | Register a Publication Table
review_duration_extremes | Review Extreme Positive Durations Without Deleting Them
run_binary_recovery | Run Binary Parameter Recovery
run_duration_recovery | Run Duration Parameter Recovery
run_group_deletion_sensitivity | Run a Group-Deletion Sensitivity Plan
run_random_slope_sensitivity | Run Random-Intercept versus Random-Slope Sensitivity
run_sbc_plan | Run a Simulation-Based Calibration Plan
run_sensitivity_suite | Run a Unified Sensitivity Suite

## -- S --

sampler_diagnostic_table | Summarise NUTS Sampler Diagnostics
save_figure_set | Save a Figure Set
save_publication_registry_figures | Save Publication Registry Figures
sbc_overview_table | SBC Overview Table
sbc_stats_table | SBC Statistics Table
schema_comparison_table | Schema-Comparison Table
score_pupil_predictions | Score posterior predictive draws against observed pupil values
sensitivity_suite_table | Sensitivity-Suite Table
simulate_advanced_pupil_timecourse | Simulate advanced dynamic pupil time courses
simulate_binary_pathology | Simulate a Dedicated Binary Pathology Scenario
simulate_binocular_pupil_timecourse | Simulate joint binocular pupil traces
simulate_declared_prior_draws | Simulate Marginal Draws from Declared gp3bayes Priors
simulate_duration_pathology | Simulate a Dedicated Duration Pathology Scenario
simulate_hierarchical_binary_data | Simulate Hierarchical Binary Data
simulate_hierarchical_duration_data | Simulate Hierarchical Lognormal Duration Data
simulate_pupil_response_shape | Simulate data from the experimental nonlinear response-shape family
simulate_pupil_timecourse | Simulate deterministic hierarchical pupil time courses
specify_advanced_pupil_timecourse_model | Specify an advanced governed pupil time-course model
specify_binary_model | Specify a Backend-Independent Binary Model
specify_binary_model_with_interaction_prior | Specify a Binary Model with a Separate Interaction Prior
specify_binocular_pupil_model | Specify a joint binocular pupil model
specify_duration_model | Specify a Backend-Independent Duration Model
specify_duration_model_with_interaction_prior | Specify a Duration Model with a Separate Interaction Prior
specify_pupil_distribution | Declare an advanced pupil observation distribution
specify_pupil_response_shape_model | Specify the experimental nonlinear pupil response-shape model
specify_pupil_timecourse_model | Specify the restricted hierarchical pupil time-course model
summarise_binary_group_variation | Summarise Binary Outcome Variation Within Groups
summarise_binary_posterior | Summarise a Binary Posterior
summarise_condition_balance | Summarise Overall Condition Balance
summarise_duration_posterior | Summarise a Duration Posterior
summarise_estimand_draws | Summarise Posterior Estimand Draws
summarise_mcmc_quality | Summarise MCMC Quality Evidence
summarise_model_posterior | Summarise an Approved gp3bayes Posterior
summarise_pupil_posterior | Summarise a fitted pupil posterior
summarise_sbc_result | Summarise an SBC Result
summarise_sensitivity_suite | Summarise a Sensitivity Suite

## -- T --

theme_gp3bayes | gp3bayes Publication Theme
translate_advanced_pupil_model_to_brms | Translate an advanced pupil model to brms without fitting
translate_binary_model_to_brms | Translate a Binary Model Specification to brms
translate_binary_model_with_interaction_prior | Translate an Advanced Binary Specification to brms
translate_binocular_pupil_model_to_brms | Translate a binocular specification to a brms multivariate formula
translate_duration_model_to_brms | Translate a Duration Model Specification to brms
translate_duration_model_with_interaction_prior | Translate an Advanced Duration Specification to brms
translate_pupil_model_to_brms | Translate an approved pupil model to brms
translate_pupil_response_shape_to_brms | Translate the experimental response-shape model to brms

## -- V --

validate_analysis_manifest | Validate an Analysis Manifest
validate_backend_environment | Validate a Bayesian Backend Environment
validate_gp3bayes_object | Validate a gp3bayes Object
validate_gp3bayes_schema | Validate an Object Against a Frozen gp3bayes Schema
validate_prior_specification | Validate a Prior Specification
validate_publication_registry | Validate a Publication Registry
validate_pupil_leave_future_out | Execute or materialize leave-future-out validation
validate_pupil_model | Validate a pupil model for an explicit prediction target
validate_transformation_replay | Validate Exact Transformation Replay
variance_component_table | Variance-Component Posterior Table

## -- W --

write_analysis_bundle_report | Write an Analysis-Bundle Markdown Report
write_diagnostic_dashboard_report | Write a Diagnostic Dashboard Report
write_model_card | Write a Model Card
write_publication_registry | Write a Publication Registry
write_reproducibility_report | Write a Reproducibility Report