Contract-First Bayesian Workflows for Hierarchical Behavioural Data

Documentation for package ‘gp3bayes’ version 0.5.0

Help Pages

-- 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