Package: gp3bayes 0.5.0

Stefanos Balaskas

gp3bayes: Contract-First Bayesian Workflows for Hierarchical Behavioural Data

Provides transparent, contract-first infrastructure for Bayesian analysis of repeated-measures and hierarchical behavioural data. It supports approved Bernoulli-logit, positive lognormal duration, and governed Gaussian dynamic-pupillometry workflows with strict readiness auditing, deterministic simulation, explicit preparation and transformation replay, inspectable scale-aware priors, prior and posterior predictive checks, restricted optional fitting through 'brms' with either 'rstan' or 'cmdstanr', sampling and temporal diagnostics, explicit posterior estimands, sensitivity analysis, target-specific predictive validation, simulation-based calibration, and conservative reporting. Core contracts and validation remain backend-independent. Version 0.5 adds governed robust and distributional dynamic pupillometry, bounded ARMA residual structures, Gaussian-process trajectories, explicit measurement uncertainty and missing-data models, joint binocular analysis, predictive model comparison, functional posterior estimands, and experimental nonlinear response-shape models while preserving explicit scientific and computational governance boundaries.

Authors:Stefanos Balaskas [aut, cre, cph]

gp3bayes_0.5.0.tar.gz
gp3bayes_0.5.0.zip(r-4.7-any)gp3bayes_0.5.0.zip(r-4.6-any)gp3bayes_0.5.0.zip(r-4.5-any)
gp3bayes_0.5.0.tgz(r-4.6-any)gp3bayes_0.5.0.tgz(r-4.5-any)
gp3bayes_0.5.0.tar.gz(r-4.7-any)gp3bayes_0.5.0.tar.gz(r-4.6-any)
gp3bayes_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gp3bayes/json (API)

# Install 'gp3bayes' in R:
install.packages('gp3bayes', repos = c('https://stefanosbalaskas.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/stefanosbalaskas/gp3bayes/issues

Pkgdown/docs site:https://stefanosbalaskas.github.io

On CRAN:

Conda:

6.17 score 117 downloads 458 exports 1 dependencies

Last updated from:0ad32d8921. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK285
source / vignettesOK412
linux-releaseOK282
macos-releaseOK152
macos-oldrelOK127
windows-develOK214
windows-releaseOK185
windows-oldrelOK167
wasm-releaseOK312

Exports:advanced_pupil_trajectory_tableanalysis_bundle_tableanalysis_manifest_tableapply_transformation_recipeas_pupil_prediction_drawsassess_binary_prior_sensitivityassess_duration_prior_sensitivityassess_powerscaled_sensitivityaudit_advanced_pupil_identifiabilityaudit_backend_parityaudit_binocular_pupil_readinessaudit_design_supportaudit_duration_boundariesaudit_duration_unit_invarianceaudit_estimand_invarianceaudit_fixed_effect_designaudit_missingness_structureaudit_model_readinessaudit_model_readiness_strictaudit_prediction_supportaudit_pupil_computational_budgetaudit_pupil_measurement_contextaudit_pupil_measurement_modelaudit_pupil_missingnessaudit_pupil_predictive_calibrationaudit_pupil_readinessaudit_pupil_temporal_dependenceaudit_random_effects_supportbackend_capabilitiesbackend_environment_tablebackend_parity_tablebayesian_backend_capabilitiesbinary_calibration_errorbinary_calibration_tablebinary_calibration_uncertaintybinary_calibration_uncertainty_tablebinary_confusion_tablebinary_group_calibrationbinary_precision_recall_curvebinary_prediction_scoresbinary_roc_curvebinary_threshold_metricsbuild_model_formulacapture_gp3bayes_schemacheck_advanced_pupil_prior_predictivecheck_binary_posterior_predictivecheck_binary_ppc_detailscheck_binary_prior_predictivecheck_cmdstan_backendcheck_duration_posterior_predictivecheck_duration_ppc_detailscheck_duration_prior_predictivecheck_model_ppccheck_pupil_posterior_predictivecheck_pupil_prior_predictivecollect_model_evidencecompare_analysis_manifestscompare_estimand_sensitivitycompare_gp3bayes_schemascompare_psis_loocompare_pupil_autocorrelationcompare_pupil_lfocompare_pupil_modelscompare_pupil_sensitivity_estimandscompute_kfold_cvcompute_loo_model_weightscompute_psis_loocompute_psis_loo_from_log_likcreate_advanced_pupil_prior_specificationcreate_analysis_bundlecreate_analysis_figure_setcreate_analysis_manifestcreate_binary_model_reportcreate_brms_sbc_plancreate_complete_evidence_inventorycreate_contrast_coding_sensitivity_specificationcreate_custom_sbc_plancreate_diagnostic_dashboardcreate_diagnostic_dashboard_figurescreate_duration_model_reportcreate_duration_unit_sensitivity_specificationcreate_figure_setcreate_group_deletion_sensitivity_plancreate_loo_influence_atlascreate_model_cardcreate_model_contractcreate_model_evidence_reportcreate_model_specificationcreate_prediction_contrast_profilecreate_prediction_gridcreate_prediction_profilecreate_prediction_surfacecreate_predictive_distribution_atlascreate_predictor_scaling_sensitivity_specificationcreate_prior_specificationcreate_publication_registrycreate_publication_table_setcreate_pupil_advanced_sensitivity_suitecreate_pupil_arma_speccreate_pupil_contractcreate_pupil_gp_speccreate_pupil_lfo_plancreate_pupil_measurement_modelcreate_pupil_missingness_speccreate_pupil_model_setcreate_pupil_sensitivity_suitecreate_pupil_validation_plancreate_random_slope_sensitivity_plancreate_reporting_checklistcreate_sensitivity_suite_plancreate_transformation_recipedesign_support_tabledetect_binary_separationdiagnose_advanced_pupil_fitdiagnose_binary_fitdiagnose_duration_fitdiagnose_model_fitdiagnose_pupil_fitdiagnostic_dashboard_tableduration_pit_tableduration_prediction_scoresduration_qq_tableduration_quantile_calibrationduration_tail_checkestimand_sensitivity_tableestimate_binocular_pupil_trajectoryestimate_model_estimandsestimate_pupil_aucestimate_pupil_dynamic_contrastestimate_pupil_peakestimate_pupil_peak_latencyestimate_pupil_residual_scaleestimate_pupil_response_parametersestimate_pupil_threshold_durationestimate_pupil_trajectoryestimate_pupil_trajectory_derivativeestimate_pupil_windowestimate_standardized_duration_estimandsestimate_standardized_probability_contrastevaluate_pathological_simulationevidence_inventory_tableextract_expected_predictionsextract_linear_predictionsextract_log_likelihoodextract_posterior_drawsextract_posterior_predictionsextract_sampler_diagnosticsfit_advanced_pupil_modelfit_advanced_pupil_model_backendfit_advanced_pupil_model_cmdstanrfit_binary_modelfit_binary_model_backendfit_binary_model_cmdstanrfit_binocular_pupil_modelfit_duration_modelfit_duration_model_backendfit_duration_model_cmdstanrfit_pupil_modelfit_pupil_model_backendfit_pupil_model_cmdstanrfit_pupil_response_shape_modelfreeze_analysis_manifestfreeze_gp3bayes_schemagazepoint_pupil_mapping_tablegp3bayes_specification_traceabilitygroup_deletion_sensitivity_tablegroup_effect_draws_tablegroup_effect_rank_probability_tablegroup_effect_tablegroup_prediction_summarygrouped_prediction_checkidentify_identifier_like_predictorsidentify_loo_influential_observationsidentify_mcmc_issuesinspect_gazepoint_pupil_schemainteraction_prior_summaryinvert_transformation_recipeloo_diagnostic_tableloo_flagged_dataloo_group_influence_tableloo_influence_atlas_tableloo_influence_summaryloo_pointwise_tableloo_summary_tablemanifest_comparison_tablematerialize_pupil_advanced_sensitivity_scenariomaterialize_pupil_sensitivity_scenariomcmc_diagnostic_tablemissingness_audit_tablemodel_card_tablemodel_comparison_tablemodel_evidence_tablemodel_weights_tablemodel_workflow_statusplot_advanced_pupil_simulationplot_advanced_pupil_trajectoryplot_autocorrelationplot_backend_environment_ggplot_backend_parity_ggplot_binary_calibrationplot_binary_calibration_uncertaintyplot_binary_group_calibrationplot_binary_precision_recallplot_binary_rocplot_binary_threshold_metricsplot_binocular_pupil_trajectoryplot_design_support_ggplot_diagnostic_dashboardplot_duration_pitplot_duration_qqplot_duration_quantile_calibrationplot_duration_tailplot_estimand_intervalsplot_estimand_sensitivity_ggplot_exceedance_probabilityplot_group_deletion_sensitivityplot_group_effect_distributionplot_group_effect_rank_probabilityplot_group_effectsplot_group_predictionsplot_grouped_prediction_checkplot_loo_group_elpdplot_loo_group_influenceplot_loo_influenceplot_loo_influence_rankplot_loo_pareto_vs_elpdplot_loo_pointwise_elpdplot_manifest_comparison_ggplot_mcmc_qualityplot_missingness_ggplot_model_comparisonplot_model_evidence_ggplot_model_weightsplot_posterior_areasplot_posterior_correlationsplot_posterior_densityplot_posterior_intervalsplot_posterior_pairsplot_powerscale_sensitivity_ggplot_ppc_statisticplot_prediction_contrast_profileplot_prediction_drawsplot_prediction_gradientplot_prediction_interval_widthplot_prediction_intervalsplot_prediction_profileplot_prediction_rank_probabilitiesplot_prediction_score_uncertaintyplot_prediction_supportplot_prediction_surfaceplot_prediction_surface_uncertaintyplot_predictive_atlas_statisticsplot_predictive_coverageplot_predictive_quantile_envelopeplot_predictive_residualsplot_prior_posterior_contractionplot_prior_posterior_densityplot_prior_posterior_intervalsplot_prior_posterior_shiftplot_prior_sensitivityplot_prior_sensitivity_scenariosplot_pupil_autocorrelation_comparisonplot_pupil_dynamic_contrastplot_pupil_estimandplot_pupil_gp_hyperparametersplot_pupil_identifiability_auditplot_pupil_lfoplot_pupil_measurement_auditplot_pupil_measurement_uncertaintyplot_pupil_missingnessplot_pupil_model_comparisonplot_pupil_model_complexityplot_pupil_observed_trajectoryplot_pupil_posterior_trajectoryplot_pupil_ppcplot_pupil_predictive_calibrationplot_pupil_readinessplot_pupil_residual_acfplot_pupil_residual_scaleplot_pupil_residual_spectrumplot_pupil_response_parametersplot_pupil_sensitivityplot_pupil_temporal_dependenceplot_pupil_trajectory_derivativeplot_pupil_validationplot_random_intercept_variance_partitionplot_random_slope_sensitivityplot_rank_diagnosticsplot_recovery_biasplot_recovery_coverageplot_recovery_estimatesplot_recovery_fit_statusplot_recovery_rmseplot_reporting_checklistplot_sampler_diagnosticsplot_sampling_diagnosticsplot_sbc_coverage_ggplot_sbc_ecdf_ggplot_sbc_rank_ggplot_sbc_simulated_vs_estimated_ggplot_schema_comparison_ggplot_sensitivity_suite_ggplot_uncertainty_decompositionplot_variance_componentsposterior_correlation_tableposterior_interval_tableposterior_predictive_statisticposterior_predictive_summary_tableposterior_probability_tablepowerscale_sensitivity_tablepowerscale_sequence_for_fitppc_statistic_tablepredict_advanced_pupil_trajectorypredict_binary_probabilitypredict_durationpredict_modelpredict_pupil_trajectoryprediction_contrastprediction_contrast_profile_tableprediction_draws_longprediction_exceedance_probabilityprediction_gradient_tableprediction_interval_widthprediction_pairwise_contrastsprediction_profile_tableprediction_rank_probabilitiesprediction_score_uncertaintyprediction_score_uncertainty_tableprediction_support_tableprediction_surface_tableprediction_tableprediction_uncertainty_decompositionpredictive_coverage_tablepredictive_distribution_atlas_tablepredictive_quantile_envelopepredictive_residualspreflight_model_specificationprepare_binocular_pupil_timecourseprepare_hierarchical_binary_dataprepare_hierarchical_duration_dataprepare_pupil_timecourseprior_posterior_bridgeprior_posterior_distance_tableprior_posterior_draws_longprior_posterior_summary_tableprior_sensitivity_scenario_tableprior_sensitivity_tableprior_specification_tablepublication_registry_tablepupil_advanced_capabilitiespupil_advanced_compatibility_tablepupil_advanced_mapping_tablepupil_advanced_specification_tablepupil_autocorrelation_tablepupil_binocular_agreement_tablepupil_binocular_correlationpupil_binocular_differencepupil_condition_contrastpupil_distribution_tablepupil_dynamic_contrast_tablepupil_gp_hyperparameterspupil_gp_tablepupil_identifiability_tablepupil_measurement_audit_tablepupil_measurement_uncertainty_tablepupil_missingness_tablepupil_model_cardpupil_model_card_tablepupil_model_comparison_tablepupil_model_weightspupil_ppc_tablepupil_readiness_tablepupil_residual_acfpupil_residual_scale_tablepupil_residual_spectrumpupil_response_parameter_tablepupil_sensitivity_tablepupil_specification_tablepupil_trajectory_derivative_tablepupil_trajectory_tablepupil_validation_tablerandom_intercept_variance_partitionrandom_intercept_variance_partition_tablerandom_slope_sensi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Dependencies:withr

Advanced Dynamic Pupillometry in gp3bayes 0.5
Scope | A backend-free advanced workflow | Declare an advanced model | Translate, fit, diagnose, and estimate
Rendered fromadvanced-dynamic-pupillometry-0-5.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Bounded ARMA and Temporal Diagnostics
Audit first; do not select an order from a plot | Governed ARMA orders | Post-fit residual comparison
Rendered fromarma-and-temporal-diagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Computational Governance and Model Cards
Complexity is audited before Stan | Model card
Rendered fromcomputational-governance-and-model-cards.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Experimental Interpretable Pupil Response Shape
Rendered fromexperimental-pupil-response-shape.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Functional Dynamics and Predictive Calibration
Purpose | Backend-free simulation | Fit declaration | Posterior derivatives | Predictive calibration on held-out data
Rendered fromfunctional-dynamics-and-predictive-calibration.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Gaussian-Process Pupil Trajectories
Approximate GP is the default | Hyperparameters are posterior estimands
Rendered fromgaussian-process-pupil-trajectories.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Governed Predictive Model Comparison
Leave-future-out is an explicit refit workflow
Rendered fromgoverned-pupil-model-comparison.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Joint Binocular Pupil Models
Rendered frombinocular-pupil-models.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Measurement Uncertainty and Missing Pupil Data
Measurement uncertainty is declared, not silently corrected | Joint brms translation
Rendered frommeasurement-error-and-missing-pupil-data.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Robust and Distributional Pupil Models
Why separate location and residual scale? | Candidate specifications are explicit | Posterior residual-scale trajectory
Rendered fromrobust-distributional-pupil-models.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Synthetic Advanced Pupillometry Gallery
Observed trajectories | Stored latent mean | Temporal dependence | Missingness | Computational audit | Binocular example
Rendered fromsynthetic-advanced-pupillometry-gallery.Rmdusingknitr::rmarkdown

Last update: 2026-08-18
Started: 2026-08-18

Baseline, gaze/PFE, and luminance sensitivity
Prespecify consequential analysis choices | Materialize, do not rank
Rendered frompupil-baseline-gaze-luminance-sensitivity.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Bayesian dynamic pupillometry: governed foundation
Scope | Deterministic synthetic example | Restricted specification | Interpretation boundary
Rendered frombayesian-dynamic-pupillometry.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Fitting hierarchical pupil time-course models
Approved family | Translation without fitting | Prior-predictive gate | Full-MCMC backends
Rendered fromfitting-pupil-timecourse-models.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Gazepoint pupil-data interoperability
Verified Open Gaze fields | 3-D pupil diameter
Rendered fromgazepoint-pupil-interoperability.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Posterior pupil trajectories and declared estimands
Lightweight posterior-draw contract | Trajectory uncertainty | Declared contrasts and windows
Rendered frompupil-trajectories-and-estimands.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Preparing and auditing pupil time courses
Preparation is not preprocessing automation | Explicit baseline transformation | Readiness evidence | Measurement-context audit
Rendered frompupil-preparation-and-auditing.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Pupil posterior predictive checks and temporal diagnostics
Posterior predictive evidence | Temporal residual review
Rendered frompupil-ppc-and-temporal-diagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Synthetic Gazepoint pupillometry case study
Purpose | A Gazepoint-like mapping audit | Contract through specification | Backend and post-fit stages | Sensitivity
Rendered fromsynthetic-gazepoint-pupillometry-case-study.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Validation for temporally dependent pupil data
Start with the prediction target | Execution
Rendered frompupil-temporal-validation.Rmdusingknitr::rmarkdown

Last update: 2026-08-15
Started: 2026-08-15

Advanced Predictive Diagnostics
Rendered fromadvanced-predictive-diagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Complete Public API Map
Audits | Checks | Constructors and bundles | Execution workflows | Explicit writers | Extraction | Freezing and reproducibility | Model fitting | Other public workflows | Plots and graphics | Prediction | Readers | Simulation | Summaries | Tables and adapters | Validation
Rendered frompublic-api-map.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Declared Priors versus Fitted Posteriors
Rendered fromdeclared-prior-versus-posterior.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
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End-to-End Evidence and Publication Showcase
Rendered fromend-to-end-evidence-showcase.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Evidence Graphics and Governance
Rendered fromevidence-graphics-and-governance.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
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Grouped PSIS-LOO Influence
Rendered fromgrouped-loo-influence.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Hierarchical Effect and Variance Atlases
Rendered fromhierarchical-effect-atlas.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Hierarchical Effects and Predictive Uncertainty
Grouped posterior predictive checks | Descriptive uncertainty decomposition
Rendered fromhierarchical-effects-and-uncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

LOO Influence and Predictive Model Comparison
Rendered fromloo-influence-and-model-comparison.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Model Cards and Reporting Inventories
Rendered frommodel-cards-and-reporting-inventories.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Parameter Recovery Diagnostics for Publication
Rendered fromrecovery-diagnostics-for-publication.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Pointwise LOO Influence Atlases
Rendered fromloo-influence-atlas.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Posterior Exploration and Publication Graphics
Backend-independent posterior tables | Publication graphics | Fitted-model extraction
Rendered fromposterior-exploration-and-graphics.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Prediction Contrasts, Rankings, and Groups
Rendered fromprediction-contrasts-ranking-and-groups.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Prediction Profiles, Surfaces, and Contrast Profiles
Rendered fromprediction-profiles-surfaces-and-contrasts.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Prediction, Calibration, and Scoring
Fitted predictions
Rendered fromprediction-calibration-and-scoring.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Predictive Distribution and Calibration Uncertainty
Rendered frompredictive-distribution-and-calibration-uncertainty.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
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Publication Registries and Diagnostic Dashboards
Rendered frompublication-registries-and-dashboards.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
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Publication-Ready Analysis Bundles
Explicit output
Rendered frompublication-analysis-bundles.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
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Quality Hardening and Failure Contracts
Public API contract | Lightweight post-fit adapters | Explicit failure boundaries | Prediction diagnostics | Output safety | Why examples are selective
Rendered fromquality-hardening-and-failure-contracts.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

Sensitivity Atlases
Rendered fromsensitivity-atlas.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
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Simulation-Based Calibration Diagnostics
Rendered fromsbc-publication-diagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-08-13
Started: 2026-08-13

A Reproducible 0.2.0 Release Case Study
Purpose | 1. Simulate known data | 2. Declare the analysis contract | 3. Preflight the design | 4. Prepare and specify | 5. Freeze analysis provenance | 6. Optional dual-backend fitting | 7. Unified posterior review | 8. Cross-backend consistency | 9. Evidence and compatibility
Rendered fromrelease-case-study.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-08-10

A Stable Unified Workflow API
Why a unified API? | Build a backend-independent specification | Inspect workflow progress | Fit through either approved backend | What the unified layer does not do
Rendered fromstable-unified-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-08-10

Analysis Manifests and Reproducible Bayesian Workflows
A manifest is an analysis contract about the analysis contract | Create a manifest before fitting | Freeze only when the analysis-defining fields are ready | Compare analysis provenance
Rendered fromreproducible-analysis-manifests.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-08-10

Backend Portability and Installation
Audit installed components | CmdStanR setup | Full MCMC only
Rendered frombackend-portability.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-07-26

Backend Reliability, Parity and Object Schemas
Two interchangeable implementation backends, one modeling contract | Posterior-summary parity | Object-schema compatibility
Rendered frombackend-reliability.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-08-10

End-to-End Hierarchical Binary Workflow
Scope | Simulate a known data-generating process | Declare the model contract | Prepare and audit the data | Specify priors and inspect prior implications | Translate and fit with the optional backend | Diagnose, interpret, and validate | Prior sensitivity and simulation recovery | Structured reporting
Rendered frombinary-end-to-end.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-07-23

End-to-End Hierarchical Lognormal Duration Workflow
Scope | Simulate durations with stored truth | Declare the duration contract | Prepare, convert, and audit | Specify priors and check prior implications | Translate and fit through the restricted backend | Diagnostics and posterior interpretation | Sensitivity, recovery, and reporting
Rendered fromduration-end-to-end.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-07-23

Pre-fit Design-Support Diagnostics
Diagnose the design before invoking Stan | Missingness is described, not repaired | Fixed-effect geometry | Repetition, crossing and random slopes | One combined preflight
Rendered frompre-fit-design-diagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-08-10

Unified Sensitivity Suites and Evidence Inventories
Orchestration without automatic robustness claims | Declare a suite before running it | Evidence is an inventory
Rendered fromsensitivity-evidence-workflow.Rmdusingknitr::rmarkdown

Last update: 2026-08-10
Started: 2026-08-10

Optional Bayesian Backend Installation
Core installation | Optional fitting and validation dependencies | Windows toolchain check | Backend preflight | Minimal compilation smoke test | Clean-process package checks
Rendered fromoptional-backend-installation.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-07-23

First-Class Estimands and Sensitivity Workflows
Why estimands are first-class | Binary probability standardisation | Duration median and predictive-tail estimands | Structural sensitivity | Participant and item deletion | Parameterisation sensitivity | Exact K-fold validation
Rendered fromestimands-and-sensitivity.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-07-26

Specification Closure: Strict Readiness and Governed Validation
Purpose | Binary strict readiness | Identifier-like predictors are review signals | Duration extremes, impossible ranges, and censoring | Traceability
Rendered fromspecification-closure.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-07-26

Transformation Replay and Detailed Posterior Predictive Checks
Replay recorded transformations | Detailed binary PPC | Detailed duration PPC
Rendered fromtransformation-replay-and-detailed-ppc.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-07-26

Advanced Optional Bayesian Workflows
Capability audit | Separate interaction priors | Full-MCMC backend selection | Separation screening | PSIS-LOO and model averaging | Power-scaling sensitivity | Simulation-based calibration
Rendered fromadvanced-optional-workflows.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-07-26

Pathological Simulation Scenarios
Binary scenarios | Duration scenarios
Rendered frompathological-simulation-scenarios.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-07-26

Prior Sensitivity and Simulation-Based Recovery
Different validation questions | Prior-scale sensitivity | Simulation-based recovery | Minimum repetition rule | Failure handling | Interpretation
Rendered fromsensitivity-and-recovery.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-23

Sampling Diagnostics and Conservative Decisions
Evidence layers | Numerical diagnostic contract | No automatic convergence statement | Diagnostic plots | Responding to failures | Reporting language
Rendered fromposterior-diagnostics.Rmdusingknitr::rmarkdown

Last update: 2026-07-23
Started: 2026-07-23

Readme and manuals

Help Manual

Help pageTopics
Summarise an advanced pupil trajectoryadvanced_pupil_trajectory_table
Analysis-Bundle Status Tableanalysis_bundle_table
Summarise Manifest Componentsanalysis_manifest_table
Apply a Recorded Transformation Recipeapply_transformation_recipe
Create a lightweight pupil prediction object from frozen drawsas_pupil_prediction_draws
Convert a pupil contract to a transparent tableas.data.frame.gp3bayes_pupil_contract
Convert a pupil estimand to a data frameas.data.frame.gp3bayes_pupil_estimand
Assess Binary Prior Sensitivityassess_binary_prior_sensitivity
Assess Duration Prior Sensitivityassess_duration_prior_sensitivity
Assess Power-Scaled Prior and Likelihood Sensitivityassess_powerscaled_sensitivity
Audit empirical support for an advanced pupil model specificationaudit_advanced_pupil_identifiability
Audit Posterior Parity Across rstan and cmdstanraudit_backend_parity
Audit binocular pupil availability and agreement descriptivelyaudit_binocular_pupil_readiness
Audit Overall Design Supportaudit_design_support
Audit Duration Range and Censoring Boundariesaudit_duration_boundaries
Audit Duration-Unit Invarianceaudit_duration_unit_invariance
Audit Estimand Invariance Against a Declared Toleranceaudit_estimand_invariance
Audit the Fixed-Effects Design Matrixaudit_fixed_effect_design
Audit Missingness Structure Before Model Fittingaudit_missingness_structure
Audit Data Readiness for an Approved Model Contractaudit_model_readiness
Run a Strict Model-Readiness Auditaudit_model_readiness_strict
Audit Prediction Supportaudit_prediction_support
Audit computational complexity before fitting an advanced pupil modelaudit_pupil_computational_budget
Audit pupil measurement and confound contextaudit_pupil_measurement_context
Audit a declared measurement model against dataaudit_pupil_measurement_model
Audit missingness in an advanced pupil specificationaudit_pupil_missingness
Audit posterior predictive calibration on explicit evaluation dataaudit_pupil_predictive_calibration
Audit pupil-timecourse readinessaudit_pupil_readiness
Audit empirical temporal dependence before model fittingaudit_pupil_temporal_dependence
Audit Random-Effects Supportaudit_random_effects_support
Report Bayesian Backend Capabilitiesbackend_capabilities
Backend-Environment Tablebackend_environment_table
Backend-Parity Tablebackend_parity_table
Report Optional Bayesian Backend Capabilitiesbayesian_backend_capabilities
Binary Calibration Errorbinary_calibration_error
Binary Calibration Tablebinary_calibration_table
Binary Calibration Uncertaintybinary_calibration_uncertainty
Binary Calibration-Uncertainty Tablebinary_calibration_uncertainty_table
Binary Confusion Tablebinary_confusion_table
Grouped Binary Calibrationbinary_group_calibration
Binary Precision-Recall Curvebinary_precision_recall_curve
Binary Prediction Scoresbinary_prediction_scores
Binary ROC Curvebinary_roc_curve
Binary Threshold-Metric Curvebinary_threshold_metrics
Build an Approved Model Formulabuild_model_formula
Capture the Structural Schema of a gp3bayes Objectcapture_gp3bayes_schema
Check advanced pupil priors through prior-only simulationcheck_advanced_pupil_prior_predictive
Check Binary Posterior Predictive Behaviourcheck_binary_posterior_predictive
Run Detailed Binary Posterior Predictive Checkscheck_binary_ppc_details
Check Binary Prior Predictive Behaviourcheck_binary_prior_predictive
Check the CmdStanR Backendcheck_cmdstan_backend
Check Duration Posterior Predictive Behaviourcheck_duration_posterior_predictive
Run Detailed Duration Posterior Predictive Checkscheck_duration_ppc_details
Check Duration Prior Predictive Behaviourcheck_duration_prior_predictive
Check Posterior Predictive Behaviourcheck_model_ppc
Run pupil-specific posterior predictive checkscheck_pupil_posterior_predictive
Check the approved pupil priors predictivelycheck_pupil_prior_predictive
Collect Model Evidence Without Declaring Model Adequacycollect_model_evidence
Compare Analysis Manifestscompare_analysis_manifests
Compare Estimand Sensitivity Across Alternative Fitscompare_estimand_sensitivity
Compare gp3bayes Object Schemascompare_gp3bayes_schemas
Compare Models with PSIS-LOOcompare_psis_loo
Compare residual autocorrelation across fitted advanced modelscompare_pupil_autocorrelation
Compare executed leave-future-out validationscompare_pupil_lfo
Compare fitted pupil models predictivelycompare_pupil_models
Compare declared pupil sensitivity estimandscompare_pupil_sensitivity_estimands
Compute Governed Exact K-Fold Cross-Validationcompute_kfold_cv
Compute LOO Model-Averaging Weightscompute_loo_model_weights
Compute PSIS-LOO for a gp3bayes Fitcompute_psis_loo
Compute PSIS-LOO from a Log-Likelihood Matrixcompute_psis_loo_from_log_lik
Create an advanced pupil prior specificationcreate_advanced_pupil_prior_specification
Create a Structured Post-Fit Analysis Bundlecreate_analysis_bundle
Create Publication Figures from an Analysis Bundlecreate_analysis_figure_set
Create an Analysis Manifestcreate_analysis_manifest
Create a Structured Binary Model Reportcreate_binary_model_report
Create a brms-Based Simulation-Based Calibration Plancreate_brms_sbc_plan
Create a Complete Evidence Inventorycreate_complete_evidence_inventory
Create a Contrast-Coding Sensitivity Specificationcreate_contrast_coding_sensitivity_specification
Create an Expert Custom SBC Plancreate_custom_sbc_plan
Create a Diagnostic Dashboard Objectcreate_diagnostic_dashboard
Create Diagnostic Dashboard Figurescreate_diagnostic_dashboard_figures
Create a Structured Duration Model Reportcreate_duration_model_report
Create a Duration-Unit Sensitivity Specificationcreate_duration_unit_sensitivity_specification
Create a Named Figure Setcreate_figure_set
Create a Group-Deletion Sensitivity Plancreate_group_deletion_sensitivity_plan
Create a LOO Influence Atlascreate_loo_influence_atlas
Create a gp3bayes Model Cardcreate_model_card
Create an Approved Bayesian Model Contractcreate_model_contract
Create a Model Evidence Reportcreate_model_evidence_report
Create a Complete Model Specificationcreate_model_specification
Create a Prediction Contrast Profilecreate_prediction_contrast_profile
Create a Governed Prediction Gridcreate_prediction_grid
Create a Numeric Prediction Profilecreate_prediction_profile
Create a Two-Dimensional Prediction Surfacecreate_prediction_surface
Create a Posterior-Predictive Distribution Atlascreate_predictive_distribution_atlas
Create a Predictor-Scaling Sensitivity Specificationcreate_predictor_scaling_sensitivity_specification
Create a Backend-Independent Prior Specificationcreate_prior_specification
Create a Publication Registrycreate_publication_registry
Extract Publication Tables from an Analysis Bundlecreate_publication_table_set
Create a pre-fit advanced pupillometry sensitivity suitecreate_pupil_advanced_sensitivity_suite
Create an explicit bounded ARMA configurationcreate_pupil_arma_spec
Create a governed pupil-timecourse contractcreate_pupil_contract
Create a Gaussian-process configuration for pupil trajectoriescreate_pupil_gp_spec
Create an explicit leave-future-out validation plancreate_pupil_lfo_plan
Create a governed measurement-uncertainty specificationcreate_pupil_measurement_model
Create a governed missingness specificationcreate_pupil_missingness_spec
Create a named set of fitted pupil modelscreate_pupil_model_set
Create a governed pupil sensitivity suitecreate_pupil_sensitivity_suite
Create an explicit pupil predictive-validation plancreate_pupil_validation_plan
Create a Random-Slope Sensitivity Plancreate_random_slope_sensitivity_plan
Create a Reporting Checklistcreate_reporting_checklist
Create a Sensitivity Suite Plancreate_sensitivity_suite_plan
Create a Reusable Transformation Recipecreate_transformation_recipe
Design-Support Tabledesign_support_table
Detect Separation in the Binary Fixed-Effects Screendetect_binary_separation
Diagnose an advanced pupil fitdiagnose_advanced_pupil_fit
Diagnose a Fitted Binary Modeldiagnose_binary_fit
Diagnose a Fitted Duration Modeldiagnose_duration_fit
Diagnose an Approved gp3bayes Fitdiagnose_model_fit
Diagnose temporal and sampling behaviour of a pupil fitdiagnose_pupil_fit
Diagnostic Dashboard Tablediagnostic_dashboard_table
Duration Probability-Integral-Transform Tableduration_pit_table
Duration Prediction Scoresduration_prediction_scores
Duration Predictive Q-Q Tableduration_qq_table
Duration Quantile Calibrationduration_quantile_calibration
Duration Tail Checkduration_tail_check
Estimand Sensitivity Tableestimand_sensitivity_table
Estimate joint binocular posterior trajectoriesestimate_binocular_pupil_trajectory
Estimate the Approved Primary Estimandsestimate_model_estimands
Estimate area under a declared pupil-response windowestimate_pupil_auc
Estimate a dynamic posterior contrast between two pupil conditionsestimate_pupil_dynamic_contrast
Estimate posterior peak pupil response inside a declared windowestimate_pupil_peak
Estimate posterior peak latency inside a declared windowestimate_pupil_peak_latency
Estimate the residual-scale trajectory from a distributional modelestimate_pupil_residual_scale
Estimate nonlinear response-shape parametersestimate_pupil_response_parameters
Estimate posterior duration above a prespecified dynamic thresholdestimate_pupil_threshold_duration
Estimate posterior pupil trajectoriesestimate_pupil_trajectory
Estimate posterior temporal derivatives of a pupil trajectoryestimate_pupil_trajectory_derivative
Estimate a declared-window mean pupil responseestimate_pupil_window
Estimate Design-Standardised Duration Estimandsestimate_standardized_duration_estimands
Estimate a Design-Standardised Binary Probability Contrastestimate_standardized_probability_contrast
Evaluate a Pathological Simulation Against the Contract Gateevaluate_pathological_simulation
Evidence Inventory Tableevidence_inventory_table
Extract Expected Posterior Predictionsextract_expected_predictions
Extract Linear-Predictor Drawsextract_linear_predictions
Extract Pointwise Log-Likelihood Drawsextract_log_likelihood
Extract Posterior Draws from a gp3bayes Fitextract_posterior_draws
Extract Posterior Predictive Drawsextract_posterior_predictions
Extract NUTS Sampler Diagnosticsextract_sampler_diagnostics
Fit an advanced pupil model using rstanfit_advanced_pupil_model
Fit an advanced pupil model through an approved brms backendfit_advanced_pupil_model_backend
Fit an advanced pupil model using cmdstanrfit_advanced_pupil_model_cmdstanr
Fit an Approved Hierarchical Binary Modelfit_binary_model
Fit a Binary Model with a Selected Full-MCMC Backendfit_binary_model_backend fit_binary_model_cmdstanr
Fit a joint binocular pupil modelfit_binocular_pupil_model
Fit an Approved Hierarchical Lognormal Duration Modelfit_duration_model
Fit a Duration Model with a Selected Full-MCMC Backendfit_duration_model_backend fit_duration_model_cmdstanr
Fit a pupil model through the fixed rstan routefit_pupil_model
Fit the restricted pupil time-course model with an approved backendfit_pupil_model_backend
Fit a pupil model through the fixed cmdstanr routefit_pupil_model_cmdstanr
Fit the experimental nonlinear response-shape modelfit_pupil_response_shape_model
Freeze an Analysis Manifestfreeze_analysis_manifest
Freeze a gp3bayes Object Schemafreeze_gp3bayes_schema
Return the Gazepoint pupil mapping audit tablegazepoint_pupil_mapping_table
Specification-Closure Traceability Matrixgp3bayes_specification_traceability
Group-Deletion Sensitivity Tablegroup_deletion_sensitivity_table
Group-Level Posterior Draw Tablegroup_effect_draws_table
Group-Level Rank-Probability Tablegroup_effect_rank_probability_table
Group-Level Effect Tablegroup_effect_table
Group Prediction Summarygroup_prediction_summary
Grouped Posterior Predictive Checkgrouped_prediction_check
Identify Identifier-Like Numeric Predictorsidentify_identifier_like_predictors
Identify Influential PSIS-LOO Observationsidentify_loo_influential_observations
Identify MCMC Diagnostic Flagsidentify_mcmc_issues
Inspect verified Gazepoint pupil and gaze fieldsinspect_gazepoint_pupil_schema
Summarise Separate Interaction Prior Metadatainteraction_prior_summary
Invert a Recorded Transformation Recipeinvert_transformation_recipe
LOO Diagnostic Tableloo_diagnostic_table
Flagged LOO Observation Dataloo_flagged_data
Aggregate LOO Influence by a Declared Grouploo_group_influence_table
LOO Influence Atlas Tableloo_influence_atlas_table
LOO Influence Summaryloo_influence_summary
Pointwise LOO Tableloo_pointwise_table
LOO Summary Tableloo_summary_table
Manifest-Comparison Tablemanifest_comparison_table
Materialize one advanced sensitivity scenariomaterialize_pupil_advanced_sensitivity_scenario
Materialize one declared pupil sensitivity scenariomaterialize_pupil_sensitivity_scenario
Modern MCMC Diagnostic Tablemcmc_diagnostic_table
Missingness-Audit Tablemissingness_audit_table
Model-Card Evidence Tablemodel_card_table
LOO Model-Comparison Tablemodel_comparison_table
Model-Evidence Tablemodel_evidence_table
LOO Model-Weight Tablemodel_weights_table
Summarise Workflow Stage Completionmodel_workflow_status
Plot simulated advanced pupil trajectoriesplot_advanced_pupil_simulation
Plot an advanced posterior pupil trajectoryplot_advanced_pupil_trajectory
Autocorrelation Diagnostic Plotplot_autocorrelation
Plot Backend Environment Checks with ggplot2plot_backend_environment_gg
Plot Backend Parity with ggplot2plot_backend_parity_gg
Binary Calibration Plotplot_binary_calibration
Plot Binary Calibration Uncertaintyplot_binary_calibration_uncertainty
Grouped Binary Calibration Plotplot_binary_group_calibration
Binary Precision-Recall Plotplot_binary_precision_recall
Binary ROC Plotplot_binary_roc
Binary Threshold-Metric Plotplot_binary_threshold_metrics
Plot binocular posterior trajectoriesplot_binocular_pupil_trajectory
Plot Design-Support Components with ggplot2plot_design_support_gg
Plot Diagnostic Dashboard Availabilityplot_diagnostic_dashboard
Duration PIT Plotplot_duration_pit
Duration Predictive Q-Q Plotplot_duration_qq
Duration Quantile-Calibration Plotplot_duration_quantile_calibration
Duration Tail-Check Plotplot_duration_tail
Estimand Interval Plotplot_estimand_intervals
Plot Estimand Sensitivity with ggplot2plot_estimand_sensitivity_gg
Prediction Exceedance-Probability Plotplot_exceedance_probability
Plot Group-Deletion Sensitivityplot_group_deletion_sensitivity
Plot Group-Effect Posterior Distributionsplot_group_effect_distribution
Plot Group-Effect Rank Probabilitiesplot_group_effect_rank_probability
Group-Effect Plotplot_group_effects
Group Prediction Plotplot_group_predictions
Grouped Posterior Predictive Plotplot_grouped_prediction_check
Plot Grouped Pointwise ELPD Contributionplot_loo_group_elpd
Plot Grouped LOO Influenceplot_loo_group_influence
LOO Influence Plotplot_loo_influence
Plot Ranked LOO Influenceplot_loo_influence_rank
Plot Pareto-k versus Pointwise ELPDplot_loo_pareto_vs_elpd
Plot Pointwise LOO ELPDplot_loo_pointwise_elpd
Plot Manifest Differences with ggplot2plot_manifest_comparison_gg
MCMC Review-Flag Plotplot_mcmc_quality
Plot Missingness Fractions with ggplot2plot_missingness_gg
LOO Model-Comparison Plotplot_model_comparison
Plot Model-Evidence Availability with ggplot2plot_model_evidence_gg
LOO Model-Weight Plotplot_model_weights
Posterior Area Plotplot_posterior_areas
Posterior Correlation Plotplot_posterior_correlations
Posterior Density Plotplot_posterior_density
Posterior Interval Plotplot_posterior_intervals
Posterior Pairs Plotplot_posterior_pairs
Plot Power-Scale Sensitivity with ggplot2plot_powerscale_sensitivity_gg
Posterior Predictive Statistic Plotplot_ppc_statistic
Plot a Prediction Contrast Profileplot_prediction_contrast_profile
Prediction-Draw Distribution Plotplot_prediction_draws
Plot Prediction-Profile Gradientsplot_prediction_gradient
Prediction Interval-Width Plotplot_prediction_interval_width
Prediction-Interval Plotplot_prediction_intervals
Plot a Prediction Profileplot_prediction_profile
Prediction Rank-Probability Plotplot_prediction_rank_probabilities
Plot Prediction Score Uncertaintyplot_prediction_score_uncertainty
Prediction-Support Plotplot_prediction_support
Plot a Prediction Surfaceplot_prediction_surface
Plot Prediction-Surface Uncertaintyplot_prediction_surface_uncertainty
Plot Predictive Atlas Statisticsplot_predictive_atlas_statistics
Predictive-Coverage Plotplot_predictive_coverage
Plot Posterior-Predictive Quantile Envelopeplot_predictive_quantile_envelope
Predictive-Residual Plotplot_predictive_residuals
Plot Prior-to-Posterior Contractionplot_prior_posterior_contraction
Plot Declared Prior and Posterior Densitiesplot_prior_posterior_density
Plot Prior and Posterior Intervalsplot_prior_posterior_intervals
Plot Prior-to-Posterior Location Shiftplot_prior_posterior_shift
Plot Prior-Scale Sensitivityplot_prior_sensitivity
Plot Prior-Sensitivity Scenario Maximaplot_prior_sensitivity_scenarios
Plot residual autocorrelation comparisonplot_pupil_autocorrelation_comparison
Plot a dynamic pupil condition contrastplot_pupil_dynamic_contrast
Plot declared-window pupil estimandsplot_pupil_estimand
Plot Gaussian-process hyperparametersplot_pupil_gp_hyperparameters
Plot advanced identifiability/design-support auditplot_pupil_identifiability_audit
Plot leave-future-out scoresplot_pupil_lfo
Plot gaze/PFE and luminance measurement-context evidenceplot_pupil_measurement_audit
Plot measurement-uncertainty auditplot_pupil_measurement_uncertainty
Plot missing-response fraction over timeplot_pupil_missingness
Plot predictive model comparisonplot_pupil_model_comparison
Plot advanced model computational complexityplot_pupil_model_complexity
Plot observed pupil trajectoriesplot_pupil_observed_trajectory
Plot posterior pupil trajectories or condition differencesplot_pupil_posterior_trajectory
Plot pupil posterior-predictive evidenceplot_pupil_ppc
Plot posterior predictive calibrationplot_pupil_predictive_calibration
Plot pupil readiness evidenceplot_pupil_readiness
Plot pupil residual autocorrelationplot_pupil_residual_acf
Plot posterior residual scale over timeplot_pupil_residual_scale
Plot residual spectrumplot_pupil_residual_spectrum
Plot experimental nonlinear response parametersplot_pupil_response_parameters
Plot pupil sensitivity scenarios or result comparisonsplot_pupil_sensitivity
Plot empirical temporal-dependence auditplot_pupil_temporal_dependence
Plot posterior pupil trajectory derivativeplot_pupil_trajectory_derivative
Plot pupil validation evidenceplot_pupil_validation
Plot Random-Intercept Variance Partitionplot_random_intercept_variance_partition
Plot Random-Slope Sensitivityplot_random_slope_sensitivity
Rank-Diagnostic Plotplot_rank_diagnostics
Plot Recovery Standardized Biasplot_recovery_bias
Plot Recovery Coverageplot_recovery_coverage
Plot Repetition-Level Recovery Estimatesplot_recovery_estimates
Plot Recovery Fit Statusplot_recovery_fit_status
Plot Recovery RMSEplot_recovery_rmse
Plot a Reporting Checklistplot_reporting_checklist
Sampler-Diagnostic Plotplot_sampler_diagnostics
Plot Sampling Diagnosticsplot_sampling_diagnostics
SBC Coverage Plotplot_sbc_coverage_gg
SBC ECDF-Difference Plotplot_sbc_ecdf_gg
SBC Rank-Histogram Plotplot_sbc_rank_gg
SBC Simulated-versus-Estimated Plotplot_sbc_simulated_vs_estimated_gg
Plot Schema Differences with ggplot2plot_schema_comparison_gg
Plot a Sensitivity Suite with ggplot2plot_sensitivity_suite_gg
Prediction-Uncertainty Plotplot_uncertainty_decomposition
Variance-Component Plotplot_variance_components
Plot Governed Exact K-Fold Resultsplot.gp3bayes_kfold_cv
Plot a Strict Readiness Auditplot.gp3bayes_strict_readiness_audit
Posterior Correlation Tableposterior_correlation_table
Posterior Interval Tableposterior_interval_table
Posterior Predictive Statistic Checkposterior_predictive_statistic
Posterior Predictive Summary Tableposterior_predictive_summary_table
Posterior Direction and ROPE Probability Tableposterior_probability_table
Power-Scale Sensitivity Tablepowerscale_sensitivity_table
Create a Power-Scaling Sequencepowerscale_sequence_for_fit
Posterior Predictive Statistic Tableppc_statistic_table
Predict an advanced pupil trajectorypredict_advanced_pupil_trajectory
Binary Event-Probability Predictionspredict_binary_probability
Duration Predictionspredict_duration
Posterior Prediction for Approved gp3bayes Modelspredict_model
Predict governed pupil trajectoriespredict_pupil_trajectory
Posterior Prediction Contrastprediction_contrast
Prediction Contrast Profile Tableprediction_contrast_profile_table
Convert Prediction Draws to Long Formprediction_draws_long
Posterior Exceedance Probabilitiesprediction_exceedance_probability
Prediction-Profile Gradient Tableprediction_gradient_table
Prediction Interval Width Tableprediction_interval_width
Pairwise Prediction Contrastsprediction_pairwise_contrasts
Prediction Profile Tableprediction_profile_table
Posterior Ranking Probabilities for Prediction Rowsprediction_rank_probabilities
Posterior Uncertainty in Prediction Scoresprediction_score_uncertainty
Prediction Score-Uncertainty Tableprediction_score_uncertainty_table
Prediction-Support Tableprediction_support_table
Prediction Surface Tableprediction_surface_table
Prediction Summary Tableprediction_table
Decompose Prediction Uncertainty Descriptivelyprediction_uncertainty_decomposition
Posterior Predictive Coverage Tablepredictive_coverage_table
Predictive Distribution Atlas Tablepredictive_distribution_atlas_table
Posterior-Predictive Quantile Envelopepredictive_quantile_envelope
Posterior Predictive Residualspredictive_residuals
Preflight an Approved Model Specificationpreflight_model_specification
Prepare binocular pupil data without averaging eyesprepare_binocular_pupil_timecourse
Prepare Hierarchical Binary Dataprepare_hierarchical_binary_data
Prepare Hierarchical Duration Dataprepare_hierarchical_duration_data
Prepare a pupil time course under explicit transformationsprepare_pupil_timecourse
Create a Declared-Prior versus Posterior Bridgeprior_posterior_bridge
Prior-versus-Posterior Distance Tableprior_posterior_distance_table
Long Prior and Posterior Draw Tableprior_posterior_draws_long
Prior-versus-Posterior Summary Tableprior_posterior_summary_table
Prior Sensitivity Scenario Tableprior_sensitivity_scenario_table
Prior Sensitivity Tableprior_sensitivity_table
Prior-Specification Tableprior_specification_table
Publication Registry Tablepublication_registry_table
Report the gp3bayes 0.5 advanced-pupillometry capability boundarypupil_advanced_capabilities
Report governed compatibility rules for 0.5 advanced modelspupil_advanced_compatibility_table
Inspect the resolved 0.5 pupil column mappingpupil_advanced_mapping_table
Tabulate an advanced pupil model specificationpupil_advanced_specification_table
Tabulate a temporal-dependence auditpupil_autocorrelation_table
Summarise binocular posterior agreementpupil_binocular_agreement_table
Extract posterior residual binocular correlationpupil_binocular_correlation
Estimate posterior right-minus-left binocular differencespupil_binocular_difference
Estimate a posterior condition-difference trajectorypupil_condition_contrast
Tabulate a pupil distribution declaration or advanced specificationpupil_distribution_table
Tabulate a dynamic pupil contrastpupil_dynamic_contrast_table
Extract Gaussian-process hyperparameterspupil_gp_hyperparameters
Tabulate GP hyperparameterspupil_gp_table
Tabulate advanced pupil identifiability/design-support auditpupil_identifiability_table
Extract a pupil measurement-context tablepupil_measurement_audit_table
Summarise measurement uncertainty declared in a modelpupil_measurement_uncertainty_table
Tabulate missingness audit resultspupil_missingness_table
Build an auditable advanced pupil model cardpupil_model_card
Tabulate a pupil model cardpupil_model_card_table
Tabulate model comparisonpupil_model_comparison_table
Compute explicit predictive model weightspupil_model_weights
Extract pupil PPC evidence tablespupil_ppc_table
Extract pupil readiness tablespupil_readiness_table
Summarise residual autocorrelation for a pupil fitpupil_residual_acf
Tabulate posterior residual scalepupil_residual_scale_table
Compute a descriptive residual spectrumpupil_residual_spectrum
Tabulate nonlinear response parameterspupil_response_parameter_table
Extract pupil sensitivity scenarios or comparison resultspupil_sensitivity_table
Convert a pupil specification to a publication-ready tablepupil_specification_table
Tabulate posterior pupil trajectory derivativespupil_trajectory_derivative_table
Convert a pupil trajectory to a tablepupil_trajectory_table
Extract a pupil validation tablepupil_validation_table
Random-Intercept Latent Variance Partitionrandom_intercept_variance_partition
Random-Intercept Variance-Partition Tablerandom_intercept_variance_partition_table
Random-Slope Sensitivity Tablerandom_slope_sensitivity_table
Read a Frozen Analysis Manifestread_analysis_manifest
Read a Frozen gp3bayes Object Schemaread_gp3bayes_schema
Recovery Estimate Tablerecovery_estimate_table
Recovery Fit-Status Tablerecovery_fit_status_table
Recovery Parameter Summary Tablerecovery_parameter_table
Register a Publication Figureregister_publication_figure
Register a Publication Tableregister_publication_table
Review Extreme Positive Durations Without Deleting Themreview_duration_extremes
Run Binary Parameter Recoveryrun_binary_recovery
Run Duration Parameter Recoveryrun_duration_recovery
Run a Group-Deletion Sensitivity Planrun_group_deletion_sensitivity
Run Random-Intercept versus Random-Slope Sensitivityrun_random_slope_sensitivity
Run a Simulation-Based Calibration Planrun_sbc_plan
Run a Unified Sensitivity Suiterun_sensitivity_suite
Summarise NUTS Sampler Diagnosticssampler_diagnostic_table
Save a Figure Setsave_figure_set
Save Publication Registry Figuressave_publication_registry_figures
SBC Overview Tablesbc_overview_table
SBC Statistics Tablesbc_stats_table
Schema-Comparison Tableschema_comparison_table
Score posterior predictive draws against observed pupil valuesscore_pupil_predictions
Sensitivity-Suite Tablesensitivity_suite_table
Simulate advanced dynamic pupil time coursessimulate_advanced_pupil_timecourse
Simulate a Dedicated Binary Pathology Scenariosimulate_binary_pathology
Simulate joint binocular pupil tracessimulate_binocular_pupil_timecourse
Simulate Marginal Draws from Declared gp3bayes Priorssimulate_declared_prior_draws
Simulate a Dedicated Duration Pathology Scenariosimulate_duration_pathology
Simulate Hierarchical Binary Datasimulate_hierarchical_binary_data
Simulate Hierarchical Lognormal Duration Datasimulate_hierarchical_duration_data
Simulate data from the experimental nonlinear response-shape familysimulate_pupil_response_shape
Simulate deterministic hierarchical pupil time coursessimulate_pupil_timecourse
Specify an advanced governed pupil time-course modelspecify_advanced_pupil_timecourse_model
Specify a Backend-Independent Binary Modelspecify_binary_model
Specify a Binary Model with a Separate Interaction Priorspecify_binary_model_with_interaction_prior
Specify a joint binocular pupil modelspecify_binocular_pupil_model
Specify a Backend-Independent Duration Modelspecify_duration_model
Specify a Duration Model with a Separate Interaction Priorspecify_duration_model_with_interaction_prior
Declare an advanced pupil observation distributionspecify_pupil_distribution
Specify the experimental nonlinear pupil response-shape modelspecify_pupil_response_shape_model
Specify the restricted hierarchical pupil time-course modelspecify_pupil_timecourse_model
Summarise Binary Outcome Variation Within Groupssummarise_binary_group_variation
Summarise a Binary Posteriorsummarise_binary_posterior
Summarise Overall Condition Balancesummarise_condition_balance
Summarise a Duration Posteriorsummarise_duration_posterior
Summarise Posterior Estimand Drawssummarise_estimand_draws
Summarise MCMC Quality Evidencesummarise_mcmc_quality
Summarise an Approved gp3bayes Posteriorsummarise_model_posterior
Summarise a fitted pupil posteriorsummarise_pupil_posterior
Summarise an SBC Resultsummarise_sbc_result
Summarise a Sensitivity Suitesummarise_sensitivity_suite
gp3bayes Publication Themetheme_gp3bayes
Translate an advanced pupil model to brms without fittingtranslate_advanced_pupil_model_to_brms
Translate a Binary Model Specification to brmstranslate_binary_model_to_brms
Translate an Advanced Binary Specification to brmstranslate_binary_model_with_interaction_prior
Translate a binocular specification to a brms multivariate formulatranslate_binocular_pupil_model_to_brms
Translate a Duration Model Specification to brmstranslate_duration_model_to_brms
Translate an Advanced Duration Specification to brmstranslate_duration_model_with_interaction_prior
Translate an approved pupil model to brmstranslate_pupil_model_to_brms
Translate the experimental response-shape model to brmstranslate_pupil_response_shape_to_brms
Validate an Analysis Manifestvalidate_analysis_manifest
Validate a Bayesian Backend Environmentvalidate_backend_environment
Validate a gp3bayes Objectvalidate_gp3bayes_object
Validate an Object Against a Frozen gp3bayes Schemavalidate_gp3bayes_schema
Validate a Prior Specificationvalidate_prior_specification
Validate a Publication Registryvalidate_publication_registry
Execute or materialize leave-future-out validationvalidate_pupil_leave_future_out
Validate a pupil model for an explicit prediction targetvalidate_pupil_model
Validate Exact Transformation Replayvalidate_transformation_replay
Variance-Component Posterior Tablevariance_component_table
Write an Analysis-Bundle Markdown Reportwrite_analysis_bundle_report
Write a Diagnostic Dashboard Reportwrite_diagnostic_dashboard_report
Write a Model Cardwrite_model_card
Write a Publication Registrywrite_publication_registry
Write a Reproducibility Reportwrite_reproducibility_report