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Changelog

Source: NEWS.md

gp3bayes 0.2.0.9001

  • Aligned DESCRIPTION, README, citation metadata, package-level help, backend-installation guidance, CRAN comments, and pkgdown deployment metadata with the complete 0.2.0.9001 development API and dual rstan/cmdstanr backend support.

Specification closure

  • Adds strict readiness checks for overall condition imbalance, binary group outcome variation, identifier-like numeric predictors, fixed-effect rank, duration extremes, declared duration ranges, censoring signals, and optional separation screening.

  • Adds reusable transformation recipes with forward replay, inversion, and exact replay validation for retained rows.

  • Adds first-class design-standardised binary probability contrasts and duration median, ratio, and predictive-quantile estimands.

  • Adds governed structural, group-deletion, contrast-coding, predictor-scaling, and duration-unit sensitivity workflows without automatic model selection or exclusion.

  • Adds detailed family-specific posterior predictive checks and plotting helpers.

  • Adds a governed exact K-fold adapter through brms::kfold() as an optional predictive-validation fallback/complement to PSIS-LOO.

  • Adds an auditable specification-traceability matrix, examples, smoke tests, and three integrated articles.

  • Added optional power-scaling sensitivity integration through priorsense.

  • Added conservative PSIS-LOO diagnostics, influence inspection, model comparison, and stacking or pseudo-BMA weights through loo.

  • Added fixed-effects separation screening through detectseparation.

  • Added simulation-based calibration plans and plots through SBC.

  • Added restricted full-MCMC backend selection between rstan and cmdstanr.

  • Added coefficient-specific interaction-prior defaults for binary and duration contracts.

  • Added dedicated binary and duration pathology generators, evaluations, plots, tests, examples, smoke tests, and three integrated articles.

gp3bayes 0.1.1

  • Prepared the first CRAN submission candidate.
  • Added Zenodo DOI documentation and current release-status wording.
  • Added explicit copyright-holder metadata for the initial CRAN submission.

gp3bayes 0.1.0

  • Created the independent gp3bayes package scaffold.
  • Defined the initial scope as contract-first Bayesian workflows for hierarchical behavioural data.
  • Restricted initial development to hierarchical Bernoulli-logit and hierarchical lognormal-duration model families.
  • Added package-level documentation and explicit interpretation boundaries.
  • Added the initial deterministic scope test using testthat edition 3.
  • Added the MIT licence.
  • Added standard GitHub Actions workflows for cross-platform R CMD check and pkgdown deployment.
  • Added canonical repository, issue-tracker, and pkgdown website metadata.
  • Added create_model_contract() for the two approved initial model families with neutral column mappings and explicit methodological specifications.
  • Added a concise gp3bayes_model_contract print method and deterministic validation tests.
  • Added audit_model_readiness() for backend-independent assessment of outcome validity, declared columns, missingness, repeated measurements, item and trial structure, predictors, interactions, time terms, and requested participant-level random slopes.
  • Added structured gp3bayes_readiness_audit results with explicit pass, warning, and failure statuses and a concise print method.
  • Added build_model_formula() for deterministic, backend-independent construction of approved fixed-effects, interaction, participant, item, time, and optional participant-level random-slope structures.
  • Added create_prior_specification() and validate_prior_specification() for explicit binary-logit and lognormal-duration prior records without creating executable backend objects.
  • Added create_model_specification() to combine a model contract, successful readiness audit, approved formula, and validated priors into one inspectable backend-independent specification.
  • Added concise print methods and deterministic validation tests for formulas, priors, compatibility checks, and complete specifications.
  • Added simulate_hierarchical_binary_data() for deterministic hierarchical Bernoulli-logit simulation with participant effects, optional crossed item effects, optional participant condition slopes, controlled imbalance, and a stored true-parameter record.
  • Added prepare_hierarchical_binary_data() for explicit binary-outcome mapping, condition coding, recorded predictor scaling, missing-data decisions, readiness auditing, and fixed-effects matrix construction.
  • Added specify_binary_model() to combine prepared data with the approved binary contract, restricted hierarchical formula, and validated backend-independent prior specification.
  • Added check_binary_prior_predictive() for deterministic simulation of family-specific prior predictions and structured plausibility checks without fitting a model or requiring a Bayesian backend.
  • Added concise print methods, generated documentation, and 89 focused tests for the backend-independent binary workflow foundation.
  • Added repository and installed-package citation metadata through CITATION.cff and inst/CITATION.
  • Refined the package description to match the currently implemented backend-independent contract, readiness, simulation, preparation, specification, and prior-predictive functionality.
  • Added restricted binary model translation from approved package specifications to brms Bernoulli-logit formulas and priors.
  • Added optional full-MCMC fitting through the fixed brms and rstan sampling route without unrestricted formulas or backend arguments.
  • Added conservative fit metadata that records sampling settings while explicitly withholding convergence and posterior-adequacy claims.
  • Added conservative binary posterior diagnostics covering R-hat, bulk and tail ESS, divergences, maximum-treedepth saturation, and chain-level energy diagnostics.
  • Added posterior summaries, binary posterior predictive checks, prior-scale sensitivity, simulation-based recovery, diagnostic plots, and structured Markdown model reports.
  • Diagnostic, predictive, sensitivity, and recovery statuses never create automatic convergence, adequacy, robustness, or validation claims.
  • Added the complete hierarchical lognormal duration workflow for strictly positive finite uncensored outcomes.
  • Added deterministic duration simulation, explicit unit conversion and preparation, model specification, prior predictive checks, restricted brms translation, and full MCMC fitting through rstan.
  • Zero, negative, censored, truncated, shifted, survival, Gamma, Weibull, and mixture outcomes remain outside the approved duration contract.
  • Added conservative duration posterior diagnostics, posterior summaries with median-ratio interpretation, posterior predictive checks, prior-scale sensitivity, simulation-based recovery, and structured Markdown reports.
  • Duration validation statuses remain separate from automatic convergence, adequacy, robustness, causal, or substantive claims.
  • Added integrated end-to-end binary and duration vignettes.
  • Added dedicated articles for sampling diagnostics, prior sensitivity and recovery, and optional backend installation.
  • Added a repository-only audit covering exports, Rd aliases, pkgdown reference topics, articles, built pages, and optional dependencies.
  • Aligned DESCRIPTION, citation metadata, README, package documentation, and the curated pkgdown reference and article indices with the complete scope.