shrinkr 0.4.5

Documentation

• Improved CRAN compatibility. Updated package metadata and documentation following CRAN review comments, including expanding Markov chain Monte Carlo

  2000. on first use in the DESCRIPTION file.

• Modernized examples. Reworked documentation examples so lightweight examples are executable and self-contained. Replaced unnecessary \dontrun{} blocks with executable examples or \donttest{} where appropriate.

• Protected computationally intensive examples. Kept examples that require fitting Bayesian hierarchical models with Stan inside \dontrun{} because they are not suitable for routine CRAN example checks.

• Improved method documentation examples. Added small example objects for selected shrinkr_fit and mixture-method documentation so examples no longer depend on objects created in other help pages.

Vignettes

• Restored graphical parameters. Updated the federated_learning vignette to save and restore graphical settings after calls to par(), avoiding persistent changes to the user’s plotting environment.

shrinkr 0.4.4

New Features

• New vignette: vignette("map_prior_with_beastt"). Demonstrates how to build a robust meta-analytic-predictive (MAP) prior by pairing shrinkr with the beastt package. shrinkr runs the hierarchical meta-analysis across historical control arms and returns the MAP as a distributional object, which beastt then robustifies (robustify_norm()) and combines with the internal control arm (calc_post_norm()) to form the control posterior and report an effective sample size. The worked example uses a continuous outcome with known SD, and the prior is calibrated with sample_prior_predictive() / prior_pairwise_differences().

Documentation

• Added the new MAP-prior vignette to the website articles index and the README Documentation section.
• Minor documentation fixes ahead of CRAN submission: package version references synchronized to 0.4.4, and small cross-reference and formatting tidy-ups in roxygen docs and man pages.

shrinkr 0.4.3

Bug Fixes

• Fixed inverse-gamma prior translation in R/utils.R. The branch handling dist_inverse_gamma priors on tau was reading from params$shape and params$scale, but distributional::parameters() returns those fields as s and r. The check !is.null(params$shape) && !is.null(params$scale) was always FALSE, so the branch silently failed and downstream code relied on a format-string regex fallback to rescue the parsing. End-to-end posteriors were correct (the fallback happened to parse format() output identically to what the explicit branch should have produced), but the code path was fragile. The branch now reads params$s / params$r from parameters(tau_raw) (the unwrapped distribution, not the possibly-truncated wrapper) and dispatches correctly without needing the fallback.
• Fixed uniform prior translation in R/utils.R. The dist_uniform branch was reading from tau_raw$min and tau_raw$max, but distributional stores the bounds as l and u. Same pattern as the IG bug: branch silently failed, format-string fallback rescued it. The branch now reads tau_raw$l / tau_raw$u and dispatches correctly.

Internal Changes

• Removed unused stan_code() generic and methods from R/prior_system.R. The generic and its 9 distributional-family methods were vestiges of an earlier, abandoned design where Stan code was assembled at runtime from prior strings. shrinkr’s actual workflow handles all prior dispatch internally inside the precompiled Stan model (inst/stan/stage2_shrinkage.stan) via integer prior codes and parameter arrays. The dead code path was never reached at runtime; removing it drops ~120 lines of source, 9 S3method entries from NAMESPACE, and 10 .Rd files from man/. prior_mixture() and prior_spike_slab() remain unchanged.
• Removed the format-string regex fallback in R/utils.R. Roughly 85 lines across the mu and tau translation paths used format(prior) string parsing as a last-resort dispatch when the explicit class-based branches missed. With the inverse-gamma fix above, every supported prior now dispatches via class-based checks, making the fallback redundant. Removing it leaves a cleaner, more transparent failure mode: an unsupported prior raises a clear error rather than silently passing through a regex parser.

shrinkr 0.4.2

License

• shrinkr is now released under GPL (>= 3). Previous versions did not carry a formal open-source license. The LICENSE field in DESCRIPTION now reads GPL (>= 3) and the full license text is shipped in LICENSE. This formalizes the terms under which the package may be used, modified, and redistributed.

Breaking Changes

• Renamed compute_theta_contrasts() to theta_contrasts() for consistency with the other theta-family functions (extract_theta(), summarise_theta()). The old name has been removed; update calls accordingly.

New Features

• summarise_mu_tau() / summarize_mu_tau(): Summarize hyperparameters (mu, tau, tau_squared) in the same format as summarise_theta(). Returns posterior mean, sd, quantiles, and convergence diagnostics (rhat, ess_bulk, ess_tail) when multiple chains are available. Closes a naming-symmetry gap: previously extract_mu_tau() existed but had no summary counterpart.

Internal Changes

• Migrated Stan array syntax to the array[N] type name form in inst/stan/stage2_shrinkage.stan. The function signature for builtin_tau_prior_lpdf() and the tau_params / custom_params data declarations previously used the pre-2.26 syntax (real[] params, real tau_params[6], real custom_params[10]), which emitted stanc3 deprecation warnings and will become errors in a future Stan release. No user-visible change in behavior; R-side data passing is unaffected.

shrinkr 0.4.1

Bug Fixes

• Fixed Stan model sampling speed regression: Restored std_normal() prior on the inactive parameterization vector (z when centered, theta_c when non-centered). In 0.4.0, the inactive vector had no sampling statement, giving it an implicit improper uniform prior. This caused Stan’s NUTS sampler to waste effort exploring unbounded space, significantly slowing sampling. The fix constrains the inactive vector without affecting the model.

Documentation

• Minor formatting improvements to README.

shrinkr 0.4.0

Breaking Changes

• Removed parse_priors(): The legacy formula-based prior interface has been removed. Use distributional objects (e.g., dist_normal(), dist_student_t()) directly with shrink() via the hierarchical_priors argument.

• Removed shrinkage_factor from Stan generated quantities. This quantity (tau^2 / (tau^2 + 1)) was misleading because it assumed standardized Stage 1 variance. Use tau_squared directly for heterogeneity assessment.

• Removed group column from fit_mixture() output. The column was always 1L and served no purpose. The variable column identifies subgroups.

• prior_mixture() and prior_spike_slab() now return native distributional objects via distributional::dist_mixture(). This replaces the previous custom dist_mixture class. All distributional operations (sampling, density, format, quantiles) work automatically. Code that accessed $components or $weights fields directly will need updating.

• prior_spike_slab() must be truncated for tau: Since tau is a scale parameter, spike-and-slab priors must be wrapped with dist_truncated(..., lower = 0). sample_prior_predictive() now errors (rather than warns) if tau draws are negative. Example: tau = dist_truncated(prior_spike_slab(), lower = 0).

New Features

• Mixture prior support now works end-to-end: prior_mixture() and prior_spike_slab() now correctly flow through to Stan for both mu and tau priors. Previously, these were exported but not wired into the .coerce_priors_to_stan() pipeline.

• Truncated mu priors: mu now supports truncation via dist_truncated(dist_normal(0, 5), lower = 0). This enables constraining the global mean to a scientifically meaningful range.

• prior_pairwise_differences(): New function to compute the prior-implied distribution of |theta_i - theta_j| from prior predictive samples. Includes print() and plot() S3 methods. The pooled view uses a skyblue density (matching the hyperparameter panel) and the by-pair view uses lightcoral violins (matching the theta panel). Useful for calibrating priors following the recommendation to inspect pairwise difference distributions before fitting.

• Re-exported as_draws_df() from the posterior package so users can call as_draws_df(fit) without explicitly loading posterior.

Bug Fixes

• Safe Cholesky factorization: .as_chol_factor() now uses a jitter-and-retry strategy (1e-10 through 1e-4) with Matrix::nearPD() fallback instead of passing a non-lower-triangular eigen decomposition to Stan. The old fallback could silently produce invalid cholesky_factor_cov input.

• Stan model no longer exposes unused parameters: The inactive parameterization (z when centered, theta_c when non-centered) is constrained with a std_normal() prior so it doesn’t appear as a meaningful parameter in output.

• Fixed all vignette references: Standardized to underscore naming (getting_started, brms_integration, tidy_bayesian_workflow, federated_learning) throughout R docs, man pages, vignettes, and README. Removed references to nonexistent vignettes (mathematical-foundation, two_stage_demo, tidybayes-integration).

• Mixture component extraction handles truncated normals: The internal .extract_normal_params() helper correctly unwraps dist_truncated(dist_normal()) to extract the underlying mean and sd for Stan mixture priors. This is needed for dist_truncated(prior_spike_slab(), lower = 0) to work.

Testing

• New test-prior-system.R with 41 tests covering:
  • prior_mixture() and prior_spike_slab() object creation and sampling
  • .coerce_priors_to_stan() for all mu types (Normal, Student-t, truncated, mixture)
  • .coerce_priors_to_stan() for all tau types (8 built-in + mixture + error cases)
  • .as_chol_factor() safety (positive-definite, near-singular, bad matrices)
  • sample_prior_predictive() validation and tau positivity enforcement
  • prior_pairwise_differences() structure, edge cases, and probability calibration
  • fit_mixture() output structure (no group column, quantiles present)
  • End-to-end shrink() with spike-and-slab tau, truncated mu, mixture mu
  • Verification that shrinkage_factor is absent from output
• Updated existing tests for 0.4.0 API changes:
  • test-shrinkr.R: Updated mixture prior tests for distributional::dist_mixture
  • test-extraction.R: Updated as.data.frame.shrinkr_mixture to expect no group column

Documentation

• README substantially improved:

  • Defined theta on first mention in Quick Start
  • Clarified what K_max controls and how mclust selects K via BIC
  • Explained implied_range in prior predictive section
  • Added “Why a Mixture of Normals?” section with universal approximation justification and K_max sensitivity guidance
  • Noted that standard rstan/bayesplot diagnostic tools work on fit$fit
  • Added examples for truncated mu, spike-and-slab (with truncation), and pairwise contrasts
  • Highlighted use cases where normal approximation is insufficient (small subgroups, rare events)
  • Fixed vignette names in Documentation section

• Getting started vignette: Added section on prior_pairwise_differences() with explanation of clinical calibration for pairwise |theta_i - theta_j|.

• Package version references synchronized to 0.4.0 throughout.

shrinkr 0.3.2

• Vignettes hosted on website only: Small package changes to host vignettes on website and not include in build.
  • This will improve CRAN compatibility later

shrinkr 0.3.1

New Features

• Federated Learning Vignette: Added comprehensive vignette demonstrating shrinkr’s application to federated learning scenarios (vignette("federated_learning")). The vignette covers:
  • Multi-hospital mortality prediction example with privacy-preserving analysis
  • Two federated learning paths: full posteriors vs. summary statistics
  • Critical guidance on Bayesian CLT assumptions for summary statistics
  • Normality diagnostics with concrete counter-examples when CLT fails
  • Privacy comparison showing data transfer requirements (200 KB vs. 16 bytes)
  • Best practices for data governance, quality control, and transparent reporting
  • Advanced scenarios including heterogeneous models and iterative updates

Improvements

• Plot Layout Enhancement: Improved plot.shrinkr_fit() default visualization:
  • Optimized spacing and arrangement of plot elements for better readability
  • Enhanced visual distinction between Stage 1 (independent) and Stage 2 (shrunken) estimates
  • Clearer presentation of global mean and credible intervals
  • More intuitive display of shrinkage effects across groups

Documentation

• Added detailed warnings about Bayesian CLT assumptions when using summary statistics instead of full posterior samples
• Emphasized mixture approximation (Path A) as the safer default for federated learning
• Provided explicit normality checking procedures with QQ plots and diagnostic statistics
• Clarified when each federated learning path is appropriate vs. when it can lead to bias

shrinkr 0.3.0

First Internal Release

This release focuses on core functionality with a clean, stable API for internal use at GSK.

Core Features

• Two-stage Bayesian hierarchical shrinkage framework: Separate Stage 1 model fitting from Stage 2 hierarchical shrinkage
• Flexible prior specification via the distributional package for standard prior families:
  • Normal, Student-t, Cauchy, Lognormal
  • Heavy-tailed: Inverse-Gamma, Half-Cauchy, Half-t
  • Bounded: Uniform
  • Truncated distributions
  • Mixture priors: spike-and-slab

Main Functions

• fit_mixture(): Approximate Stage 1 posteriors with Gaussian mixture models
• shrink(): Apply hierarchical shrinkage with custom priors
• prior_spike_slab(): Create spike-and-slab mixture priors for testing homogeneity
• prior_mixture(): Create custom mixture priors with multiple components
• sample_prior_predictive(): Generate prior predictive samples for prior elicitation

Prior Specification & Checking

• Specify priors using distributional package syntax
• Test prior implications with sample_prior_predictive()
• Visualize prior predictive distributions
• Check implied ranges and spread of effects before fitting

Extraction & Analysis

• extract_mu_tau(): Extract global parameter estimates (mean and heterogeneity)
• summarise_theta() / summarize_theta(): Summarize group-level estimates with credible intervals
• compute_theta_contrasts(): Compute pairwise group comparisons
• plot() methods: Visualize shrinkage effects and mixture approximation quality

Input Methods

• Full posterior samples (recommended): Provide mixture approximation that captures posterior uncertainty
• Point estimates: Use MLE + variance vector or covariance matrix when full posteriors unavailable

Integration

• Works with tidybayes and posterior packages for tidy workflows
• Compatible with outputs from Stan, NIMBLE, JAGS, and brms
• Supports both univariate and multivariate parameters

Documentation

• Comprehensive vignettes:
  • Getting Started: Basic workflow and examples
  • Integration with tidyBayes ecosystem
  • Working with brms models
• Complete function documentation with examples

Package Quality

• Comprehensive test suite
• All functions documented with roxygen2
• Proper NAMESPACE management
• Precompiled Stan models for efficiency

Technical Details

• Built on rstan for Markov chain Monte Carlo (MCMC) sampling
• Uses mclust for mixture model fitting
• Integrates with posterior and distributional packages
• Supports centered and non-centered parameterizations
• Vectorized Stan code for computational efficiency

shrinkr 0.2.0 (Development)

• Prototype version with extended prior system
• Experimental features for prior selection

shrinkr 0.1.0 (Development)

• Initial development version
• Core two-stage framework established