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Release Notes

All notable changes to SeroEpi are documented on this page. This project adheres to Semantic Versioning and the Keep a Changelog specification.

[Unreleased]

Added

  • Surveillance Cohort & Semantic Variable Engine (seroepi.dataset, seroepi.variables, seroepi.dist):
  • Immutable Polars-backed Dataset container with \(O(1)\) identity-mapped Variable lookup (Trait, Spatial, Temporal, Target, and composable multi-variable Criterion expressions).
  • Sparse CSR pairwise SNP distance matrices (GenomicDistances) and outbreak-aware clonal cluster deduplication (TransmissionEstimator).
  • Asynchronous PathogenwatchClient and UN/World Bank demographic WorldBankClient with bundled KlebnetNeonatalSepsis and CountryData assets.
  • Stratified Aggregation & Bayesian Prevalence Estimators (seroepi.aggregate, seroepi.estimators):
  • Aggregator sufficiency-reduction transformer compatible with scikit-learn pipelines.
  • Analytical/frequentist UnpooledEstimator (Wilson, Clopper-Pearson, Jeffreys, Dirichlet) and BootstrapEstimator.
  • JAX/NumPyro hierarchical Bayesian partial-pooling models (HierarchicalMCMCEstimator NUTS and HierarchicalSVIEstimator SVI) for Binomial and Beta-Binomial / Dirichlet-Multinomial likelihoods.
  • Multi-Valent Formulation Optimization (seroepi.estimators.formulation):
  • Formulation and FormulationComparison meta-estimators supporting pooled or equal-stratum weights, Leave-One-Stratum-Out (LOSO) cross-validation, and permutation/Bayesian False Discovery Rate (BH/BY) differential enrichment testing.
  • Publication-Grade Altair Plotting & Live PyShiny App (seroepi.plotting, seroepi.app):
  • Theme-aware Altair plotters (ChoroplethPlotter, BarPlotter, HeatmapPlotter, PyramidPlotter, UpSetPlotter, FormulationCoveragePlotter, FormulationStabilityPlotter, DifferentialPrevalencePlotter, RankShiftPlotter).
  • Modular OOP PyShiny web application (HomeTab, DatasetTab, EstimationTab, FormulationTab) deployed on Posit Connect Cloud and embedded in the documentation site.

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