Changes in version 0.0.2 (2026-10-16)                  

  - Document return classes, output components, and their interpretation
    for the eight functions identified during CRAN review.
  - Require an explicit output_dir in run_ga_batch(). Calls that
    previously relied on the default "results" directory must now supply
    that argument.
  - Replace both disabled genetic-algorithm examples with small,
    self-contained examples that run during package checks and show the
    actual returned fields.

                        Changes in version 0.0.1                        

MCMC reference distributions

  - Return self-normalized estimates of the uniform combination score
    distribution, with a separate reference conditional on support
    strictly greater than beta.
  - Return the weight-based effective sample size for both references.
    Weights use exact capped scores before histogram binning and are
    rescaled for stability.
  - Add weight_ess() and uniform_score_reference() for explicit
    post-processing.
  - Add optional burn_in and store_trace arguments to the generic and
    PWP MCMC interfaces. Rejected moves contribute repeated states to
    the retained sample.

Sampling and score corrections

  - Correct unsigned subtraction in the hypergeometric upper tail: zero
    observed exposed events now give score zero, instead of an erroneous
    infinite score.

  - Both MCMC proposal types now operate on fixed-size subsets of
    distinct nodes, including ancestor-descendant pairs. Global
    proposals are uniform; local proposals exclude occupied destinations
    and use the corresponding Hastings correction. These corrections
    change trajectories from earlier development versions even when the
    same seed is supplied.

  - A positive prob_type1 is required to connect the observed state
    space. Initialization constructs a supported state and reports
    impossible sizes.

  - Correct hierarchical membership when a single observed descendant
    covers multiple selected ancestors. Genetic-algorithm validity rules
    are unchanged.

  - Exhaustive size-two references enumerate supported unordered pairs
    once, excluding self-pairs, and use unit weights. Previous reference
    outputs should be regenerated before comparison with corrected MCMC
    output.

  - Sort within-patient observations before computing medians in
    Wilcoxon post-processing and residual scores; scores no longer
    depend on row order.

  - Expose optional id_column in the depth-vector MCMC interface for
    continuous patient-level scores.

  - Validate finite temperatures, score caps, integer size controls and
    burn-in; support n_results = 0 and allow user interruption during
    long runs.

Package maintenance

  - Align the package declaration with the maintainer-selected GPL-3
    license.

  - Require C++17, which covers the language features used by the
    package.

  - Make saved-result helpers independent of implicitly attached
    tidyverse packages.

  - Guard traversal above tree roots and empty dissimilarity matrices;
    compute parent links for depth-vector trees as for data-frame trees.

  - Declare optional visualization dependencies and report missing
    dependencies.

  - Replace placeholder help pages; document the capped target and
    reference space.

  - Use explicit exports, preserving documented public helpers and
    keeping native engines and test helpers internal.

  - Replace the test dependency on emcAdr with an independent synthetic
    tree.

  - Add tests for weighting, ESS, filtering, burn-in, proposal support
    and exhaustive calibration, and a multi-platform R CMD check
    workflow.