Changes in version 0.1.4 (2026-04-17)                  

  - Documentation / vignettes:
    
      - Added a new "Quick Start with bifrost" vignette with a minimal
        end-to-end simulated example.
      - Clarified searchOptimalConfiguration() documentation around
        acceptable tree inputs, recommended mvgls() methods ("H&L" vs
        "LL"), and the role of error = TRUE.
      - Reworked the README to foreground installation, documentation,
        and citation guidance.
      - Added two pkgdown-only background articles on multivariate
        Brownian motion / shifts and on whole-tree PCA / model-selection
        issues.

  - Citation / metadata:
    
      - Updated package authorship metadata to reflect the current
        author list.
      - Updated citation("bifrost") for the live bioRxiv preprint and
        the in-press application paper.
      - Added the foundational mvMORPH citations to the package citation
        metadata.
      - Added a formatted citation section and dynamic bioRxiv badge to
        the README.

  - Maintenance:
    
      - Disabled a deprecated vignette-preview step in GitHub Actions
        CI.

                 Changes in version 0.1.3 (2026-01-21)                  

  - Addressed CRAN reviewer feedback following review of 0.1.2:
    
      - Added explicit return-value documentation (@return / \value{})
        for the exported print.bifrost_search() method, clarifying that
        the function returns the input object invisibly and is called
        for its printing side effects.

  - Plotting:
    
      - plot_ic_acceptance_matrix() gains an optional baseline_ic
        argument to plot and compute diff(IC) relative to the true
        no-shift baseline (useful when matrix_data begins at the first
        evaluated shift model rather than the true baseline).

  - Documentation / vignettes:
    
      - Updated the jaw-shape vignette with additional static figures
        (evolutionary correlation heatmap, IC-trajectory plot, and
        branch-rate visualization) and improved plotting annotations.

                        Changes in version 0.1.2                        

  - Addressed CRAN reviewer feedback following review of 0.1.1:
    
      - plot_ic_acceptance_matrix() now saves and restores the user’s
        graphical parameters via an immediate on.exit() (prevents
        leaking par() settings across calls).

  - Plotting:
    
      - Added rate_limits argument to plot_ic_acceptance_matrix()
        (default c(-400, 150)) to control the secondary y-axis limits
        for the rate-of-improvement overlay (validated numeric length-2,
        finite).

  - Search results output:
    
      - Added a bifrost_search S3 class and print.bifrost_search()
        method for searchOptimalConfiguration() results (compact console
        summary; optional ASCII IC-history plot via txtplot when
        store_model_fit_history = TRUE; prints IC weights when present).
      - Print output includes a citation hint (citation("bifrost"));
        package citation metadata updated in inst/CITATION.

  - IC weights / no-shift behavior:
    
      - Standardized ic_weights output across serial and parallel
        uncertainty-weight modes; always returns a data.frame with
        consistent columns, and returns an empty data.frame with the
        same schema when no shifts are detected.
      - When no shifts are detected, model_no_uncertainty now returns
        the baseline mvgls model (instead of NULL).

  - Documentation / vignettes / tests:
    
      - Updated jaw-shape vignette chunk printing of ic_weights to avoid
        RStudio paged/Unicode rendering issues.
      - Expanded and stabilized unit tests and CI configuration
        (including Config/testthat/parallel: false).

                        Changes in version 0.1.1                        

  - Addressed CRAN reviewer feedback following review of 0.1.0:
      - Replaced all uses of shorthand T/F with TRUE/FALSE.
      - Ensured all informational output is suppressible via
        message()/warning() and controlled by a verbose flag.
      - Redirected all on-disk output generated during model fitting to
        tempdir() to comply with CRAN file system policies and avoid
        writing to the user’s working directory.
      - Ensured graphical parameters and global options are restored
        using immediate on.exit() calls.
      - Refined parallelization behavior to be CRAN-safe and
        cross-platform:
          - Parallel candidate evaluation uses future with multicore on
            Unix outside RStudio and multisession otherwise.
          - BLAS/OpenMP threads are capped to one per worker during
            parallel execution to avoid CPU oversubscription.
          - Sequential execution remains the default when num_cores = 1.
      - Improved documentation clarity around parallel execution,
        verbosity, and model fit history storage.

                        Changes in version 0.1.0                        

  - Initial CRAN submission.