Changes in version 2.3.1 (2026-03-13)                  

Major changes

  - Correlation engine overhaul. ResIN now uses a unified, more
    efficient correlation backend that supports:
      - cor_method = "pearson" (fully supported across
        weighted/unweighted settings, pairwise/listwise missingness, and
        optional p-value pruning)
      - cor_method = "polychoric" (currently supported for unweighted
        correlation estimation; unsupported option combinations
        transparently fall back to Pearson correlation)
  - New missingness control for correlations. Added missing_cor =
    c("pairwise","listwise") to explicitly control missing-data handling
    during correlation estimation (default: "pairwise").

Weighted correlations

  - Improved weights interface. Survey weights can now be supplied
    either as:
      - a numeric vector of length nrow(df), or
      - a character scalar naming a weights column in df (e.g., weights
        = "psweights").
        When weights is supplied as a column name and node_vars = NULL,
        the weights column is automatically excluded from the
        response-node variables used for estimation.

Edge pruning

  - New multiple-testing option for pruning. Added
    remove_nonsignificant_method, enabling Benjamini–Hochberg FDR
    control ("fdr") as an alternative to raw p-value pruning
    ("default"). sign_threshold is interpreted as the raw p-value cutoff
    under "default" and as the target FDR level under "fdr".
  - EBICglasso retired. EBICglasso and EBICglasso_arglist are retained
    for backwards compatibility but are deprecated and ignored as
    of 2.3.0. This feature is not statistically appropriate for the
    rank-deficient one-hot encoded ResIN correlation matrix.

Bootstrapping workflow (S3 methods & robustness)

  - Added/expanded S3 methods and documentation for ResIN bootstrap
    workflow objects:
      - ResIN_boots_prepped and ResIN_boots_executed now have clearer
        print/summary behavior.
      - ResIN_boots_execute() is more robust (handles failed iterations
        gracefully) and improves progress-bar formatting.
  - ResIN_boots_extract() now supports multi-quantity extraction and
    improved summarizing behavior, including consistent data-frame
    output for summaries.

Conversion of ResIN objects for interoperability and manipulation in other software environments

  - Added conventional S3 conversions for ResIN objects:
      - as.igraph.ResIN(), as.qgraph.ResIN(), as.gephi.ResIN()
      - as.network.ResIN() (statnet/network ecosystem), with
        as.network() re-exported for convenience
  - Added lightweight cross-language export helpers:
      - as.networkx.ResIN() exports NetworkX compatible edge & node CSV
        tables for Python workflows (loadable via pandas + networkx).
      - as.graphsjl.ResIN() exports Graphs.jl compatible edge & node CSV
        tables for Julia workflows (with integer vertex IDs suitable for
        Graphs.jl), while preserving node/edge metadata as table
        columns.
  - Legacy conversion functions (e.g., ResIN_to_igraph(),
    ResIN_to_qgraph(), ResIN_to_gephi()) are retained for compatibility
    and delegate to the new conversion methods where appropriate.

Improved Multimodal network estimation and plotting features

  - Enhanced the optional multimodal output (multimodal = TRUE) to
    return tidy, analysis-ready tables in addition to graph objects:
    
      - ResIN_edgelist_multimodal: participant–response edge list (one
        row per observed response node selection).
      - ResIN_nodeframe_multimodal: vertex table containing node
        identifiers, node type (participant vs response node), layout
        coordinates, and available metadata.

  - Improved multimodal plotting:
    
      - Response nodes are now rendered larger than participant nodes
        for improved visual separation.
      - multimodal plots now reuse key analytic settings from the main
        ResIN workflow where applicable (e.g., covariate/cluster-based
        colouring via plot_whichstat).
      - When plot_whichstat = "cluster", the legend title includes the
        clustering algorithm and reports participant/response counts per
        detected cluster.

  - Added flexible edge overlay controls for multimodal plots via
    multimodal_edge_overlay:
    
      - "none": no edges drawn
      - "multimodal": draw participant–response edges only
      - "ResIN": draw the original ResIN (response–response) edges as an
        overlay, with line width optionally mapped via plot_edgestat
      - "both": draw ResIN edges as a base layer and multimodal edges on
        top ResIN edge overlays are mapped to the multimodal layout
        coordinates to ensure visual alignment with the multimodal node
        geometry.

  - Added adjecency matrix retaining negative edges as part of
    aux_objects

Bug fix for cluster Leiden function call

Documentation

  - Improved help page titles and vignette metadata (more informative
    package-level index display).
  - Added/updated documentation for new S3 classes/methods, conversions,
    and pruning options.

                 Changes in version 2.3.0 (2026-03-02)                  

  - Prior release.