ResIN 2.3.1

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.

ResIN 2.3.0

• Prior release.