richCluster 2.0.0 (2026-09-15)

Important: results differ from earlier versions

This release fixes several problems in the similarity and clustering core, listed below. Results may differ from those of richCluster 1.0.2 and earlier, and we recommend re-running affected analyses with 2.0.0.
cluster_result objects saved with an earlier version should be recomputed from the input enrichment tables rather than re-plotted. The bundled example object has been regenerated.
There is no compatibility mode that restores the earlier behaviour; see “Reproducing results from richCluster 1.0.2” below.

Kappa similarity now counts the genes shared by two terms correctly.
Corrected the cluster merge logic so that qualifying clusters are merged as documented.
linkage_method = "single" and linkage_method = "complete" now apply single and complete linkage respectively; earlier versions had the two exchanged.
linkage_method = "ward" now implements Ward’s minimum-variance criterion; earlier versions used average linkage for this option.
distance_metric = "jaccard" now returns the Jaccard index, |A intersect B| / |A union B|.
Kappa now returns 1 for two terms whose identical gene sets span the whole gene universe.
david_cluster() now repeats its merge stage until no pair of final clusters exceeds the multiple-linkage threshold.

In cluster() and runRichCluster(), negative kappa values are set to 0, so kappa similarity lies on a [0, 1] scale. This non-negative similarity is a deliberate choice for clustering and differs from an unmodified Cohen’s kappa. david_cluster() uses unmodified kappa, as the DAVID algorithm does.
cluster() now selects terms on the adjusted p-value by default, matching its documentation. The new filter_on argument selects the column ("Padj" or "Pvalue").
distance_cutoff and linkage_cutoff are strict thresholds throughout: a score must exceed the cutoff to link or merge.
Results are now reproducible across macOS, Linux and Windows: cluster numbering, term order and tie-breaking follow a canonical term order, and merge_enrichment_results() orders its rows independently of the locale.
Cluster numbers are now contiguous and consistent with those used by the plotting functions. The representative term of a cluster is the term with the smallest value in the requested significance column.
full_network() no longer includes self-loops, and cluster_hmap() now produces unique row labels.
The diagonal of the exported similarity matrix is 1.
term_hmap() now returns a plotly object drawn by heatmaply, like cluster_hmap(), and the iheatmapr dependency has been removed.

distance_metric = "dice" adds the Dice coefficient.
cluster() and runRichCluster() gain gene_delim, the separator used to split gene lists (default ",").
cluster(), david_cluster() and runRichCluster() gain verbose (default FALSE); progress output is silent unless verbose = TRUE.

Warnings and errors carry stable condition classes: richCluster_filter_on_fallback, richCluster_colname_collision, richCluster_duplicate_terms and richCluster_missing_geneid.
merge_enrichment_results() adds a DatasetCount column and warns when an input dataset repeats a Term value.
david_cluster() validates its parameters, and an input too large for the similarity matrix (above about 46,000 terms) stops early with an informative error.

To reproduce an existing figure or table, install 1.0.2 in a separate library with remotes::install_version("richCluster", "1.0.2"). Use 2.0.0 for new analyses.