NEWS

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comparpq 0.1.3

• Add param compute_dist to list_phyloseq()

comparpq 0.1.2

• Add params significance, test and p_alpha to div_pq() to report tuckey hsd paired-test using letters.
• gg_hill_lpq() new function to visualize Hill diversity correlations across pairs of phyloseq objects in a list_phyloseq. Produces a faceted scatter plot (pairs × Hill orders) with optional 1:1 line, regression line, and per-panel correlation annotation, enabling visual assessment of REPRODUCIBILITY, ROBUSTNESS, and REPLICABILITY.
• gg_bubbles_pq() now uses merge_lpq() when a list_phyloseq is passed, merging into a single phyloseq and faceting by source_name instead of building separate patchwork panels. diff_contour now works with any facet_by variable (not just list_phyloseq), highlighting taxa unique to each facet level with a distinct contour color from diff_contour_colors. No longer limited to 2 or 3 objects. New match_by parameter controls how taxa are matched when merging list_phyloseq objects.
• gg_bubbles_pq() new ggplot2-based circle-packed bubble plot of taxa abundances. Unlike bubbles_pq(), it does not require d3js/Observable and supports faceting by a @sam_data variable to display one bubble chart per level. Uses packcircles for layout computation.
• compare_refseq() new function to compare reference sequences (refseq slot) between two phyloseq objects, identifying shared and unique ASVs/OTUs by name and by DNA sequence content, including detection of same-name-different-sequence and same-sequence-different-name mismatches. Computes mean nearest-neighbor k-mer distance for unique sequences.
• Add function apply_to_lpq() to apply a function to each phyloseq object in a list_phyloseq
• estim_cor_lpq() new function to compute bootstrap correlation/regression across a list_phyloseq
• estim_cor_pq() new function to compute bootstrap correlation and regression CIs for diversity vs numeric variables
• estim_diff_lpq() new function to run estimation statistics (effect sizes + CIs) across a list_phyloseq
• estim_diff_pq() new function for estimation statistics (Gardner-Altman/Cumming plots) comparing diversity across groups via dabestr
• merge_lpq() new function to merge a list_phyloseq into a single phyloseq object where each original phyloseq becomes one sample. Taxa can be matched by reference sequences (match_by = "refseq", default) or by taxa names (match_by = "names").
• simple_venn_pq() new function to draw Venn diagrams of shared taxa across 2-4 sample groups using pure ggplot2 (no external Venn package needed), with support for multiple taxonomic ranks and compact, clearly labeled circles/ellipses.
• simple_venn_pq() now accepts a list_phyloseq object as input, automatically merging it via merge_lpq() before drawing the Venn diagram.