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name: diversity-tables description: "Compute scikit-bio community diversity metrics and prepare BIOM-style table-like inputs for count workflows." disable-model-invocation: true metadata: disco-role: operating license: BSD 3-Clause

Diversity Tables

Use this sub-skill when a task asks for alpha diversity, beta diversity, phylogenetic diversity, UniFrac, large beta-distance computation, BIOM-style tables, table-like count matrices, or table augmentation for biological community data.

Read First

• references/api-reference.md for callable signatures, return types, metric discovery, table orientation, and augmentation APIs.
• references/workflows.md for input preparation, alpha/beta runs, Faith PD/UniFrac setup, block decomposition, and dense/table conversions.
• references/troubleshooting.md for invalid counts, sample/taxon length errors, callable-vs-string metrics, tree/taxa mismatch, table axis confusion, optional backend limits, and validate=False risks.
• scripts/diversity_table_smoke.py for a deterministic smoke check covering sobs, Bray-Curtis, Faith PD, UniFrac, and Table dense conversion.

Typical Routing

• Compute richness, evenness, observed features, Chao1, Faith PD, or any per-sample metric with skbio.diversity.alpha_diversity.
• Compute Bray-Curtis, Jaccard, Euclidean, weighted UniFrac, unweighted UniFrac, or SciPy pairwise distances with skbio.diversity.beta_diversity.
• Use skbio.diversity.block_beta_diversity when many samples or features make full beta diversity expensive and block/map-reduce execution is appropriate.
• Use skbio.diversity.partial_beta_diversity only for explicit ID pairs and with caution because uncomputed distances are represented as zeros.
• Use skbio.table.Table, skbio.table.example_table, pandas DataFrames, NumPy arrays, or other supported table-like inputs when rows are samples and columns are features/taxa.
• Use skbio.table.mixup, aitchison_mixup, compos_cutmix, or phylomix only as table augmentation helpers for synthetic biological count/composition workflows.

Boundaries

• Route tree construction, rooting, branch-length repair, and detailed TreeNode validation to ../trees-phylogeny/SKILL.md.
• Route statistical testing, ordination, PERMANOVA/ANOSIM, and visualization of resulting DistanceMatrix objects to ../statistics-ordination/SKILL.md.
• Route BIOM/TSV/FASTA/Newick file reading and metadata parsing to ../io-metadata/SKILL.md.
• Keep this sub-skill focused on count/table preparation, diversity drivers, metrics, outputs, and table augmentation.