bio-ecological-genomics-biodiversity-metrics
Calculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized rarefaction. Use when quantifying biodiversity from species abundance or incidence data, comparing diversity across sites, or constructing rarefaction curves. Not for clinical 16S microbiome alpha/beta diversity (see microbiome/diversity-analysis).
npx skills add BioTender-max/awesome-bio-agent-skills --skill biodiversity-metrics --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: ggplot2 3.5+, vegan 2.6+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Biodiversity Metrics **"Calculate species diversity for my ecological samples"** → Compute Hill number diversity (richness, Shannon, Simpson) with coverage-based rarefaction/extrapolation using iNEXT, and partition beta diversity into turnover and nestedness components with betapart. - R: `iNEXT::iNEXT()` for coverage-based rarefaction and extrapolation - R: `betapart::beta.multi()` for beta diversity partitioning Calculates alpha diversity using Hill numbers, coverage-based rarefaction/extrapolation, and beta diversity partitioning into turnover and nestedness components. ## Hill Numbers Framework Hill numbers unify diversity indices into a single parametric family controlled by order q: | Order (q) | Name | Sensitivity | Equivalent Index | |-----------|------|-------------|----------------
- Version Compatibility
- Hill Numbers Framework
- iNEXT Coverage-Based Rarefaction
- Point Estimates at Standardized Coverage
- Asymptotic Diversity Estimation
- iNEXT.3D: Taxonomic, Phylogenetic, and Functional Diversity
- Classic Diversity with vegan
- Beta Diversity Partitioning with betapart
- Interpreting Beta Diversity Components
- Visualization
- Related Skills
What does the bio-ecological-genomics-biodiversity-metrics skill do?
Calculates species richness, diversity, and turnover using the Hill number framework with iNEXT coverage-based rarefaction/extrapolation, asymptotic diversity estimation, and beta diversity partitioning (betapart turnover vs nestedness). Compares assemblages using coverage-standardized rather than size-standardized rarefaction. Use when quantifying biodiversity from species abundance or incidence data, comparing diversity across sites, or constructing rarefaction curves. Not for clinical 16S microbiome alpha/beta diversity (see microbiome/diversity-analysis).
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill biodiversity-metrics --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.