Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add GPTomics/bioSkills --skill community-ecologygit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/gptomics/bioskills/community-ecology)<a href="https://agentmods.dev/skills/gptomics/bioskills/community-ecology"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/community-ecology/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/gptomics/bioskills/community-ecology"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/community-ecology.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00232 | $0.06529 |
| Opus 5 | $0.00116 | $0.03265 |
| Sonnet 5 | $0.00046 | $0.01306 |
| Haiku 4.5 | $0.00023 | $0.00653 |
Grade A, and why
bio-ecological-genomics-community-ecology scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 8d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 336 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: vegan 2.6+, indicspecies 1.7+, Hmsc 3.0+, sjSDM 1.0+, ade4 1.7+, picante 1.8+, ggplot2 3.5+
Before using code patterns, verify installed versions match. If versions differ:
- R:
packageVersion('<pkg>')then?function_nameto 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.
Community Ecology
"Test how environmental gradients structure my species communities" -> Constrained ordination (CCA / RDA / db-RDA) with explicit dispersion testing alongside PERMANOVA, indicator-species analysis with group-size correction, Joint Species Distribution Models for residual covariance and prediction, and trait-environment testing with statistically corrected permutation schemes.
- R:
vegan::rda(),vegan::dbrda(),vegan::adonis2()for ordination and PERMANOVA - R:
vegan::betadisper()for the mandatory PERMDISP companion to PERMANOVA - R:
HmscorsjSDMfor joint species distribution modeling - R:
indicspecies::multipatt(..., func = 'IndVal.g')for indicator species
The Single Most Important Modern Insight -- Always run PERMDISP alongside PERMANOVA
Anderson & Walsh 2013 Ecol Monogr 83(4):557-574 established that PERMANOVA's pseudo-F is sensitive to dispersion heterogeneity — a significant PERMANOVA can reflect centroid difference, dispersion difference, or both. Running PERMANOVA without PERMDISP is the single most common methodological failure in community-ecology papers. If betadisper is significant alongside a significant PERMANOVA, the location-difference conclusion is not supported by the data alone; the two could be entirely a dispersion artifact.
A second cornerstone insight: residual species-species covariance in Joint Species Distribution Models is NOT a clean estimator of biotic interaction (Pollock 2014, reaffirmed by Zurell 2018 and Poggiato 2021). It reflects unmeasured covariates, dispersal limitation, sampling artifacts, AND any genuine biotic interactions, in unknown proportions. Skills that interpret residual covariance as interaction are over-interpreting.
What ships with it
3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 8d ago First seen · 336 lines · 232 tokens per session scan A ed2585abdf0b
bio-ecological-genomics-community-ecology is a skill published in the GitHub repository GPTomics/bioSkills (1,201 stars, last pushed 27d ago), licensed MIT. It adds 232 tokens to every session and 6,529 once invoked, about $0.0012 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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