ecology-skills

Claude Skills

A collection of custom skills for Claude Code, built for ecology research workflows.

Skills extend Claude Code's capabilities with domain-specific analysis pipelines, structured outputs, and integrations with academic databases. Each skill lives in its own subfolder and is loaded into Claude Code via the skills plugin.

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Skills

ecology-literature-review

A structured literature review tool for ecologists. Supply papers as PDFs, pasted text, or DOIs and the skill analyses each one through two complementary lenses:

6-Question Reading Framework

1. Motivation — what did the authors want to know?
2. Approach / Methods — what did they do?
3. Field Context — why was it done that way?
4. Results — what do the data show?
5. Interpretation — how did the authors interpret their findings?
6. Next Steps — what should be done next?

9 Ecological Dimensions

• Taxonomic coverage
• Spatial coverage
• Temporal coverage
• Study design & scale
• Data sources
• Ecosystem / habitat type
• Conservation & management implications
• Limitations, gaps & future directions
• Study region coordinates (decimal degrees, extracted verbatim from paper text)

Output: A Word document (.docx) containing two comparison matrix tables (papers × framework questions; papers × ecological dimensions), full per-paper profiles, a cross-paper synthesis, bibliography, and an audit log. Also writes a companion .md file and per-paper staged .md files to feed the atomic-literature-note skill.

Literature search (opt-in): The skill can search for papers on request using OpenAlex (free, no credentials required) or Consensus (if available). Search is not run automatically — it must be explicitly requested.

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atomic-literature-note

Creates atomic literature notes and concept notes in the Obsidian ecology vault. Two modes:

• Atomic note — one concise note per paper (~1 page), filed in the correct topic folder. Reads metadata and highlights from Zotero (via MCP), direct PDFs, or staged .md files produced by ecology-literature-review. Supports single-paper and batch workflows.
• Concept note — a half-page summary of an ecological term, auto-populated with vault papers that use the concept.

Trigger phrases: "make a note for [paper]", "create an atomic note", "summarise this paper for Obsidian", "create a concept note for [term]".

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hypothesis-forge

Generates 2–5 candidate hypothesis notes from tensions already recorded in the vault. Harvests four evidence streams — concept-note tensions/open questions, counter-claims in atomic notes, papers marked changed_my_thinking: yes, and recent idea notes — then synthesises falsifiable hypotheses pre-linked to supporting and contradicting vault evidence.

Vault-internal only — no web search. Every citekey in the output must already exist in the vault.

Trigger phrases: "forge hypotheses", "generate candidate hypotheses from my vault", "what tensions in my concept notes could become hypotheses?".

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vault-weekly-synthesis

Weekly briefing (~40 lines) of vault activity and hypothesis health. Scans recently modified atomic notes, identifies recurring concepts not yet captured as concept notes, surfaces any changed_my_thinking papers added this week, and checks hypothesis health (status, staleness, orphan detection).

Trigger phrases: "weekly synthesis", "vault synthesis", "what did I read this week", "check my hypotheses".

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Install

Option A — Claude Code (plugin marketplace)

This repo is packaged as a Claude Code plugin marketplace. In Claude Code, run:

/plugin marketplace add agreenville/claude-skills
/plugin install ecology-skills@agreenville-claude-skills
/reload-skills

Skills will then be available as ecology-skills:<skill-name> — e.g. ecology-skills:ecology-literature-review.

The repo is public — anyone can install directly with the command above.

Option B — Claude.ai or Claude Desktop (download and upload)

If you're using Claude.ai or Claude Desktop instead of Claude Code:

1. Go to the Releases page and download ecology-literature-review.zip from the latest release. (Each tagged release auto-bundles every folder under skills/ into its own zip.)
2. Upload the zip via:
   • Claude.ai — Settings → Capabilities → Skills → Upload a skill
   • Claude Desktop — Settings → Customise → Skills → Upload a skill
3. The skill triggers automatically on relevant phrases (e.g. "I'm starting a literature review on pollinators").

If you'll be running the .docx generation step in Claude.ai's sandbox, the bundled package.json lets the sandbox install docx on first run. The zip excludes node_modules to keep it small.

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