BioGeoBEARS Biogeographic Analysis
Validates tree/geography input, scaffolds a full BioGeoBEARS analysis folder, and generates a ready-to-run RMarkdown script.
Test report
- Verdict
- Tested · Works
- Score
- Tested
- Jul 16, 2026
- Environment
- Claude Code 2.x (agent harness)
- Upstream re-checked
- Aug 10, 2026 · 4461f6a
Ran the bundled validator on real toy data end-to-end: it correctly reformatted a CSV distribution table into PHYLIP format, then caught three real, distinct errors on a deliberately broken file (a space in a species name, wrong binary-code length, an invalid character) and a tree/geography species mismatch, each with a precise line-numbered message -- exactly the kind of debugging a baseline manual setup would burn 20+ minutes discovering by trial and error.
Scored on four weighted criteria — install, triggering, output vs. baseline, docs. How scoring works
- Installs cleanly 5/5
- Triggers reliably 5/5
- Output vs. baseline 8/10
- Docs & honesty 5/5
What BioGeoBEARS Biogeographic Analysis does
Sets up phylogenetic biogeographic (ancestral range) analyses using the R package BioGeoBEARS: validates and reformats geography files against tree tips, creates an organized analysis directory, and generates a customized RMarkdown script that fits and compares the six standard DEC/DIVALIKE/BAYAREALIKE(+J) models. Triggers on requests to reconstruct ancestral ranges, analyze species distributions on a phylogeny, or run BioGeoBEARS.
How to install BioGeoBEARS Biogeographic Analysis
git clone https://github.com/brunoasm/my_claude_skills
mkdir -p ~/.claude/skills
cp -r my_claude_skills/biogeobears ~/.claude/skills/biogeobears
Skills live in ~/.claude/skills/ (global) or .claude/skills/
(per-project). Restart Claude Code after installing.
Commands — how to trigger BioGeoBEARS Biogeographic Analysis
-
/biogeobearsValidates tree/geography input, scaffolds a full BioGeoBEARS analysis folder, and generates a ready-to-run RMarkdown script.
It also activates on plain-language prompts like these:
-
Set up a BioGeoBEARS analysis folder for my phylogeny dataset -
Validate my geography file against my tree tips for ancestral ranges -
Generate an RMarkdown script comparing DEC and DIVALIKE+J models
Frequently asked questions
- Is the BioGeoBEARS Biogeographic Analysis skill free?
- Yes. The skill itself is free from brunoasm/my_claude_skills. SkillProof publishes the install command and an independent test verdict at no cost.
- Does BioGeoBEARS Biogeographic Analysis work with Claude Code?
- We tested it with Claude Code 2.x (agent harness) on Jul 16, 2026. Verdict: Tested · Works. Ran the bundled validator on real toy data end-to-end: it correctly reformatted a CSV distribution table into PHYLIP format, then caught three real, distinct errors on a deliberately broken file (a space in a species name, wrong binary-code length, an invalid character) and a tree/geography species mismatch, each with a precise line-numbered message -- exactly the kind of debugging a baseline manual setup would burn 20+ minutes discovering by trial and error.
- What is the BioGeoBEARS Biogeographic Analysis SkillProof Score?
- 9.2/10 — installs cleanly 5/5, triggers reliably 5/5, output vs. baseline 8/10, docs & honesty 5/5.
- How do I install BioGeoBEARS Biogeographic Analysis?
- Copy the install command from this page, run it in your terminal, and restart Claude Code. Skills live in ~/.claude/skills/ (global) or .claude/skills/ inside a project.
- Can I use BioGeoBEARS Biogeographic Analysis with Cursor, Copilot, Gemini CLI, Codex or other AI tools?
- The SKILL.md format is native to Claude (Claude Code, Desktop, claude.ai). The instructions inside adapt to other assistants: Cursor rules, GitHub Copilot instructions, Windsurf rules, Custom GPTs, AGENTS.md for OpenAI Codex, and GEMINI.md for Google Gemini CLI — our conversion guides cover each, and the free converter on the tools page does the wrapping for you.