biogeobears
CommunityReconstruct ancestral ranges with BioGeoBEARS.
Authorbrunoasm
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill automates complete phylogenetic biogeographic analyses using BioGeoBEARS in R. It handles input validation, analysis setup, model comparison, and visualizations, dramatically reducing setup time and ensuring reproducible workflows.
Core Features & Use Cases
- Input validation and reformatting: checks phylogenetic trees and geography data, formats inputs for BioGeoBEARS.
- Automated workflow generation: creates an organized analysis folder structure and a customized RMarkdown script that fits multiple biogeographic models (DEC, DEC+J, DIVALIKE, DIVALIKE+J, BAYAREALIKE, BAYAREALIKE+J).
- Model comparison & visualization: compares models with AIC/AICc/AIC weights, and generates publication-ready visualizations (pie charts and text labels) of ancestral ranges.
- Use Case: Reconstruct ancestral ranges along a phylogeny and compare biogeographic models to infer dispersal/extinction patterns.
Quick Start
Gather your tree and geography files, then run the included workflow to execute a full BioGeoBEARS analysis with automatic results generation.
Dependency Matrix
Required Modules
anthropic>=0.40.0pybtex>=0.24.0rispy>=0.6.0json-repair>=0.25.0jsonschema>=4.20.0pandas>=2.0.0openpyxl>=3.1.0pyreadr>=0.5.0requests>=2.31.0
Components
scriptsreferencesassets
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: biogeobears Download link: https://github.com/brunoasm/my_claude_skills/archive/main.zip#biogeobears Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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