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biogeobears

Automate BioGeoBEARS phylogenetic biogeography analyses in R with RMarkdown workflows.

3|1|Updated Dec 21, 2025
Search Tags:#bioinformatics#phylogenetics#data-validation#biogeography#rmarkdown#ancestral-range
One-click install
npx skills add https://github.com/I-Onlabs/claude-code-skills --skill biogeobears-i-onlabs
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: biogeobears
Source: https://github.com/I-Onlabs/claude-code-skills/tree/main/biogeobears
Command: npx skills add https://github.com/I-Onlabs/claude-code-skills --skill biogeobears-i-onlabs

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

BioGeoBEARS analyses are powerful but involve multiple preprocessing steps, directory setup, model configuration, and result visualization; this skill automates the full end-to-end biogeographic workflow on phylogenies in R, promoting reproducibility and efficiency.

Core Features & Use Cases

  • Validate and reformat phylogenetic trees and geographic distribution data for BioGeoBEARS workflows.
  • Create an organized project directory with input, scripts, and results ready for analysis.
  • Generate a parameterized RMarkdown workflow that fits multiple biogeographic models (DEC, DEC+J, DIVALIKE, DIVALIKE+J, BAYAREALIKE, BAYAREALIKE+J) and compares them with AIC/AICc and likelihood tests.
  • Produce publication-ready visualizations of ancestral ranges on trees and an HTML report for sharing results.
  • Use Case: A researcher wants to assess historical biogeography for a clade across several geographic areas and compare models to identify the best-supported scenario.

Quick Start

Provide your phylogenetic tree and geography data, and the system will generate a complete BioGeoBEARS analysis package with a parameterized RMarkdown script and ready-to-run outputs.

Frequently Asked Questions about biogeobears

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate BioGeoBEARS ancestry range analysis in RMarkdown?▼

To automate BioGeoBEARS ancestral range analysis, this Skill generates a parameterized RMarkdown workflow that fits multiple biogeographic models and produces interactive HTML reports. It handles directory setup, model configuration, and visualization automatically.

What is the best way to compare DEC and DIVALIKE models for phylogenetic biogeography?▼

Comparing DEC and DIVALIKE models for phylogenetic biogeography is handled by generating scripts that fit these models and evaluate them using AIC, AICc, and likelihood tests. The workflow identifies the best-supported biogeographic scenario for your clade.

How do I validate phylogenetic tree and geographic distribution data for biogeography?▼

Validating phylogenetic tree and geographic distribution data for biogeography requires checking formatting and compatibility. This Skill validates and reformats input data to ensure it meets BioGeoBEARS workflow requirements before analysis begins.

Can I create publication-ready plots of ancestral ranges on phylogenetic trees?▼

You can create publication-ready plots of ancestral ranges on phylogenetic trees using the visualization outputs generated by this Skill. It automatically produces these visuals alongside interactive HTML reports for sharing biogeographic results.

Do I need to manually set up directories for BioGeoBEARS analysis?▼

You do not need to manually set up directories for BioGeoBEARS analysis. This Skill creates an organized project directory with separate folders for input data, scripts, and results ready for immediate analysis execution.

What biogeographic models are supported by automated RMarkdown workflows?▼

Automated RMarkdown workflows support DEC, DEC+J, DIVALIKE, DIVALIKE+J, BAYAREALIKE, and BAYAREALIKE+J biogeographic models. The generated scripts fit all these models to your phylogeny and compare them statistically.

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