Agent skill · research science · aiskillstore
biogeobears
Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to analyze species distributions on phylogenies. Handles input file validation, data reformatting, RMarkdown workflow generation, and result visualization.
Why this skill is useful
Adds executable scripts for validating and reformatting input files, along with RMarkdown workflow generation for biogeographic analyses.
What it needs
Requires python, r installed locally. About 9k tokens when loaded. Last updated 2026-08-07. 405 stars on the source repository.
What this skill does
BioGeoBEARS Biogeographic Analysis Overview BioGeoBEARS (BioGeography with Bayesian and Likelihood Evolutionary Analysis in R Scripts) performs probabilistic inference of ancestral geographic ranges on phylogenetic trees. This skill helps set up complete biogeographic analyses by: 1. Validating and reformatting input files (phylogenetic tree and geographic distribution data) 2. Generating organized analysis folder structure 3. Creating customized RMarkdown analysis scripts 4. Guiding users through parameter selection and model choices 5. Producing publication-ready visualizations When to Use This Skill Use this skill when users request: "Analyze biogeography on my phylogeny" "Reconstruct ancestral ranges for my species" "Run BioGeoBEARS analysis" "Which areas did my ancestors occupy?" "Test biogeographic models (DEC, DIVALIKE, BAYAREALIKE)" The skill triggers when users mention phylogenetic biogeography, ancestral area reconstruction, or provide tree + distribution data. Required Inputs Users must provide: 1. Phylogenetic tree (Newick format, .nwk, .tre, or .tree file) Must be rooted Tip labels will be matched to geography file Branch lengths required 2. Geographic distribution data (any tabular format) Species names (matching tree tips) Presence/absence data for different geographic areas Can be CSV, TSV, Excel, or already in PHYLIP format Workflow Step 1: Gather Information When a user requests a BioGeoBEARS analysis, ask for: 1. Input file paths: "What is the path to your phylogenetic tree file?" "What is the path to your geographic distribution file?" 2. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills aiskillstore/biogeobears