Do I need R installed to use this skill?

While the skill sets up the analysis structure and scripts, you will need R and the BioGeoBEARS package installed on your local environment to execute the generated scripts.

How does the skill handle species name mismatches?

It includes a validation step that checks tip labels in your tree against the names in your geographic data, helping you identify and fix mismatches before running the analysis.

What file formats are required for this analysis?

You need a phylogenetic tree in Newick format (.nwk, .tre) and geographic distribution data in tabular format (CSV, TSV, or PHYLIP).

Which biogeographic models are supported?

The skill supports the standard BioGeoBEARS suite: DEC, DIVALIKE, and BAYAREALIKE, along with their +J (founder-event speciation) variants.

BioGeoBEARS Biogeographic Analysis

Name: BioGeoBEARS Biogeographic Analysis
Author: brunoasm

bybrunoasm

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データサイエンスとML

Sets up and executes probabilistic inference of ancestral geographic ranges on phylogenetic trees using BioGeoBEARS in R.

概要

This skill streamlines the complex process of biogeographic reconstruction by automating the preparation, validation, and execution of BioGeoBEARS analyses. It handles file conversion for phylogenetic trees and distribution data, sets up organized project structures, generates customized RMarkdown scripts, and guides users through selecting optimal parameters for models like DEC, DIVALIKE, and BAYAREALIKE. It is ideal for researchers looking to perform ancestral range estimation without manually writing boilerplate R code.

主な機能

Step-by-step guidance on model selection and parameter optimization.
Production of publication-ready visualizations including pie charts and text labels.
Automated validation and reformatting of phylogenetic tree and geography files.
3 GitHub stars
Generation of organized directory structures for reproducible research.
Customizable RMarkdown analysis scripts for six different biogeographic models.

ユースケース

Comparing multiple biogeographic models (DEC, DIVALIKE, BAYAREALIKE) with and without founder-event speciation (+J).
Automating the setup of R-based phylogenetic analysis pipelines for large datasets.
Reconstructing ancestral geographic ranges for a specific biological group.

概要

主な機能

Step-by-step guidance on model selection and parameter optimization.
Production of publication-ready visualizations including pie charts and text labels.
Automated validation and reformatting of phylogenetic tree and geography files.
3 GitHub stars
Generation of organized directory structures for reproducible research.
Customizable RMarkdown analysis scripts for six different biogeographic models.

ユースケース

Comparing multiple biogeographic models (DEC, DIVALIKE, BAYAREALIKE) with and without founder-event speciation (+J).
Automating the setup of R-based phylogenetic analysis pipelines for large datasets.
Reconstructing ancestral geographic ranges for a specific biological group.