Can I use standard CSV files for geographic distribution?

Yes, the skill includes a validation and reformatting tool that converts standard tabular presence/absence data (CSV/TSV) into the specialized PHYLIP format required by BioGeoBEARS.

What input formats are required for the phylogeny?

The skill supports standard Newick formats (.nwk, .tre, or .tree). The tree must be rooted and include branch lengths for proper model inference.

Does this skill execute the R analysis directly?

The skill prepares the entire environment, including validated data, scripts, and directory structures. You then execute the generated RMarkdown or shell script in your local R environment to run the heavy computation.

Which biogeographic models can I compare?

It facilitates comparison across all six standard BioGeoBEARS models: DEC, DEC+J, DIVALIKE, DIVALIKE+J, BAYAREALIKE, and BAYAREALIKE+J.

BioGeoBEARS Biogeographic Analysis

Name: BioGeoBEARS Biogeographic Analysis
Author: brunoasm

bybrunoasm

•

데이터 과학 및 ML

Automates the setup, validation, and execution of phylogenetic ancestral range reconstruction using BioGeoBEARS in R.

소개

This skill streamlines the complex process of phylogenetic biogeographic analysis by automating input file validation for trees and geographic data. It handles the tedious task of reformatting datasets into PHYLIP format, generates organized analysis directory structures, and produces customized RMarkdown scripts for testing various biogeographic models. It is an essential tool for evolutionary biologists and ecologists looking to reconstruct ancestral ranges and produce publication-ready visualizations with statistical rigor.

주요 기능

Support for comprehensive model testing (DEC, DIVALIKE, BAYAREALIKE, and +J variants)
Automated visualization setup for pie chart and text-based ancestral range plots
Validation and reformatting of Newick trees and geographic distribution data
Automated generation of structured analysis folders and RMarkdown workflows
3 GitHub stars
Built-in Python scripts for converting CSV/TSV files to BioGeoBEARS-compatible formats

사용 사례

Testing the statistical fit of founder-event speciation (+J) versus traditional dispersal models
Standardizing biogeographic analysis pipelines for reproducible research in R
Reconstructing the ancestral geographic ranges of a species group across evolutionary time

소개

주요 기능

Support for comprehensive model testing (DEC, DIVALIKE, BAYAREALIKE, and +J variants)
Automated visualization setup for pie chart and text-based ancestral range plots
Validation and reformatting of Newick trees and geographic distribution data
Automated generation of structured analysis folders and RMarkdown workflows
3 GitHub stars
Built-in Python scripts for converting CSV/TSV files to BioGeoBEARS-compatible formats

사용 사례

Testing the statistical fit of founder-event speciation (+J) versus traditional dispersal models
Standardizing biogeographic analysis pipelines for reproducible research in R
Reconstructing the ancestral geographic ranges of a species group across evolutionary time