Frequently Asked Questions (FAQ)

General Questions

What is this project about?

Islands Biogeography is a research project investigating biodiversity patterns in island archipelagos. We examine both marine ecosystems (corals and fish) and terrestrial ecosystems (plants and birds), using taxonomic (species-based) and functional (trait-based) approaches.

Key Questions:

• How do island distance and isolation affect biodiversity?
• Do taxonomic and functional diversity patterns differ?
• What environmental factors drive species turnover?

Who is behind this project?

Lead Researcher: Luiza Waechter
Affiliation: BioScales Lab
Collaborators: [Field teams and research institutions]

How can I cite this project?

@software{waechter2026islands,
  author = {Waechter, Luiza},
  title = {Islands Biogeography: Beta-diversity patterns in island archipelagos},
  year = {2026},
  url = {https://github.com/BioScalesLab/Islands_Biogeography}
}

Or in text format:

Waechter, L. (2026). Islands Biogeography: Beta-diversity patterns in island 
archipelagos. BioScales Lab. Retrieved from 
https://github.com/BioScalesLab/Islands_Biogeography

Is this project open source?

Yes! The code is licensed under the MIT License, making it free to use, modify, and distribute for both commercial and non-commercial purposes.

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Getting Started

How do I install the required packages?

The easiest way is to use the pacman package:

if (!require("pacman")) install.packages("pacman")
pacman::p_load(tidyverse, glmmTMB, brms, ggplot2, tidybayes, bayestestR)

This will automatically install any missing packages.

How long does the full analysis take to run?

• Full Bayesian models: 2-4 hours (depending on hardware)
• Correlation analysis: ~10 minutes
• Visualization: ~5 minutes

You can run just the correlations and plots for a quick overview.

What are the system requirements?

Minimum:

• R 4.0+
• 4 GB RAM
• 5 GB disk space

Recommended:

• R 4.2+
• 8+ GB RAM
• Multi-core processor
• 10+ GB disk space

Can I run this on Mac/Windows/Linux?

Yes! The project is fully cross-platform. It runs on:

• ✅ macOS
• ✅ Windows
• ✅ Linux (including Ubuntu, CentOS, Fedora)

How do I update the packages?

# Update all packages
update.packages()

# Or update specific packages
pacman::p_update()

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Data Questions

Where can I find the data?

The processed, analysis-ready data is in the Data/ directory:

• 12 CSV files with taxonomic and functional diversity data
• Full data dictionary in Data/README.md

Can I access the raw data?

Raw field data is archived separately for data security and privacy reasons. Contact luizawaechter.s@gmail.com for access requests.

What are the data sources?

Marine:

• Coral and fish survey data from reef monitoring programs
• Multiple island archipelagos globally

Terrestrial:

• Bird and plant surveys from ecological monitoring
• Native species only (non-introduced)

Can I use this data in my research?

Yes, with proper citation. See the citation section above.

Are there size limits for the data files?

Large files (>50 MB) are managed with Git LFS (Git Large File Storage). They download automatically but require LFS to be installed.

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Analysis Questions

What do the models do?

The models examine relationships between:

• Response: Beta-diversity (species turnover between islands)
• Predictors: Geographic distance, isolation time, island size, climate
• Random Effects: Archipelago grouping

What does beta-diversity mean?

Beta-diversity measures how different species communities are between two locations. High beta-diversity means communities are very different; low beta-diversity means they're similar.

We use the Sørensen index, which ranges from 0 (identical) to 1 (completely different).

Why do you compare taxonomic and functional diversity?

Different metrics reveal different patterns:

• Taxonomic diversity: Species presence/absence
• Functional diversity: Ecological traits and roles

Functional diversity can be maintained even if species composition changes.

What's the difference between GLMM and Bayesian models?

• GLMM (glmmTMB): Frequentist approach, faster computation
• Bayesian (brms): Incorporates prior information, better uncertainty estimates

We run both for comparison.

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Technical Questions

How do I increase computation speed?

# Use more parallel processing cores
options(mc.cores = parallel::detectCores())

# Reduce MCMC iterations (less precise but faster)
# In brms models, reduce iter and chains parameters

What if I get memory errors?

# Reduce parallel processing
options(mc.cores = 2)

# Run models one at a time instead of all at once
# Use a subset of data for testing

How do I debug errors in the code?

1. Check the error message carefully
2. Verify your working directory: getwd()
3. Confirm all data files are present: list.files("Data/")
4. Check package versions: packageVersion("glmmTMB")
5. Open an issue on GitHub if you can't resolve it

Can I modify the code?

Absolutely! See CONTRIBUTING.md for guidelines.

How do I contribute my changes?

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Submit a pull request

See CONTRIBUTING.md for detailed instructions.

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Troubleshooting

I'm getting "package not found" errors

Install the missing package:

install.packages("package_name", repos = "https://cloud.r-project.org/")

Or use pacman:

pacman::p_load(package_name)

The data won't load

Check your working directory:

getwd()

# Set to Data folder
setwd("Data/")

# List available files
list.files()

Models won't converge

This is common with complex data. Try:

1. Reduce model complexity (fewer predictors)
2. Increase iterations: iter = 4000, warmup = 2000
3. Use priors to guide the model
4. Check for multicollinearity in predictors

I get different results each time

This is normal for Bayesian models (random sampling). To reproduce exactly:

set.seed(12345)
# Run model

The plots don't look right

Check that ggplot2 is loaded:

library(ggplot2)

And verify the data format:

str(your_data)

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Collaboration & Contributing

Can I contribute to this project?

Yes! We welcome contributions from the community. See CONTRIBUTING.md.

What types of contributions are welcome?

• Bug reports and fixes
• Code improvements
• Documentation enhancements
• New analyses or features
• Data corrections
• Visualization improvements

How do I report a bug?

Open a GitHub issue with:

1. Description of the bug
2. Steps to reproduce
3. Expected vs. actual behavior
4. Error message (if applicable)
5. Your environment (R version, OS, package versions)

What if I find a security issue?

Please report it to luizawaechter.s@gmail.com rather than opening a public issue. See SECURITY.md.

Can I use this code in my publication?

Yes! Please cite the repository and our work. See citation guidelines above.

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Advanced Questions

How do I add new data to the analysis?

1. Add your CSV file to Data/
2. Update Data/README.md with file description
3. Load it in your analysis script
4. Submit a pull request if you want to merge changes

How do I create custom models?

1. Load your data
2. Scale variables if needed
3. Use glmmTMB() or brms::brm() to fit
4. Use summary(), plot(), predict() for results

See Island_Betadiversity_models.R for examples.

How do I modify the plots?

The plots use ggplot2. You can:

1. Change themes: + theme_minimal()
2. Adjust colors: + scale_color_manual()
3. Add facets: + facet_wrap(~group)
4. Customize labels: + labs(title = "Custom Title")

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Contact & Support

How do I contact the project lead?

Email: luizawaechter.s@gmail.com
Response Time: 24-48 hours

Where can I ask questions?

1. GitHub Discussions: For project questions
2. GitHub Issues: For bugs and feature requests
3. Email: For urgent or sensitive matters
4. Documentation: Check README.md and QUICKSTART.md

How do I stay updated?

• Watch the GitHub repository for updates
• Star to show support
• Subscribe to GitHub notifications
• Check CHANGELOG.md for version updates

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Useful Links

• Quick Start Guide - Get running in 5 minutes
• Contribution Guidelines - How to contribute
• Data Dictionary - Understand your data
• Project Configuration - Detailed project info
• Code of Conduct - Community guidelines
• Security Policy - Report vulnerabilities

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Last Updated: January 30, 2026
Contact: luizawaechter.s@gmail.com
Repository: BioScalesLab/Islands_Biogeography

Can't find what you're looking for? Open an issue or email us!