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Advancing fungal dispersal ecology through traits and data harmonization

Welcome to the fungal dispersal repository, an integral part of the Environmental Data Science Innovation and Inclusion Lab (ESIIL). This repository is the central hub for our working group, encompassing our project overview, proposals, team member information, codebase, and more.

Our Project

Dispersal is a key mechanism driving the geographic distributions of species on Earth, but dispersal theory and methods are based primarily on macroorganisms with microbial dispersal paradigms emerging only recently. In fungi, numerous traits related to dispersal (e.g. spore traits, fruiting body traits, dispersal syndromes) are likely linked to fungal biogeographic patterns, but these hypotheses remain largely untested. We aim to harmonize fungal dispersal trait data with DNA sequence-based taxon occurrence data to test trait-based predictions regarding the dispersal capabilities of fungi across spatial scales. We will also assess the potential for fungal dispersal to buffer against range shifts predicted with global climate change. This work will contribute to our understanding of global fungal biodiversity and ecosystem function, as well as aid in predicting plant and human fungal disease outbreaks. Finally, we will integrate fungal dispersal models with global climate change predictions to assess the potential for fungal range shifts in a changing world.

Documentation

  • Access detailed documentation on our GitHub Pages site.
  • Find comprehensive guides, tutorials, and additional resources.

Project Proposal

Fungal Dispersal Working Group Proposal_11-1-23.pdf

Group Members

  • PI: Dr. Bala Chaudhary, Dartmouth College.
  • Co-PI: Dr. Cameron Egan, University of Southern California.
  • Co-PI: Dr. Kabir Peay, Stanford University.
  • Co-technical lead: Dr. Carlos A. Aguilar-Trigueros, University of Jyväskylä.
  • Co-technical lead: Sarah Cuprewich, Dartmouth College.
  • Member: Dr. Michelle Afkhami, University of Miami.
  • Member: Dr. Priscilla Chaveri, Bowie State University.
  • Member: Dr. Jennifer Martiny, University of California-Irvine.
  • Member: Dr. Veera Norros, Finnish Environment Institute.
  • Member: Dr. Anne Pringle, University of Wisconsin-Madison.
  • Member: Dr. Adriana Romero-Olivares, New Mexico State University.
  • Member: Dr. Agnese Seminara, University of Genoa.
  • Member: Dr. Ryan Stephens, Eastern Tennessee State University.

Code Repository

This section of the repository will include all the code developed for the project. You can structure it as follows:

  • Analysis Code: Scripts for data analysis, statistical modeling, etc.
  • Data Processing: Scripts for cleaning, merging, and managing datasets.
  • Visualization: Code for creating figures, charts, and interactive visualizations.

Meeting Notes and Agendas

Meeting notes and agendas will be regularly updated here to keep all group members informed and engaged with the progress and direction of the project.

Contributing to This Repository

We welcome contributions from all group members. To maintain the quality and integrity of the repository, please adhere to the following guidelines:

  • Make sure all commits have a clear and concise message.
  • Document any major changes or decisions in the meeting notes.
  • Review and merge changes through pull requests to ensure oversight.

Getting Help

If you encounter any issues or have questions about how to contribute, please refer to the ESIIL Support Page or contact the repository maintainers directly. https://cu-esiil.github.io/Postdoc_OASIS/resources/cyverse_hacks/

Customize Your Repository

As a new working group, you'll want to make this repository your own. Here's how to get started:

  1. Edit This Readme: Replace the placeholder content with information about your specific project. Ensure that the introduction, project overview, and objectives clearly reflect your group's research focus.

  2. Update Group Member Bios: Add details about each group member's expertise, role in the project, and professional background. Include links to personal or professional web pages to foster community engagement and collaboration.

  3. Organize Your Code: Structure your codebase in a way that is logical and accessible. Use directories and clear naming conventions to make it easy for all members to find and contribute to different parts of the project.

  4. Document Your Data: Include a data directory with README files explaining the datasets, sources, and any preprocessing steps. This will help new members understand and work with the project's data effectively.

  5. Outline Your Methods: Create a detailed METHODS.md file where you describe the methodologies, software, and tools you will be using in your research. This transparency will support reproducibility and collaborative development.

  6. Set Up Project Management: Utilize the 'Issues' and 'Projects' features on GitHub to track tasks, discuss ideas, and manage your workflow. This can help in maintaining a clear view of progress and priorities.

  7. Add a License: Choose and include an appropriate open-source license for your project, ensuring that the broader community understands how they can use and contribute to your work.

  8. Create Contribution Guidelines: Establish a CONTRIBUTING.md file with instructions for members on how to propose changes, submit issues, and contribute code.

  9. Review and Merge Workflow: Decide on a workflow for reviewing and merging changes. Will you use branch protection? Who will have merge privileges? Document this process to avoid confusion.

  10. Establish Communication Channels: Beyond GitHub, set up additional communication channels like Slack, Discord, or email lists for quick and informal discussions.

Remember, the goal is to make your repository clear, accessible, and useful for all current and future members of your working group. Happy researching!

Last update: 2024-11-21