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Katya Jay

Welcome to the tundra_shrub_expansion repository, part of the Environmental Data Science Innovation and Inclusion Lab (ESIIL). This repository serves as the central hub for our research at ESIIL, hosting the project description, proposals, bio, codebase, and more.

Project Summary

Woody encroachment, driven by climate warming, disturbance, and altered nutrient cycling, is occurring across ecosystems globally with significant implications for surface energy balance and ecosystem functions and services. These vegetation shifts modify biogeochemical and biophysical processes locally, altering ecosystem energy, water, and carbon (C) fluxes. While there is widespread agreement that woody encroachment has regional and global consequences that can create non-linear climate feedbacks, the underlying biological processes are poorly incorporated into land models that are used for climate change projections.

Two related challenges must be addressed to incorporate shrub encroachment into land models. First, studies using modeling approaches to explore shrub encroachment have largely assumed arbitrary increases in cover, demonstrating a need for predictive tools to understand the mechanisms driving these transitions. Second, land models have largely overlooked trait-environmental relationships even though plant traits vary with environmental conditions and trait differences between encroaching shrubs and resident species are likely critical in shaping ecosystem responses and climate feedbacks. By leveraging big datasets in combination with remote sensing techniques, machine learning approaches, and process-based ecosystem modeling, my project will tackle these challenges and increase our ability to incorporate vegetation dynamics into regional and global land model predictions. I will integrate diverse, open datasets at local and regional scales to quantify woody encroachment rates while helping to develop a pipeline for using these datasets in ecological studies with land models in other ecosystems.

Project Proposal

Collaborators and Co-Authors

  • Will Wieder: Will is a project scientist in the Terrestrial Scientists Section (TSS) within the Climate and Global Dynamics Laboratory (CGD) at the National Center for Atmospheric Research (NCAR) and a research affiliate in the Institute of Arctic and Alpine Research at the University of Colorado, Boulder. He is interested in global biogeochemical cycles, working to improve the ecological theory represented in models like the Community Land Model (CLM), and facilitating greater exchange between geoscientific and biological sciences disciplines.
  • Katie Suding: Katie is a Distinguished Professor of Ecology and Evolutionary Biology and a Fellow of the Institute of Arctic and Alpine Research at the University of Colorado, Boulder. She is interested in integrating across community and ecosystem scales to study the effects of various global change drives on ecosystem function in grassland, rangeland, and alpine tundra systems, combining long-term monitoring, modeling, and experimental approaches to inform land management and restoration efforts.
  • Cibele Amaral: Cibele is the Interim Analytics Hub Director and a Remote Sensing Data Scientist at Earth Lab and ESIIL at the University of Colorado, Boulder. She is interested in ecosystem ecology and management, remote sensing, and big data analytics, producing science and open-source tools that support sustainable development, climate change adaptation, and biodiversity conservation.

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.

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: 2024-05-09