This is the central hub for information pertaining to ESIIL Postdocs
Welcome to the CU-ESIIL 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 your project description, proposals, bio, codebase, and more.
The dead remains of habtitat-forming organisms, known as material legacies, can influecne ecoloigcal processes during periods of recovery after disturbance, and thereby shape ecosystem resilience. Using the NSF Long Term Ecological Research network, we aim to quantify the effects of material legacies of foundation species in marine and terrestrial ecosystems.
Under global change, contemporary ecosystems are subject to shifting regimes of disturbance that create novel environmental conditions in which ecosystem recovery takes place. An emerging focus of ecology is to understand how material legacies – biogenic material left after disturbance – affect patterns of community assembly and properties of resilience (i.e., the rate and extent of ecosystem recovery). A particularly unresolved aspect of this focus is how the material legacies of foundation species (organisms that create the biological structures of ecosystems) affect ecosystem resilience. Here, we aim to leverage the LTER network to assess material legacy effects on ecosystem resilience across 12 terrestrial and marine ecosystem types. Specifically, we will utilize time series of ecosystem response metrics and material legacies following disturbances to evaluate the rate and extent of ecosystem recovery (Objective 1). Then, we will create a qualitative summary of the types of material legacies in each system, the ecological processes they influence, and the effects these legacies have on resilience (Objective 2). This research will help us achieve a generalized understanding of the impacts of material legacies and ensure we are best equipped to manage these legacies as they become more or less prevalent under changing global conditions.
Images of material legacies of foundation species in various ecosystems: a) dead standing trees in a forest after a drought or pest outbreak; b) dead oyster shells on an oyster reef after a hypoxic event or marine heatwave; c) dead marshgrass after a heat stress event; d) dead standing coral skeletons after heatwave-induced coral bleaching or predator outbreak.
- Katharine Suding: Lead PI of Niwot Ridge LTER
- Jill Johnstone: Investigator at Bonanza Creek LTER.
- Aubrey Barker-Plotkin: PI of Harvard Forest LTER.
- Matt Betts: Lead PI of Andrews Forest LTER.
Link to Github repo for code used to create analyses and visualizations for this project: https://github.com/kkopecky711/LTER-material-legacy-synthesis.git
- 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.
When you meet with your advisor, collaborators, or a team, you should take notes here.
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.
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.
As a new working group, you'll want to make this repository your own. Here's how to get started:
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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.
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Update Bio: Add details about your expertise, role in the project, and professional background. Include links to personal or professional web pages to foster community engagement and collaboration.
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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.
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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.
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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.
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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.
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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.
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Create Contribution Guidelines: Establish a CONTRIBUTING.md file with instructions for members on how to propose changes, submit issues, and contribute code.
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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.
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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!