DDL Lab Retreat 2025: Extinction Through the Lens of Co-Occurring Species

Key Questions

• Given a community in which one or more species went extinct, why did other species in the community not go extinct?
• How did land coverage change in this area?
• What are the environmental factors that led to the extinction or survival of the species?

Repo Structure

This repo has the following basic structure.

├─ environment.yml     <- Basic Python dependencies for Conda environment.
├── README.md           <- The top-level README for developers.
│
├── data                <- If data sets are too large for repo include in .gitignore and download/provide locally. If
│   │                      multiple data sets are used, create a seperate folder for each data set. Also data sets might
│   │                      be merged. Each subfolder (i.e. data stage) should contain a data description (e.g. URL etc.).
│   ├── case_studies    <- Data regarding ranges of selected extinct species and ranges of the extant overlap species
│   ├── spatial_data    <- Polygon, rasters and reference grids containing information descrbing relevant landscape and range data
│
├── results             <- Final analysis docs.
│   ├── figures         <- Generated graphics and figures to be used in reporting, presentations or papers
│   ├── presentations   <- Presentation slides (e.g. pptx) for conferences, seminars etc.
│   ├── submissions     <- Final submission files (e.g. csv, docx, pdf) including versioning (e.g. v1). Folder also
│   │                      contains revisions & resubmissions (create subfolders if applicable).
│   ├── tables          <- Generated tables to be used in reporting or papers
│
├── .gitignore          <- Avoids uploading data, credentials, outputs, system files etc.
│
├── srcPy                    <- Python source code for use in this project.
│
├── src_R                    <- R source code for use in this project.

Acknowledgment

Initial project structure was created following the structure in this repo.