COVID-19 Lockdowns & Animal Movement

Repository containing code for analysis of animal movement in relation to COVID-19 lockdowns in the United States. This is part of the larger "COVID-19 Bio-logging Initiative", organized by the International Bio-loggin Initiative (www.bio-logging.net).

Contact information for this repo: scott.yanco@yale.edu

Code Usage

The code in this repository anticipates the following minimal directory structure to run:

/project_root  
  |  
  +--/analysis          # *This repository*  
  |   |  
  |   +--/docs          # Supporting documentation (other than README.md)  
  |   |  
  |   +--/src           # Source code directory, includes top level workflow script
  |   |   |
  |   |   +--/funs      # Source code for custom functions called by other scripts
  |   |   | 
  |`  |   +--/hpc       # Scripts for submitting jobs to Slurm manager
  |   |   |
  |   |   +--/workflow  # Scripts that execute elements of the workflow
  |   |   |
  |   |   +--/poc       # Scripts that are in active development or scratch scripts excl;uded from workflow
  |   |   |
  |   |   ...           # Other directories as needed for particular non-workflow tasts (e.g., method validation analyses, interim vizualization scripts, etc.) 
  |   |  
  |   +--/ctfs          # Control files  
  |   |
  |   +--/conda_envs    # Stores .yml files wiwth conda environment recipes
  |  
  +--/raw_data          # Raw data stored as initially received, inlcuding mosey_db
  |  
  +--/processed_data    # Any processed data products, especially the wokring version of the mosey db
  |  
  +--/out               # Analytical outputs, interim products
  |  
  +--/figs              # Figures produced by this workflow
  |  
  ...                   # Other scripts as needed

Data associated with this project are far too large to be stored on GitHub and are currently private anyhow. Raw data are stored as a mosey_db, which is a SQLite relational database built to store data from MoveBank. If data become publically available the archive will be described here (or the code to build the mosey_db from MoveBank will be released).

Citation

This project is led by:

Walter Jetz (PI)¹
Ruth Oliver¹
Diego Ellis-Soto¹
Scott Yanco¹
Brett Jesmer^{1, 2}

¹Center for Biodiversity and Global Change
Department of Ecology and Evolutionary Biology
Yale University
New Haven, CT, USA

²Department of Fish and Wildlife Conservation
Virginia Tech
Blacksburg, VA, USA

Additional Information & Resources

Recently published comment article describing the opportunity: [https://www.nature.com/articles/s41559-020-1237-z](https://www.nature.com/articles/s41559-020-1237-z (open access))