Assessing spatial structure in marine populations

This repository contains code used for assessing spatial structure in marine populations. This research was conducted with Dalhousie University's Department of Engineering Mathematics & Internetworking in collaboration with Fisheries and Oceans Canada. Author is Karsten Economou.

About the research

Manuscript in progress.

Data used

The particle-track simulation, contributed to by Dr. Kira Krumhansl, Dr. Wendy Gentleman, and Karsten Economou (not included in this repository), uses the Bedford Institute of Oceanography North Atlantic Ocean model (BNAM) for field data. The species distribution model used for Placopecten magellanicus was provided by Drs. Ben Lowen and Claudio DiBacco.

Usage

See LICENSE.

Installation

All .py and .ipynb files are written in Python 3.8.

Clone the repository with

git clone https://github.com/KarstenEconomou/marine-spatial-structure

or use DownGit to download the files.

Install requirements with a virtual environment (venv) activated with

pip install -r requirements.txt

File structure

Used data, temporary files, and most output is not included in this repository. pathlib is used for referencing files in code with the cwd assumed to be the top-level project directory.

Main pipeline

Pre-simulation

1. Create initial particle locations of a uniform density: initial_positions.ipynb
2. Write a grid over the domain depicting the suitability of habitat of each cell for each genetic lineage from a .tif probability-based species distribution model: sdm_grid.ipynb

Post-simulation

1. Process simulated particle trajectories and create a flow network: network.ipynb
2. Run Infomap: community_detection.ipynb
3. Plot and analyze detected communities stored in .clu format: modules.ipynb

Utilities

• plot.py offers tailored options for plotting particles and hexagons over the domain of interest
• constants.py is a centralized hub of constants
• geneticlineage.py, hexbin.py, module.py, particle.py, particletype.py, season.py, zone.py are modules containing classes.