High population density limits predator access in Antarctic fur seal breeding colonies

Authors: Johannes Bartl , Ane Liv Berthelsen , Alexander Winterl , Cameron Fox-Clarke, Jaume Forcada , Rebecca Nagel , Joseph I. Hoffman , Ben Fabry

Installation

Prerequisites

• Python: 3.8.10
• python packages listed in requirements.txt For training a GPU is recommended - we used:
• Hardware: NVIDIA GeForce RTX 3070 (8GB VRAM)
• CUDA Toolkit: 11.2 (Required for reproducibility)
• NVIDIA Driver: 575.51 (Supports CUDA 11.2+)

Setup

1. Clone the repository:

   git clone https://github.com/fabrylab/AntarcticFurSealDensity.git
   cd AntarcticFurSealDensity

2. Install dependencies:

   pip install -r requirements.txt

This repository contains the code, models, and analysis scripts associated with the paper "Colony matters: How density shapes predator access in two Antarctic fur seal (Arctocephalus gazella) colonies".

Repository Structure

Code & Notebooks

• training.ipynb: Pipeline to train the YOLOv8 neural network.
• analysis.ipynb: Main analysis script for generating statistical results and figures.

Models

• model.pt: Trained YOLOv8-large weights file used to predict the full dataset.

Data & Detections

• FWB.csv: Neural network detection results for Freshwater Beach.
• SSB.csv: Neural network detection results for Special Study Beach.

Map Data

• FWB.kml / FWB.png / FWB_v1.cdb: Georeferencing and annotation data for Freshwater Beach.
• SSB.kml / SSB.png / SSB_v1.cdb: Georeferencing and annotation data for Special Study Beach.
• both_areas.kml / both_areas.png / both_areas_v1.cdb: Combined map data.

Dataset Access (Zenodo)

The raw imagery and primary annotation databases are hosted on Zenodo.

Dataset DOI: 10.5281/zenodo.18955385

The Zenodo dataset includes:

1. Raw Imagery: 110 high-resolution .jpg images.
2. Annotations: Corresponding .cdb (ClickPoints) databases containing ground-truth annotations.

Analysis & Figures

The analysis.ipynb notebook reproduces the following key results:

• (a) Temporal trends in abundance at Special Study Beach (Figure 2)
• (b) Abundance ratios of birds to pups between colonies (Figure 3)
• (c) Demographic patterns in seal density (Figure 4)
• (d) Spatial associations between birds and pups (Figure 5)