Spatial extinction simulations with ts-ipc

Project Structure

• application/
  • application code for simulations, using ts-ipc
• slim/
  • SLiM code, called from application code above
• analysis/
  • downstream analysis code, to be run on finished simulations

Initial Setup

SLiM (version 4) will have to be downloaded and compiled in addition to the setup of this python project, and supplied to the application code via the --SlimBin option.

Setup (using a python virtual environment)

In the cloned repository folder:

python -m venv venv
source venv/bin/activate
pip install -r requirements.txt

Spatial Extinction Workflow

• application/extinction_app.py
  • simulation driver application
  • different parameter sets accessible through subcommands
  • see python application/extinction_app.py --help
  • see parameter options with python application/extinction_app.py testing --help
• slim/spatial_extinction.slim
  • SLiM code for spatial extinction, called from application/ code above
• analysis/spatial_stats.py
  • script for spatial SampleSet analysis
  • run with base-name of finished tree sequence file

Run (with testing parameters)

In the cloned repository folder:

mkdir output
python application/extinction_app.py testing
python analysis/spatial_stats.py output/extinct