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
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.
In the cloned repository folder:
python -m venv venv
source venv/bin/activate
pip install -r requirements.txtapplication/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.slimSLiMcode for spatial extinction, called fromapplication/code above
analysis/spatial_stats.py- script for spatial
SampleSetanalysis - run with base-name of
finishedtree sequence file
- script for spatial
In the cloned repository folder:
mkdir output
python application/extinction_app.py testing
python analysis/spatial_stats.py output/extinct