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Numerical model for life history evolution of age-structured populations

Project description

PyPI version Python 3.6+

AEGIS

Aging of Evolving Genomes In Silico (AY-jis, /eɪd͡ʒɪs/)

Numerical model for life history evolution of age-structured populations under customizable ecological scenarios.

How to install

We recommend that you install aegis-sim from PyPI into a virtual environment.

$ pip install aegis-sim
Cheat sheet
# Unix/macOS
python3 -m venv aegis-venv
. aegis-venv/bin/activate
python3 -m pip install aegis-sim
# Windows
python -m venv aegis-venv
.\aegis-venv\Scripts\activate
python -m pip install aegis-sim
For developers
# Unix/macOS
git clone git@github.com:valenzano-lab/aegis.git
cd aegis
make install_dev

To check if installation is successful, run aegis -h. If it is, the output will contain Aging of Evolving Genomes In Silico; if not, it will say aegis: command not found.

How to run

  1. Create a configuration file

    Before running a custom AEGIS simulation, you must create a configuration file (in YAML format) which will contain your custom parameter values. List of modifiable parameters, and all relevant details can be found in the wiki. Default parameter values are set in the file default.yml.

    An example of a YAML file:

    # custom.yml
    
    RANDOM_SEED_: 42
    STAGES_PER_SIMULATION_: 10000
    MAX_LIFESPAN: 50
    
  2. Start the simulation

    $ aegis {path/to/file}.yml # In this case, `aegis custom.yml`
    
  3. Inspect the output

    Output files will be created in the {path/to/file} directory (in this case, in the custom directory) which will have the following structure:

    {path/to/file}/
        progress.log
        {ecosystem-number}/
            output-summary.json
            snapshots/
                demography/
                    {stage}.feather
                    ...
                genotypes/
                    {stage}.feather
                    ...
                phenotypes/
                    {stage}.feather
            visor/
                genotypes.csv
                phenotypes.csv
                spectra/
                    age_at_birth.csv
                    age_at_end_of_sim.csv
                    age_at_genetic.csv
                    age_at_overshoot.csv
                    age_at_season_shift.csv
                    cumulative_ages.csv
    

    Detailed description of the content and format of output files can be found in the wiki.

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