Population dynamics

Library to conduct experiements on population dynamics.

Installation

• To generate required log and results directories and setup virtual environment, run

bash init.sh

This step needs to be performed only once to set up your work space.

• Alternatively, you can create virtual environment manually as follows:

mkdir -p ~/venvs/population-dynamics
python3 -m venv ~/venvs/population-dynamics

• Activate virtual environment

source ~/venvs/population-dynamics/bin/activate

• Upgrade pip and setuptools

pip install --upgrade pip setuptools

• install dependencies with

pip install -r requirements.txt

Alternatively, there exists requirements_lock.txt to get a version of the environment that is tested by us in terms of dependencies. The downside of using this file to installing dependencies is that you might not get all the latest version of packages. In case, if either or the files do not setup the environment successfully, please raise an issue.

• Install causal_inference as a package within the environment in development setting if you want to use the repo in the development mode by running the following line

python setup.py develop

Running the Lotka-Volterra simulation

• The Lotka-Volterra simulator class exists in repo/causal_inference/base/lv_simulator.py.

• The Lotka-Volterra simulation parameters are fetched from repo/causal_inference/config.py. You can edit the config.py file directly to play around with the parameter values.

• You can run the simulator directly from terminal by running

python causal_inference/base/lv_simulator.py

This will take all the default arguments and configuration to run a simulation instance of lotka-volterra population dynamics.

• The simulation statistics will be saved in the repo/results directory by default.

Simulation and inference

• The simulation and inference methods are separately implemented in repo/causal_inference/base/lotka_volterra/lv_system.py.
• Currently, this inference method is experimental and may not always converge to correct optimal parameters.
• More work is needed to find a good approximation schema to initiate the parameters of the LV-system.