thk123 / ntd-model-trachoma

Trachoma Simulation Model

To run the trachoma simulation model, import the Trachoma_Simulation() function from the trachoma_simulations module in the trachoma package.

The Trachoma_Simulation() function requires the following inputs.

BetFilePath: str
    This is the path to the input CSV file with the
    random seed and beta to be used for each simulation.

MDAFilePath: str
    This is the path to the input CSV file with the
    first and last year of the simulations and with
    the first and last year of MDA.

PrevFilePath: str
    This is the path where the output CSV file with
    the simulated prevalence will be saved.

SaveOutput: bool
    If True, the last state of the simulations will
    be saved in a pickle file. If False, the last
    state of the simulations will not be saved.

OutSimFilePath: str
    This is the path where the output pickle file with
    the last state of the simulations will be saved. It
    is only required when SaveOutput = True.

InSimFilePath: str
    This is the path where the input pickle file with
    the last state of the simulations has been saved.
    If this is provided, the code will skip the burnin
    and resume the previous simulations from this state.
    If this is not provided, the code will start new
    simulations from scratch, including the burnin.

Numerous different examples are included in the Jupyter notebook trachoma_tests.ipynb in the tests folder.

How to run

Install pipenv according to the instructions for your OS, then cd to the project directory and run:

	$ pipenv install . # sets up per-project python environment ('env')
	$ pipenv shell # starts a per-project shell using that env
	(ntd-model-trachoma) $ python tests/trachoma_run.py # runs the test model scenarios