Model of a Farrow-to-Finish Swine Farm

This repository contains code and data for the farrow-to-finish swine farm model. The main components include the farrow-to-finish farm model Emulsion configuration file, a Python add-on script for farmer and animal movement simulation, and a Jupyter notebook for parameter estimation of the transmission parameters using Approximate Bayesian Computation with Sequential Monte Carlo simulation (ABC-SMC).

Repository Structure

• data/: Folder containing the data used in the simulations.
• LICENSE: License file for the repository.
• movement_12fatpens_outrans.py: Python script add-on for simulating movements in the swine model.
• parameter_estimation_notebook.ipynb: Jupyter notebook for parameter estimation using ABC.
• swine_model_weekly-12fatpens-FINAL.yaml: EMULSION file for the swine model.
• swine_model_weekly-12fatpens-weight-FINAL-swIAVs.yaml: EMULSION file for the swine model (swIAVs version).
• movement_12fatpens_swIAVs.py: Python script add-on for simulating movements in the swine model (swIAVs version).

Getting Started

Prerequisites

Ensure you have the following packages installed:

• Python 3.x
• emulsion==1.2rc5
• numpy
• pandas
• matplotlib
• pyabc
• docopt
• shutil
• uuid
• datetime
• csv
• dateutil
• random

You can install the required packages using pip:

pip install numpy pandas matplotlib pyabc docopt python-dateutil emulsion==1.2rc5 betapert