amelia327/Togo-TRANSFIL-model

TRANSFIL model of Lymphatic Filariasis in Togo # Togo TRANSFIL Model This repository (repo) is storage for a metapopulation TRANSFIL Model built to model Togo. ## Understanding the Repository Structure This repo has four main sections: - **Data fitting** - The scripts used to run and analyse the ABC-SMC data fitting aswell as a folder of posterior results for different iterations of the fitting algorithm - **Model** - The components of the mathematical model - **Simulations** - Saved simulation results under different model conditions - **main.py** - The entrypoint to the code. Initially set up with an example script, running the model 1000 times, and printing a plot of the median and interquartile lines ## Repository File Structure | main.py # run and coordinate code here | RCode.R # for geodata mapping | requirements.txt # list of required python packages for running the project +---Data_Fitting | | analyse_fitting.py # generates histograms to visualise data fitting results | | data_fitting_epsilon.py # functions to perform the ABC-SMC data fitting | | | \---abc_town_results # contains sets of data fitting final accepted results +---model | Burkina_Faso_dynamics.py # simulates refugee immigration | human_dynamics.py # simulates human, birth, death, and aging | larvae_dynamics.py # calculates larvae burden of a mosquito population | metapop_dynamics.py # moves individuals between towns | mf_dynamics.py # finds individuals' mf densities | Nigeria_dynamics.py # moves individuals to and from Nigeria | parameters.py # contains all parameter values | population.py # coordinates the model activities | testing_dynamics.py # simulates testing of the population | worm_dynamics.py # simulates individuals gaining and losing worms | \---Simulations # contains files of saved simulation data ## To keep in mind when running the code I have intentionally designed the code to be very modular, with the model broken down into functional stage …