One-Health-Research-Consulting/RVF_SIR_Model

Repository of code to simulate 34-years of RVFV transmission at a single pan in central South Africa. # Localized Rift Valley Fever Virus Persistence This repository contains code, data, and figures that support: Rostal MK, Prentice J, Ross N, Kemp A, Thompson PN, Anyamba A, Cleaveland S, Cordel C, Msimang V, van Vuren, JP, Haydon D, Karesh WB, Paweska JP, Matthews L. (2025) Localized Rift Valley Fever Virus Persistence Explains Epidemic and Interepidemic Dynamics and Guides Control Strategies. *Proceedings of the Royal Society B: Biological Sciences* DOI: 10.1098/rspb.2025.0453 --- ### RVF_SIR_Model Repository of code to simulate 34-years of RVFV transmission at a single pan in central South Africa. All code referred to below are in the *"All_Files_For_Publication" folder*. To run the simulations, run the scripts in order according to the file number. If the file name starts with the term Function or Model, then it should not be run by the user and will be called by the main scripts. If a file name starts with the term Analysis, then it may be run by the user depending on the level of analysis they would like to do. The main scripts will allow the user to run the 34-year simulation with the option of various scenarios (e.g., vaccination), run the Latin hypercube sensitivity analysis, run the variable-by-variable analyses and estimate R_0. The analysis scripts will produce plots and analyze the Latin hypercube results. The model scripts contain the parameter list, the mosquito hatching determination and the ODE function. The function scripts have all other functions defined for the analyses. **1. Run the simulation:** Start with the _“1-Run RVFV Simulations.R”_ file. The user will start by indicating whether they would like to run a specific scenario (with vaccination, without transovarial transmission (Only.q = no horizontal transmission or no.amp.vec = no transmission by _Culex_), without horizontal transmission (No.q), a low starting population of infected _Aedes_ eggs (lo.eggs), and with a higher (muC.25_higher) or lower _Culex_ (muC.25_lower) mortalit …