In SwissTPH/VivaxModelR: Simulation of Plasmodium Vivax dynamics

This document explains the structure of the various functions contained in the package. These functions are provided in the R folder.

The model code, i.e. containing the definition of the ODEs, and formulae for reproduction numbers, equilibrium relationships and transmission rate calibration are provided in the following scripts:

• VivaxFunctions.R for the models without delayed access to treatment, without RCD and without MDA.
• VivaxFunctionsDelays.R for the models with delayed access to treatment, without RCD and without MDA.
• VivaxFunctionsRCD.R for the models with RCD (with and without delayed access to treatment).
• VivaxFunctionsDelays.R for the models with MDA (with and without delayed access to treatment).
• VivaxFunctionsSto.R for the stochastic implementation of all models

Wrapper functions to apply the model to a full dataset in which each row corresponds to a different setting are available in the following scripts: - CalculateFromData.R for the models without delayed access to treatment(with and without MDA and RCD). Contains both calibration and forward simulation. - CalculateFromDataDelay.R for the models with delayed access to treatment (with and without MDA and RCD). Contains both calibration and forward simulation. - CalculateFromDataRCD.R for the calibration with RCD at baseline

Finally, high level wrapper functions are available in simulate_interventions.R and auxiliary functions in aux_functions.

SwissTPH/VivaxModelR documentation built on Feb. 14, 2024, 11:27 a.m.