VivaxModelR: developer doc

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.

Clara Champagne