HETTMO

HETerogeneous Transmission MOdel -- R package

This package contains a Bayesian workflow for modelling respiratory infectious diseases with time-varying transmission in Stan.

It includes three methods for implementing the time-varying transmission: Brownian motion, B-splines and Gaussian processes.

The package relies on functionality of cmdstanR.

More information can be found in this pre-print.

TO DO:

add instructions on how to change the age-groups.

add instructions on how to adapt the modelled ODE-system.

Install package

To install the package directly from Github in R, you can use:

library(devtools)

install_github("JudithBouman2412/HETTMO")

Generalizability of code

SEIR backbone

Here, we indicate the parts of the code that need to be adjusted to change the compartmental model that is the backbone of the workflow.

For the unstratified B-spline based model, adjust:

• the ODE-system: for standard ODE-solvers, and for the trapezoidal solver.

For the stratified B-spline based model, adjust:

• the ODE-system: for standard ODE-solvers, and for the trapezoidal solver

For the unstratified aGP based model, adjust:

• the ODE-system: for standard ODE-solvers and for the trapezoidal solver.

For the unstratified BM based model, adjust:

• the ODE-system: for standard ODE-solvers and for the trapezoidal solver.