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.
To install the package directly from Github in R, you can use:
library(devtools)
install_github("JudithBouman2412/HETTMO")
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.