malariasimple

A fast, time-discrete compartmental approximation of malariasimulation.

Installation

You can install malariasimple from GitHub with:

# install.packages("pak")
pak::pak("mrc-ide/malariasimple")

Usage

Performing a model simulation in malariasimple is a two-step process:

library(malariasimple)
#1. Define model parameters
params <- get_parameters() |>
          set_equilibrium(init_EIR = 10)

#2. Run model
out <- run_simulation(params)

Code Organisation

The model itself is written using odin2 and is found in two scripts:

• inst/odin/malariasimple_deterministic.R
• inst/odin/malariasimple_stochastic.R

Customisations occur in the parameter set-up stage, which is facilitated by the helper functions found in R/.

License

MIT