fleet: mean-field counterpart to malariasimulation

A deterministic mean-field counterpart to the malariasimulation individual-based model (IBM) of Plasmodium falciparum and P. vivax malaria, advanced one day at a time on the IBM's daily clock and built on odin2 and dust2. It reproduces the human model, structured by age and biting heterogeneity and, for P. vivax, by hypnozoite batch, coupled to the compartmental mosquito model, with the same intervention modules. It takes an unmodified malariasimulation::get_parameters() list, is seeded at the malariaEquilibrium (or malariaEquilibriumVivax) solution, and returns malariasimulation's output table, which postie post-processes as it would an IBM run. Run time does not depend on population size.

Functions

• run_simulation_ode() runs the model.

• ode_tuning() holds the discretisation settings, passed as tuning.

• default_age_lower() gives the default age grid.

The ode in two of the names is kept for compatibility: the model is a daily update, not an ODE.

vignette("fleet") is a worked introduction, and vignette("using") covers where the mean field departs from the IBM and what to do about it. Agreement with the IBM is measured in a separate project, fleetcheck.

See also

Useful links:

• https://pwinskill.github.io/fleet/

• https://github.com/pwinskill/fleet

• Report bugs at https://github.com/pwinskill/fleet/issues

Author

Maintainer: Peter Winskill p.winskill@imperial.ac.uk [copyright holder]