fleet: a mean-field (ODE) twin of malariasimulation

A fast, deterministic mean-field (ODE) counterpart to the malariasimulation individual-based model of Plasmodium falciparum malaria, built on the odin2 / dust2 stack. It reproduces the age- and biting-heterogeneity-structured human model (states S/D/A/U/Tr plus treatment and chemoprevention prophylaxis, and the six immunity functions) coupled to the compartmental mosquito model, and honours the same intervention modules. It accepts an unmodified malariasimulation::get_parameters() list, is seeded at the malariaEquilibrium fixed point, and returns malariasimulation-style outputs that feed straight into postie. A multi-decade run completes in seconds, independent of population size.

Getting started

• run_simulation_ode(): run the model; returns a wide, daily count table (P. falciparum only).

• default_age_lower(): the default graded age grid.

• ode_tuning(): solver and discretisation settings, passed as tuning =.

The count table is malariasimulation-shaped, so post-process it with postie exactly as you would an IBM run: postie::get_rates(out) and postie::get_prevalence(out, diagnostic = "lm"). See vignette("fleet") for a worked tour and vignette("using") for where and how much the ODE departs from the IBM and what to do about it. The measured agreement behind those claims is 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]