SimBA

Nimble Model Building & Simulation-Based Analytics for Malaria and other Mosquito-Transmitted Pathogens

This website was developed to support nimble model building and computation for malaria and other mosquito-transmitted pathogens using a suite R packages available from github. The software was designed for Simulation-Based Analytics (SimBA) and research for malaria and other mosquito-borne pathogens. For more information about malaria analytics – using models for policy support – please see the companion website, Robust Analytics for Malaria Policy and Adaptive Malaria Control.

The material on this site is designed around the topics needed to support model building for malaria analytics: mosquito ecology and malaria epidemiology, transmission dynamics and control. The sidebar presents an organized set of vignettes describing concepts and algorithms to support nimble model building. Many of the vignettes have examples with working code. The navigation bar (at the top) has some quick links, including a guide to some models.

This site is under construction. Please forgive the mess.

Software

The SimBA software suite was developed around an R package called ramp.xds:

  • ramp stands for Robust Analytics for Malaria Policy (RAMP). RAMP is a bespoke inferential system for malaria policy, a broad set of concepts and workflows designed around SimBA software to develop Robust Analytics for Adaptive Malaria Control.

  • xds stands for eXtensible Dynamical Systems

The SimBA software suite includes four satellite packages for ramp.xds:

  • ramp.library is a code library for ramp.xds with model families or modules for the core dynamical components.

  • ramp.control is a code library for ramp.xds with algorithms to implement various models of vector control and health-based malaria interventions

  • ramp.forcing is a code library for ramp.xds with algorithms to implement exogenous forcing by weather

  • ramp.work is a set of algorithms and functions to apply the models to various tasks

Each one of the R packages documents its own code, and some vignettes have been written that describe each individual software package. This website, SimBA, extends the package-specific documentation to demonstrate the capabilities of the whole package. The website also discusses some related R packages and other software that were developed by some of us over the years that are not part formally of SimBA.

Design

The SimBA software is based on a rigorous mathematical framework for modular model building for mosquito-transmitted pathogens, published as Spatial Dynamics of Malaria Transmission. It inherits its code base and core ideas from exDE (see below).

SimBA was designed with several goals:

  • The software should lower the costs of building, analyzing, solving, and using dynamical systems models describing the epidemiology, spatial transmission dynamics, and control of malaria and other mosquito-transmitted pathogens.

  • The models should also serve as a basis for exploring mosquito ecology and responses to vector control, with the capability to handle forcing by weather and other exogenous variables.

  • The software should be extensible to facilitate development of models with unbounded complexity. The software should support nimble model building and scalable complexity.

  • The software libraries should eventually include verified code replicating the models from most published studies.

The vignettes and documents on this website are designed to demonstrate the capabilities of the SimBA suite of R packages.

History

Publication of Spatial Dynamics of Malaria Transmission was accompanied by a software package called exDE. After publication, we began the work to extend exDE to handle exogenous forcing motivated by the need to understand malaria transmission as a changing baseline that has been modified by malaria control. By April 2024, we had added new features and found good solutions for most of the technical challenges, so we turned our attention to updating MicroMoB, software published before exDE that was developed to handle discrete-time systems. We soon recognized the benefit of merging the two, giving rise to ramp.xds, which is under active development. The two older software packages, exDE and MicroMoB are no longer under active development.

Wu SL, et al. (2023) Spatial Dynamics of Malaria Transmission. PLoS Computational Biology 19(6): e1010684.