ramp.work - Algorithms for ramp.xds

Algorithms to Develop and Apply Malaria Intelligence

Installation

ramp.work is an algorithm code library that extends ramp.xds.

To install the latest version of ramp.xds from GitHub, run the following lines of code in an R session.

library(devtools)
devtools::install_github("dd-harp/ramp.xds")

To install the latest version of ramp.work from Github, run the following line in an R session:

devtools::install_github("dd-harp/ramp.work")

What is RAMP?

RAMP -- Robust Analytics for Malaria Policy -- is a bespoke inferential system for malaria decision support and adaptive malaria control. A core goal for RAMP is to characterize, quantify, and propagate uncertainty in conventional analysis and through simulation-based analytics.

What is ramp.xds?

ramp.xds is an R software package that supports nimble model building for simulation-based analytics and malaria research. It was designed to help research scientists and policy analysts set up, analyze, solve, and apply dynamical systems models describing the epidemiology, spatial transmission dynamics, and control of malaria and other mosquito-transmitted pathogens. The software also supports nimble model building and analysis for mosquito ecology, with the capability to handle forcing by weather and other exogenous variables.

The software was designed around a rigorous mathematical framework for modular model building, described in Spatial Dynamics of Malaria Transmission (Wu SL, et al. 2023. PLoS Computational Biology)^[Wu SL, Henry JM, Citron DT, Mbabazi Ssebuliba D, Nakakawa Nsumba J, Sánchez C. HM, et al. (2023) Spatial dynamics of malaria transmission. PLoS Comput Biol 19(6): e1010684. https://doi.org/10.1371/journal.pcbi.1010684]. The mathematical framework has now been extended to cover exogenous forcing by weather and vector control.

What is ramp.work?

ramp.work is a code library with algorithms that do various work tasks for ramp.xds. These are part of a suite of R packages developed to support RAMP:

• ramp.xds. is the core computational engine for simulation-based analytics. It includes a basic set of models -- enough to design, verify, and demonstrate the basic features of modular software.

• ramp.library is an extended library of stable code that has been tested and verified. It includes a large set of model families published in peer review that are not included in ramp.xds The ability to reuse code reduces the costs of replicating studies. Through this library, ramp.xds also supports nimble model building and analytics for other mosquito-borne pathogens.

• ramp.work includes algorithms to apply the framework, include code to fit models to data and to do constrained optimization

• ramp.malaria includes a large set of models illustrating capabilities of ramp.xds

ramp.work is under active development.