Rpackages.qmd

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title: "R packages"
subtitle: "Modular Computation for Simulation-Based Analytics"
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**RAMP** (**R**obust **A**nalytics for **M**alaria **P**olicy) is an organized way of translating evidence into robust policy advice and support [Adaptive Malaria Control](https://faculty.washington.edu/smitdave/ramp/index.html). RAMP relies on simulation-based analytics implemented through **SimBA** software. Using **SimBA,** it is easy to develop site-specific dynamical systems models of malaria epidemiology, transmission dynamics, and control for scenario planning to support sub-national tailoring, monitoring and evaluation, and strategic planning.

SimBA includes sevaral software packages. Six packages implement simulation-based analytics: core computation in [`ramp.xds`](ramp.xds.html) is supported by five satellite packages. Altogether, these R packages implement a modular framework for model building describe in *Spatial Dynamics of Malaria Transmission* [@WuSL2023SpatialDynamics]. We have also included two packages to explore concepts at the cutting edge of malaria epidemiology and microsimulation. Meanwhile, some older software packages -- predecessors to **`ramp.xds`** -- have been [deprecated](deprecated.html).

## Core Computation

-   [ramp.xds](ramp.xds.html) handles core computational and analysis. It was developed to build and solve dynamical systems models for the epidemiology, transmission dynamics, and control of malaria and other mosquito-transmitted pathogens based on a well-defined mathematical framework [@WuSL2023SpatialDynamics].

    -   all packages are `ramp` branded

    -   `xds` stands for *e**X**tensible **D**ynamical **S**ystems*

-   [**`ramp.library`**](ramp.library.html) is a supplementary model library for **`ramp.xds`** that has additional modules for the core dynamical components.

-   [**`ramp.control`**](ramp.control.html) is a supplementary code library for **`ramp.xds`** that holds algorithms to implement various models of malaria control, including vector control, mass vaccination, mass drug administration, *etc.*

-   [**`ramp.forcing`**](ramp.forcing.html) is is a supplementary code library for **`ramp.xds`** that holds algorithms to implement exogenous forcing by weather and other factors.

-   [**`ramp.demog`**](ramp.demog.html) is is a supplementary code library for **`ramp.xds`** that handles human demography and stratification, including vital dynamics and age structure.

-   [**`ramp.work`**](ramp.work.html) is a set of algorithms and functions to compute scaling relationships, to fit models to data, and to apply malaria models in context.

## Deep Dives

### Microsimulation

Two packages have been developed by our team for behavioral state models for mosquitoes and microsimulation:

-   [`ramp.micro`](ramp.micro.html) was developed to explore complexity in mosquito ecology through the development and analysis of simulation models describing mosquito behavioral & spatial dynamics on point sets representing resources, which we call micro-simulation [@PerkinsTA2013HeterogeneityMixing; @CastellanosHMS2025MosquitoDispersal]

-   [`MBITES`](https://github.com/dd-harp/MBITES) is an individual-based simulation model developed to explore mosquito behavioral states [@WuSL2020MBITES].

### Malaria Epidemiology

In [`ramp.falciparum`](ramp.falciparum.html), we explore malaria epidemiology, defined in the narrow sense to describe human exposure to malaria and infection, immunity, disease, drug taking, diagnostics and detection, and infectiousness [@HenryJM2025ProbabilisticSynthesis].

## Deprecated

**`ramp.xds`** was preceded by two packages that have since been deprecated (See [Deprecated](deprecated.html)).