Malaria model scenarios¶
The EMOD malaria model is explained in detail in Malaria model overview. While the various components that comprise the model are explained with examples, it may be more useful to learn the model through hands-on implementation. The following sections will introduce sets of example files that illustrate how the malaria model works on particular topics. All files are available in the downloadable EMODScenarios folder and, in addition to the explanations below, each scenario will have a more detailed README file to cover relevant information.
Because all disease-specific EMOD simulation types are based on the generic model, the Generic model scenarios are helpful in learning the basics of modeling with EMOD, even if you intend to use one of the disease-specific simulation types.
For more information on the software architecture and inheritance, see Overview of EMOD software.
The scenarios included for learning the malaria model can be broken down into two categories: “baseline simulation scenarios,” which focus on the configuration file, and “scenarios with campaigns,” which introduce the use of a campaign file. All scenarios utilize vector-based transmission, either with the VECTOR_SIM or the MALARIA_SIM. Note that climate is an important aspect of vector-based transmission, so every scenario will utilize climate files in addition to demographic files.
These scenarios introduce users to the basic structure of the model, including the vector model, the malaria model, and how climate is important in vector-based transmission models. There are no campaign interventions included for the baseline scenarios.
This scenario introduces users to the VECTOR_SIM, which utilizes vector-based disease transmission. In this sim type, parameters for multiple vector species can be configured, but there are no malaria- specific parameters included. The purpose of this scenario is to familiarize users with the vector model, and to introduce parameters that are species-specific to the included vectors. The scenario includes three species of mosquitoes, but does not include any campaign interventions.
This scenario introduces users to the MALARIA_SIM, which builds upon the vector-transmission of the VECTOR_SIM and adds malaria-specific parameters. Specifically, users can configure malaria drug parameters, and disease parameters are specific to malaria (instead of having a more generic form). The purpose of this scenario is to introduce the user to the model features that are unique to the malaria model, and to demonstrate how they contribute to facilitate understanding of malaria epidemiology.
While climate is used in every vector and malaria simulation type, this scenario explores how differences in climate impact malaria transmission. The simulation utilizes the VECTOR_SIM to show how transmission is impacted differentially in three locations that vary in their climate. The base configuration is the same for the different locales, yet vector populations will vary drastically due to temperature, humidity, and rainfall. The purpose of this scenario is to help familiarize the user with the importance of accurate climate files, as they have a large impact on the seasonality of disease transmission.
The baseline scenarios are meant to familiarize the user with basic model functionality and setup. The scenarios in this section build upon the concepts previously demonstrated, and add in the use of campaign interventions. Each scenario below includes a campaign file, and each will demonstrate the functionality of various interventions.
Bednets are commonly used to protect individuals from malaria; in this scenario, insecticide-treated nets (ITN) are introduced as an intervention. These nets, also known as bednets, are a commonly used and effective strategy to prevent malaria transmission. The purpose of this scenario is twofold: first, the use of campaign files is introduced, and second, the use of bednets as an intervention is demonstrated.
This scenario builds upon the “Bednet distribution” scenario by combining multiple interventions. The same configuration file is used, and bednets are included; in addition to the bednets, an acquisition-blocking vaccine is included in the campaign file. The purpose of this scenario is to familiarize users with campaign files that utilize multiple strategies. Eradication programs typically rely on combinations of interventions, not a single intervention in isolation. Therefore, it is important for modelers to be familiar with creating such complex strategies.
This scenario builds upon the concept of complex strategies that was introduced in the “Bednets and pre-erythrocytic vaccines” scenario by using a combination of four interventions. The campaign file includes the bednets and acquisition-blocking vaccines that were previously introduced, and adds in indoor residual spraying (IRS) and transmission-blocking vaccines. The purpose of this scenario is to both introduce a different type of vaccine, and to demonstrate that campaign files can be layered with numerous interventions to help recreate specific situations.
This scenario uses a historical data set from the The Garki Project to examine how indoor residual spraying (IRS) and mass drug administration (MDA) impact malaria transmission. Previous scenarios introduced IRS, but utilized vaccination campaigns instead of MDA. To use MDA, the simulation type will be the MALARIA_SIM, and the configuration file will contain parameters to set the efficacy of specific drugs. As with generic vaccinations, the campaign file will then be used to distribute the vaccines to the desired portion of the population. The purpose of this scenario is twofold: first, it will allow the user to explore the Garki dataset, and second, it will introduce a new intervention (MDA).
Previous scenarios utilized individual-level interventions. This scenario introduces a node-targeted intervention. These sugar-baited traps are applied at the node instead of distributed to individuals, and are used to collect host-seeking mosquitoes. The purpose of this scenario is to familiarize the user with node-level interventions (here, sugar traps). An interesting aspect of this intervention is that the efficacy can be modified by mosquito feeding behavior and how frequently they seek sugar meals. This behavior can be configured in the configuration file.
As with the “Sugar-baited traps” scenario, this scenario utilizes a node-targeted intervention, insect-killing fences. There are several types of fences, such as photonic fences that kill mosquitoes using lasers. These fences can work to kill mosquitoes outdoors when they are either on their way into a house to seek a blood meal, or on their way out of the house to oviposit. The purpose of this scenario is to familiarize the user with node-level interventions (here, insect-killing fences).
This scenario provides more detail on how to realistically configure larval habitat for mosquitoes. Previous scenarios utilized single habitat types for the mosquitoes in the model; here, multiple habitat types can be configured for each species. As mosquito species will typically have a predominant habitat type, but opportunistically utilize other available habitat types, this is an especially important feature of the model. The purpose of this scenario is to illustrate how to configure multiple habitat types for a single vector species.