Environmental model scenarios¶
The EMOD environmental model is explained in detail in Environmental 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 a downloadable EMOD scenarios zip file and, in addition to the explanations below, each scenario will have a more detailed README file to cover relevant information.
For more information on the software architecture and inheritance, see Overview of EMOD software.
This scenario illustrates a node-level diagnostic that is a unique feature of environmentally- transmitted pathogens. The scenario uses the ENVIRONMENTAL_SIM to demonstrate the features of EnvironmentalDiagnostic, which enables the user to identify contaminated locations by sampling the environment. The value obtained is compared to a threshold value, and then it will broadcast either “positive” (the sample value is higher than the threshold), or “negative” (the sample value is lower than the threshold). For policymaking and further scenario testing, this can be used in conjunction with other interventions to target and treat contaminated areas; however this example does not include further interventions.
In its default setting, EMOD assumes that transmission within a population is homogeneous. However, it is known that the specifics of disease transmission are often more complex: populations are typically not well-mixed, people differ in susceptibility and exposure, and different groups may have heterogeneity in access to preventatives or treatments. To account for these differences, there is a model feature called Heterogeneous Intra-Node Transmission (HINT). This feature is explained in the Generic model scenarios.
Some pathogens, such as Salmonella typhi, which is responsible for typhoid fever, has a more complex transmission pathway. To adequately capture these dynamics, the ENVIRONMENTAL_SIM has two modes of transmission: a contact route and an environmental route. For these simulation types, the HINT framework has been modified into Multi-route HINT so that heterogeneous transmission can occur over both transmission routes. As a user, the main change in the code will be for the TransmissionMatrix in the demographics file: it will now have two matrices, one for “contact” and one for “environmental.”
The ENVIRONMENTAL_SIM (and the simulation types built upon its framework, such as TYPHOID_SIM) do not have climate capability. However, as many environmentally-transmitted pathogens may be impacted by seasonal effects, there is a feature that enables user-controlled seasonal attenuation of contagion.
To control seasonal impacts on environmental contagions, the model allows the user to specify a trapezoidal-shaped infectivity multiplier. This scenario is designed to illustrate the trapezoidal-shaped infectivity multiplier (seasonality) on the environmental contagion population (e.g. the amount of environmental contaminants present).