EMOD and emodpy-malaria documentation#
This documentation set describes how to use Epidemiological MODeling software (EMOD) for simulating malaria transmission and interventions and how to use emodpy-malaria for creating input files, submitting simulation jobs to a compute cluster, and more.
Epidemiological MODeling software (EMOD)#
The Institute for Disease Modeling (IDM) develops disease modeling software that is thoroughly tested and shared with the research community to advance the understanding of disease dynamics. This software helps determine the combination of health policies and intervention strategies that can lead to disease eradication. If you encounter any issues while using the software, please contact idm@gatesfoundation.org.
EMOD, is an agent-based model (ABM) that simulates the simultaneous interactions of agents in an effort to recreate complex phenomena. Each agent (such as a human or vector) can be assigned a variety of “properties” (for example, age, gender, etc.), and their behavior and interactions with one another are determined by using decision rules. These models have strong predictive power and are able to leverage spatial and temporal dynamics.
EMOD is also stochastic, meaning that there is randomness built into the model. Infection and recovery processes are represented as probabilistic Bernoulli random draws. In other words, when a susceptible person comes into contact with a pathogen, they are not guaranteed to become infected. Instead, you can imagine flipping a coin that has a λ chance of coming up tails S(t) times, and for every person who gets a “head” you say they are infected. This randomness better approximates what happens in reality. It also means that you must run many simulations to determine the probability of particular outcomes.
The EMOD documentation is broken up into disease-specific sets that provide guidance for researchers modeling particular diseases. The documentation contains only the parameters, output reports, and other components of the model that are available to use for malaria modeling.
emodpy-malaria#
emodpy-malaria is a collection of Python scripts and utilities created to streamline user interactions with EMOD and idmtools for modeling malaria. Much of the functionality is inherited from the emod_api package and emodpy package.
Additional information about how to use idmtools can be found in Welcome to idmtools. Additional information about EMOD malaria parameters can be found in EMOD parameter reference.
See Welcome to idmtools for a diagram showing how idmtools and each of the related packages are used in an end-to-end workflow using EMOD as the disease transmission model.
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