Input files¶
EMOD takes a number of files as inputs for running simulations. The input files indicate the transmission mode, population size, age distribution, disease interventions, and many more qualities that affect disease transmission. The EMOD executable (Eradication.exe) takes these input files and uses them to run a simulation of the disease dynamics.
Many of the input files are formatted as JSON (JavaScript Object Notation) files. JSON is a simple text format that uses key/value pairs to encode data. In EMOD, the key is a parameter name and the value is the setting for that parameter. For example, “Base_Incubation_Period”: 5 sets the incubation period for the disease being modeled to be five days. JSON files are easy to read and edit. For more information about JSON, see EMOD parameter reference. Some of the inputs are compiled binary files.
Primary files¶
The primary files used for EMOD simulations are the following:
- demographics file
Defines the geography and the population being modeled. Each geographic node has a location, population, and certain characteristics assigned to it. These files are often reused across multiple simulations and disease scenarios.
- configuration file
Defines many aspects of the simulation, including disease characteristics like infectivity and transmission mode and simulation characteristics like simulation length and additional input files to use.
- campaign file
Defines the events that occur during the simulation. Primarily, these are the various disease interventions that will take place, but they also include the disease outbreaks.
Supplementary files¶
There are other optional files that EMOD can use as inputs to the simulation. These files are not necessary for every simulation or every disease. For example, climate files are only used for vector-borne diseases because weather affects mosquito populations. Migration files are only used for multi-node simulations where human or vector movement is important. Because EMOD is stochastic, it requires running many simulations which may require a lot of processing power. Load-balancing and serialization files are for managing computing resources.
These files use both a JSON file for metadata and an associated binary file that contains the actual data. You will typically use these input files in their default state.
Input file IDs¶
The Institute for Disease Modeling (IDM) provides collections of climate and demographics files for many different locations in the world for download on GitHub. For instructions, see EMOD installation. Some input files were prepared using CIESIN Gridded Population of the World (GPW) population distribution and a corresponding spatial resolution grid (for example, 2.5 arc minutes) to define the initial population and extent of the nodes for country-wide input files. Therefore, the naming convention for this files usually leads with the geographic location, followed by the spatial resolution, and input file type.
All input files except configuration and campaign files include the parameter IdReference in the metadata, which is used to generate the NodeID associated with each node in a simulation. The values for IdReference and NodeID must be the same across all input files used in a simulation. See Demographics parameters for more information about NodeID generation.